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Teles GH, Xavier MR, Da Silva JM, De Souza RB, de Barros Pita W, de Morais MA. The Metabolism of Respiring Carbon Sources by Dekkera bruxellensis and Its Relation with the Production of Acetate. Appl Biochem Biotechnol 2023; 195:6369-6391. [PMID: 36867386 DOI: 10.1007/s12010-023-04398-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/04/2023]
Abstract
Dekkera bruxellensis has been studied for several aspects of its metabolism over the past years, which has expanded our comprehension on its importance to industrial fermentation processes and uncovered its industrial relevance. Acetate is a metabolite often found in D. bruxellensis aerobic cultivations, whereas its production is linked to decreased ethanol yields. In a previous work, we aimed to understand how acetate metabolism affected the fermentation capacity of D. bruxellensis. In the present work, we evaluated the role of acetate metabolism in respiring cells using ammonium or nitrate as nitrogen sources. Our results showed that galactose is a strictly respiratory sugar and that a relevant part of its carbon is lost, while the remaining is metabolised through the Pdh bypass pathway before being assimilated into biomass. When this pathway was blocked, yeast growth was reduced while more carbon was assimilated to the biomass. In nitrate, more acetate was produced as expected, which increased carbon assimilation, although less galactose was uptaken from the medium. This scenario was not affected by the Pdh bypass inhibition. The confirmation that acetate production was crucial for carbon assimilation was brought by cultivations in pyruvate. All physiological data were connected to the expression patterns of PFK1, PDC1, ADH1, ALD3, ALD5 and ATP1 genes. Other respiring carbon sources could only be properly used by the cells when some external acetate was supplied. Therefore, the results reported herein helped in providing valuable contributions to the understanding of the oxidative metabolism in this potential industrial yeast.
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Affiliation(s)
- Gilberto Henrique Teles
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235. Cidade Universitária, Recife, PE, 50.670-901, Brazil
| | - Mariana Rodrigues Xavier
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235. Cidade Universitária, Recife, PE, 50.670-901, Brazil
| | | | - Rafael Barros De Souza
- Laboratory of Microbial Metabolism, Institute of Biological Sciences, University of Pernambuco, Recife, Brazil
| | | | - Marcos Antonio de Morais
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235. Cidade Universitária, Recife, PE, 50.670-901, Brazil.
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2
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Teles GH, da Silva JM, Xavier MR, de Souza RB, de Barros Pita W, de Morais Junior MA. Metabolic and biotechnological insights on the analysis of the Pdh bypass and acetate production in the yeast Dekkera bruxellensis. J Biotechnol 2022; 355:42-52. [PMID: 35760147 DOI: 10.1016/j.jbiotec.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/01/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
The advancement of knowledge about the physiology of Dekkera bruxellensis has shown its potential for the production of fuel ethanol very close to the conventional fermenting yeast S. cerevisiae. However, some aspects of its metabolism remain uncovered. In the present study, the respiro-fermentative parameters of D. bruxellensis GDB 248 were evaluated under different cultivation conditions. The results showed that sucrose was more efficiently converted to ethanol than glucose, regardless the nitrogen source, which points out for the industrial efficiency of this yeast in sucrose-based substrate. The blockage of the cytosolic acetate production incremented the yeast fermentative efficiency by 27% (in glucose) and 14% (in sucrose). On the other hand, the presence of nitrate as inducer of acetate production reducing the production of ethanol. Altogether, these results settled the hypothesis that acetate metabolism is the main constraint for ethanol production. Besides, this acetate-generating pathway seems to exert some regulatory action on the flux and distribution of the carbon flowing throught the central metabolism. These physiological aspects were corroborated by the relative expression analysis of key genes in the crossroad to ethanol, acetate and biomass formation. All the results were discussed in the light of the industrial potential of this yeast.
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Affiliation(s)
- Gilberto Henrique Teles
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Jackeline Maria da Silva
- Laboratory of Molecular Genetics, Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
| | - Mariana Rodrigues Xavier
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Rafael Barros de Souza
- Laboratory of Microbial Metabolism, Institute of Biological Sciences, University of Pernambuco, Recife, Brazil
| | - Will de Barros Pita
- Laboratory of Molecular Genetics, Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
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3
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The effect of growth rate on the production and vitality of non-Saccharomyces wine yeast in aerobic fed-batch culture. Bioprocess Biosyst Eng 2021; 44:2655-2665. [PMID: 34499236 DOI: 10.1007/s00449-021-02634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Non-Saccharomyces wine yeasts are of increasing importance due to their influence on the organoleptic properties of wine and thus the factors influencing the biomass production of these yeasts, as starter cultures, are of commercial value. Therefore, the effects of growth rates on the biomass yield (Yx/s) and fermentation performance of non-Saccharomyces yeasts at bench and pilot scale were examined. The fermentative performance and (Yx/s) were optimised, in aerobic fed-batch cultivations, to produce commercial wine seed cultures of Lachancea thermotolerans Y1240, Issatchenkia orientalis Y1161 and Metschnikowia pulcherrima Y1337. Saccharomyces cerevisiae (Lalvin EC1118) was used as a benchmark. A Crabtree positive response was shown by L. thermotolerans in a molasses-based industrial medium, at growth rates exceeding 0.21 h-1 (µcrit), resulting in a Yx/s of 0.76 g/g at 0.21 h-1 (46% of µmax) in the aerobic bioreactor-grown fed-batch culture at bench scale. At pilot scale and 0.133 h-1 (36% of µmax), this yeast exhibited ethanol concentrations reaching 10.61 g/l, as a possible result of substrate gradients. Crabtree negative responses were observed for I. orientalis and M. pulcherrima resulting in Yx/s of 0.83 g/g and 0.68 g/g, respectively, below 32% of µmax. The Yx/s of M. pulcherrima, I. orientalis and L. thermotolerans was maximised at growth rates between 0.10 and 0.12 h-1 and the fermentative capacity of these yeasts was maximised at these lower growth rates.
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4
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Rodríguez Madrera R, Pando Bedriñana R, Suárez Valles B. Evaluation of indigenous non-Saccharomyces cider yeasts for use in brewing. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-020-03665-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Comparative proteomic analyses reveal the metabolic aspects and biotechnological potential of nitrate assimilation in the yeast Dekkera bruxellensis. Appl Microbiol Biotechnol 2021; 105:1585-1600. [PMID: 33538877 DOI: 10.1007/s00253-021-11117-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/28/2020] [Accepted: 01/16/2021] [Indexed: 10/22/2022]
Abstract
The yeast Dekkera bruxellensis is well-known for its adaptation to industrial ethanol fermentation processes, which can be further improved if nitrate is present in the substrate. To date, the assimilation of nitrate has been considered inefficient because of the apparent energy cost imposed on cell metabolism. Recent research, however, has shown that nitrate promotes growth rate and ethanol yield when oxygen is absent from the environment. Given this, the present work aimed to identify the biological mechanisms behind this physiological behaviour. Proteomic analyses comparing four contrasting growth conditions gave some clues on how nitrate could be used as primary nitrogen source by D. bruxellensis GDB 248 (URM 8346) cells in anaerobiosis. The superior anaerobic growth in nitrate seems to be a consequence of increased cell metabolism (glycolytic pathway, production of ATP and NADPH and anaplerotic reactions providing metabolic intermediates) regulated by balanced activation of TORC1 and NCR de-repression mechanisms. On the other hand, the poor growth observed in aerobiosis is likely due to an oxidative stress triggered by nitrate when oxygen is present. These results represent a milestone regarding the knowledge about nitrate metabolism and might be explored for future use of D. bruxellensis as an industrial yeast. KEY POINTS: • Nitrate can be regarded as preferential nitrogen source for D. bruxellensis. • Oxidative stress limits the growth of D. bruxellensis in nitrate in aerobiosis. • Nitrate is a nutrient for novel industrial bioprocesses using D. bruxellensis.
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6
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Leonarski E, Cesca K, Zanella E, Stambuk BU, de Oliveira D, Poletto P. Production of kombucha-like beverage and bacterial cellulose by acerola byproduct as raw material. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110075] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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7
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da Silva JM, Ribeiro KC, Teles GH, Ribeiro E, de Morais Junior MA, de Barros Pita W. Fermentation profiles of the yeast Brettanomyces bruxellensis in d-xylose and l-arabinose aiming its application as a second-generation ethanol producer. Yeast 2020; 37:597-608. [PMID: 32889766 DOI: 10.1002/yea.3519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/28/2020] [Accepted: 09/01/2020] [Indexed: 11/07/2022] Open
Abstract
The yeast Brettanomyces bruxellensis is able to ferment the main sugars used in first-generation ethanol production. However, its employment in this industry is prohibitive because the ethanol productivity reached is significantly lower than the observed for Saccharomyces cerevisiae. On the other hand, a possible application of B. bruxellensis in the second-generation ethanol production has been suggested because this yeast is also able to use d-xylose and l-arabinose, the major pentoses released from lignocellulosic material. Although the latter application seems to be reasonable, it has been poorly explored. Therefore, we aimed to evaluate whether or not different industrial strains of B. bruxellensis are able to ferment d-xylose and l-arabinose, both in aerobiosis and oxygen-limited conditions. Three out of nine tested strains were able to assimilate those sugars. When in aerobiosis, B. bruxellensis cells exclusively used them to support biomass formation, and no ethanol was produced. Moreover, whereas l-arabinose was not consumed under oxygen limitation, d-xylose was only slightly used, which resulted in low ethanol yield and productivity. In conclusion, our results showed that d-xylose and l-arabinose are not efficiently converted to ethanol by B. bruxellensis, most likely due to a redox imbalance in the assimilatory pathways of these sugars. Therefore, despite presenting other industrially relevant traits, the employment of B. bruxellensis in second-generation ethanol production depends on the development of genetic engineering strategies to overcome this metabolic bottleneck.
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Affiliation(s)
| | | | | | - Ester Ribeiro
- Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
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8
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da Silva JM, da Silva GHTG, Parente DC, Leite FCB, Silva CS, Valente P, Ganga AM, Simões DA, de Morais MA. Biological diversity of carbon assimilation among isolates of the yeast Dekkera bruxellensis from wine and fuel-ethanol industrial processes. FEMS Yeast Res 2019; 19:5372417. [PMID: 30848782 DOI: 10.1093/femsyr/foz022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Dekkera bruxellensis is considered a spoilage yeast in winemaking, brewing and fuel-ethanol production. However, there is growing evidence in the literature of its biotechnological potential. In this work, we surveyed 29 D. bruxellensis isolates from three countries and two different industrial origins (winemaking and fuel-ethanol production) for the metabolization of industrially relevant sugars. The isolates were characterized by the determination of their maximum specific growth rates, and by testing their ability to grow in the presence of 2-deoxy-d-glucose and antimycin A. Great diversity was observed among the isolates, with fuel-ethanol isolates showing overall higher specific growth rates than wine isolates. Preferences for galactose (three wine isolates) and for cellobiose or lactose (some fuel-ethanol isolates) were observed. Fuel-ethanol isolates were less sensitive than wine isolates to glucose catabolite repression (GCR) induction by 2-deoxy-d-glucose. In strictly anaerobic conditions, isolates selected for having high aerobic growth rates were able to ferment glucose, sucrose and cellobiose at fairly high rates without supplementation of casamino acids or yeast extract in the culture medium. The phenotypic diversity found among wine and fuel-ethanol isolates suggests adaptation to these environments. A possible application of some of the GCR-insensitive, fast-growing isolates in industrial processes requiring co-assimilation of different sugars is considered.
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Affiliation(s)
- Jackeline Maria da Silva
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - Denise Castro Parente
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - Carolina Santos Silva
- Department of Chemical Engineering, Federal University of Pernambuco, Recife, Brazil
| | - Patrícia Valente
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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9
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The biotechnological potential of the yeast Dekkera bruxellensis. World J Microbiol Biotechnol 2019; 35:103. [PMID: 31236799 DOI: 10.1007/s11274-019-2678-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/15/2019] [Indexed: 10/26/2022]
Abstract
Dekkera bruxellensis is an industrial yeast mainly regarded as a contaminant species in fermentation processes. In winemaking, it is associated with off-flavours that cause wine spoilage, while in bioethanol production this yeast is linked to a reduction of industrial productivity by competing with Saccharomyces cerevisiae for the substrate. In spite of that, this point of view is gradually changing, mostly because D. bruxellensis is also able to produce important metabolites, such as ethanol, acetate, fusel alcohols, esters and others. This dual role is likely due to the fact that this yeast presents a set of metabolic traits that might be either industrially attractive or detrimental, depending on how they are faced and explored. Therefore, a proper industrial application for D. bruxellensis depends on the correct assembly of its central metabolic puzzle. In this sense, researchers have addressed issues regarding the physiological and genetic aspects of D. bruxellensis, which have brought to light much of our current knowledge on this yeast. In this review, we shall outline what is presently understood about the main metabolic features of D. bruxellensis and how they might be managed to improve its current or future industrial applications (except for winemaking, in which it is solely regarded as a contaminant). Moreover, we will discuss the advantages and challenges that must be overcome in order to take advantage of the full biotechnological potential of this yeast.
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10
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Tyrawa C, Preiss R, Armstrong M, van der Merwe G. The temperature dependent functionality ofBrettanomyces bruxellensisstrains in wort fermentations. JOURNAL OF THE INSTITUTE OF BREWING 2019. [DOI: 10.1002/jib.565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Caroline Tyrawa
- Department of Molecular and Cellular Biology; University of Guelph; 50 Stone Rd. E Guelph N1G 2W1 ON Canada
| | - Richard Preiss
- Department of Molecular and Cellular Biology; University of Guelph; 50 Stone Rd. E Guelph N1G 2W1 ON Canada
- Escarpment Laboratories; 8 Smith Ave. Guelph N1E 5Y5 ON Canada
| | - Meagan Armstrong
- Department of Molecular and Cellular Biology; University of Guelph; 50 Stone Rd. E Guelph N1G 2W1 ON Canada
| | - George van der Merwe
- Department of Molecular and Cellular Biology; University of Guelph; 50 Stone Rd. E Guelph N1G 2W1 ON Canada
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11
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Tiukova IA, Pettersson ME, Hoeppner MP, Olsen RA, Käller M, Nielsen J, Dainat J, Lantz H, Söderberg J, Passoth V. Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis. PLoS One 2019; 14:e0215077. [PMID: 31042716 PMCID: PMC6493715 DOI: 10.1371/journal.pone.0215077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.
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Affiliation(s)
- Ievgeniia A. Tiukova
- Chalmers University of Technology, Department of Biology and Biological Engineering, Systems and Synthetic Biology, Göteborg, Sweden
- Swedish University of Agricultural Sciences, Department of Molecular Sciences, Uppsala, Sweden
| | - Mats E. Pettersson
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
| | - Marc P. Hoeppner
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Uppsala, Sweden
- Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology, Kiel, Germany
| | - Remi-Andre Olsen
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - Max Käller
- Royal Institute of Technology, Biotechnology and Health, School of Engineering Sciences in Chemistry, SciLifeLab, Stockholm, Sweden
- Stockholm University, Department of Biochemistry and Biophysics, SciLifeLab, Stockholm, Sweden
| | - Jens Nielsen
- Chalmers University of Technology, Department of Biology and Biological Engineering, Systems and Synthetic Biology, Göteborg, Sweden
| | - Jacques Dainat
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Uppsala, Sweden
| | - Henrik Lantz
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Uppsala, Sweden
| | - Jonas Söderberg
- Uppsala University, Department of Cell and Molecular Biology, Molecular Evolution, Uppsala, Sweden
| | - Volkmar Passoth
- Swedish University of Agricultural Sciences, Department of Molecular Sciences, Uppsala, Sweden
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12
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Peña-Moreno IC, Castro Parente D, da Silva JM, Andrade Mendonça A, Rojas LAV, de Morais Junior MA, de Barros Pita W. Nitrate boosts anaerobic ethanol production in an acetate-dependent manner in the yeast Dekkera bruxellensis. J Ind Microbiol Biotechnol 2018; 46:209-220. [PMID: 30539327 DOI: 10.1007/s10295-018-2118-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/05/2018] [Indexed: 12/29/2022]
Abstract
In the past few years, the yeast Dekkera bruxellensis has gained much of attention among the so-called non-conventional yeasts for its potential in the biotechnological scenario, especially in fermentative processes. This yeast has been regarded as an important competitor to Saccharomyces cerevisiae in bioethanol production plants in Brazil and several studies have reported its capacity to produce ethanol. However, our current knowledge concerning D. bruxellensis is restricted to its aerobic metabolism, most likely because wine and beer strains cannot grow in full anaerobiosis. Hence, the present work aimed to fulfil a gap regarding the lack of information on the physiology of Dekkera bruxellensis growing in the complete absence of oxygen and the relationship with assimilation of nitrate as nitrogen source. The ethanol strain GDB 248 was fully capable of growing anaerobically and produces ethanol at the same level of S. cerevisiae. The presence of nitrate in the medium increased this capacity. Moreover, nitrate is consumed faster than ammonium and this increased rate coincided with a higher speed of glucose consumption. The profile of gene expression helped us to figure out that even in anaerobiosis, the presence of nitrate drives the yeast cells to an oxidative metabolism that ultimately incremented both biomass and ethanol production. These results finally provide the clues to explain most of the success of this yeast in industrial processes of ethanol production.
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Affiliation(s)
| | - Denise Castro Parente
- Department of Genetics, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
| | | | | | | | | | - Will de Barros Pita
- Department of Antibiotics, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil.
- Departamento de Antibióticos, Universidade Federal de Pernambuco, Avenida Professor Artur de Sá, Cidade Universitária, 50740520, Recife, PE, Brazil.
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13
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Teles GH, da Silva JM, Mendonça AA, de Morais Junior MA, de Barros Pita W. First aspects on acetate metabolism in the yeast Dekkera bruxellensis: a few keys for improving ethanol fermentation. Yeast 2018; 35:577-584. [PMID: 30006941 DOI: 10.1002/yea.3348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/25/2018] [Accepted: 05/23/2018] [Indexed: 11/10/2022] Open
Abstract
Dekkera bruxellensis is continuously changing its status in fermentation processes, ranging from a contaminant or spoiling yeast to a microorganism with potential to produce metabolites of biotechnological interest. In spite of that, several major aspects of its physiology are still poorly understood. As an acetogenic yeast, minimal oxygen concentrations are able to drive glucose assimilation to oxidative metabolism, in order to produce biomass and acetate, with consequent low yield in ethanol. In the present study, we used disulfiram to inhibit acetaldehyde dehydrogenase activity to evaluate the influence of cytosolic acetate on cell metabolism. D. bruxellensis was more tolerant to disulfiram than Saccharomyces cerevisiae and the use of different carbon sources revealed that the former yeast might be able to export acetate (or acetyl-CoA) from mitochondria to cytoplasm. Fermentation assays showed that acetaldehyde dehydrogenase inhibition re-oriented yeast central metabolism to increase ethanol production and decrease biomass formation. However, glucose uptake was reduced, which ultimately represents economical loss to the fermentation process. This might be the major challenge for future metabolic engineering enterprises on this yeast.
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Affiliation(s)
- Gilberto Henrique Teles
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
| | - Jackeline Maria da Silva
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
| | - Allyson Andrade Mendonça
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
| | - Marcos Antonio de Morais Junior
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil.,Department of Genetics, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
| | - Will de Barros Pita
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil.,Department of Antibiotics, Federal University of Pernambuco, Recife, PE, 50760-901, Brazil
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14
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Kosel J, Cadež N, Schuller D, Carreto L, Franco-Duarte R, Raspor P. The influence of Dekkera bruxellensis on the transcriptome of Saccharomyces cerevisiae and on the aromatic profile of synthetic wine must. FEMS Yeast Res 2018. [PMID: 28633312 DOI: 10.1093/femsyr/fox018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A double compartment membrane system was constructed in order to systematically study possible microbial interactions between yeasts Saccharomyces cerevisiae and Dekkera bruxellensis and their impact on wine aroma. The presence of D. bruxellensis induced 77 transcripts of S. cerevisiae. These were mostly of unknown function; however, some were involved in thiamine biosynthesis and in amino acid and polyamine transport, suggesting a competitive relationship between the two yeast species. Among the transcripts with no biological function, 14 of them were found to be the members of the PAU gene family that is associated with response to anaerobiosis stress. In separated cultures, S. cerevisiae produced glycerol which was subsequently consumed by D. bruxellensis. The concentration of ethylphenols was reduced and we assume that they were absorbed onto the surfaces of S. cerevisiae yeast walls. Also in separated cultures, D. bruxellensis formed a typical profile of aromatic esters with decreased levels of acetate esters and increased level of ethyl esters.
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Affiliation(s)
- Janez Kosel
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.,Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar 4710-057, Braga, Portugal
| | - Neža Cadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Dorit Schuller
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar 4710-057, Braga, Portugal
| | - Laura Carreto
- RNA Biology Laboratory, CESAM, Biology Department, Aveiro University, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ricardo Franco-Duarte
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar 4710-057, Braga, Portugal
| | - Peter Raspor
- Faculty of Health Sciences, University of Primorska, Polje 42, SI-6310 Izola, Slovenia
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Bassi APG, Meneguello L, Paraluppi AL, Sanches BCP, Ceccato-Antonini SR. Interaction of Saccharomyces cerevisiae–Lactobacillus fermentum–Dekkera bruxellensis and feedstock on fuel ethanol fermentation. Antonie Van Leeuwenhoek 2018; 111:1661-1672. [DOI: 10.1007/s10482-018-1056-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
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16
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Parente DC, Cajueiro DBB, Moreno ICP, Leite FCB, De Barros Pita W, De Morais MA. On the catabolism of amino acids in the yeast Dekkera bruxellensis
and the implications for industrial fermentation processes. Yeast 2017; 35:299-309. [DOI: 10.1002/yea.3290] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/04/2017] [Accepted: 10/11/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
| | | | | | - Fernanda Cristina Bezerra Leite
- Interdepartmental Research Group in Metabolic Engineering; PE 50760-901 Brazil
- Department of Biology; Federal Rural University of Pernambuco; Recife PE 52171-900 Brazil
| | - Will De Barros Pita
- Interdepartmental Research Group in Metabolic Engineering; PE 50760-901 Brazil
- Department of Antibiotics; PE 50760-901 Brazil
| | - Marcos Antonio De Morais
- Interdepartmental Research Group in Metabolic Engineering; PE 50760-901 Brazil
- Department of Genetics; Federal University of Pernambuco; Recife PE 50760-901 Brazil
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17
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Glutamine: a major player in nitrogen catabolite repression in the yeast Dekkera bruxellensis. Antonie van Leeuwenhoek 2017. [PMID: 28631172 DOI: 10.1007/s10482-017-0888-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the present work we studied the expression of genes from nitrogen central metabolism in the yeast Dekkera bruxellensis and under regulation by the Nitrogen Catabolite Repression mechanism (NCR). These analyses could shed some light on the biological mechanisms involved in the adaptation and survival of this yeast in the sugarcane fermentation process for ethanol production. Nitrogen sources (N-sources) in the form of ammonium, nitrate, glutamate or glutamine were investigated with or without the addition of methionine sulfoximine, which inhibits the activity of the enzyme glutamine synthetase and releases cells from NCR. The results showed that glutamine might act as an intracellular sensor for nitrogen availability in D. bruxellensis, by activating NCR. Gene expression analyses indicated the existence of two different GATA-dependent NCR pathways, identified as glutamine-dependent and glutamine-independent mechanisms. Moreover, nitrate is sensed as a non-preferential N-source and releases NCR to its higher level. After grouping genes according to their regulation pattern, we showed that genes for ammonium assimilation represent a regulon with almost constitutive expression, while permease encoding genes are mostly affected by the nitrogen sensor mechanism. On the other hand, nitrate assimilation genes constitute a regulon that is primarily subjected to induction by nitrate and, to a lesser extent, to a repressive mechanism by preferential N-sources. This observation explains our previous reports showing that nitrate is co-consumed with ammonium, a trait that enables D. bruxellensis cells to scavenge limiting N-sources in the industrial substrate and, therefore, to compete with Saccharomyces cerevisiae in this environment.
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Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress. Sci Rep 2016; 6:34304. [PMID: 27678167 PMCID: PMC5039629 DOI: 10.1038/srep34304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/07/2016] [Indexed: 11/08/2022] Open
Abstract
Brettanomyces bruxellensis has been described as the main contaminant yeast in wine production, due to its ability to convert the hydroxycinnamic acids naturally present in the grape phenolic derivatives, into volatile phenols. Currently, there are no studies in B. bruxellensis which explains the resistance mechanisms to hydroxycinnamic acids, and in particular to p-coumaric acid which is directly involved in alterations to wine. In this work, we performed a transcriptome analysis of B. bruxellensis LAMAP248rown in the presence and absence of p-coumaric acid during lag phase. Because of reported genetic variability among B. bruxellensis strains, to complement de novo assembly of the transcripts, we used the high-quality genome of B. bruxellensis AWRI1499, as well as the draft genomes of strains CBS2499 and0 g LAMAP2480. The results from the transcriptome analysis allowed us to propose a model in which the entrance of p-coumaric acid to the cell generates a generalized stress condition, in which the expression of proton pump and efflux of toxic compounds are induced. In addition, these mechanisms could be involved in the outflux of nitrogen compounds, such as amino acids, decreasing the overall concentration and triggering the expression of nitrogen metabolism genes.
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Leite F, Leite DR, Pereira L, de Barros Pita W, de Morais M. High intracellular trehalase activity prevents the storage of trehalose in the yeast Dekkera bruxellensis. Lett Appl Microbiol 2016; 63:210-4. [DOI: 10.1111/lam.12609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Affiliation(s)
- F.C.B. Leite
- Interdepartmental Research Group in Metabolic Engineering; Federal University of Pernambuco; Recife PE Brazil
- Department of Biology; Federal Rural University of Pernambuco; Recife PE Brazil
| | - D.V.da R. Leite
- Interdepartmental Research Group in Metabolic Engineering; Federal University of Pernambuco; Recife PE Brazil
| | - L.F. Pereira
- Interdepartmental Research Group in Metabolic Engineering; Federal University of Pernambuco; Recife PE Brazil
| | - W. de Barros Pita
- Interdepartmental Research Group in Metabolic Engineering; Federal University of Pernambuco; Recife PE Brazil
- Department of Antibiotics; Federal University of Pernambuco; Recife PE Brazil
| | - M.A. de Morais
- Interdepartmental Research Group in Metabolic Engineering; Federal University of Pernambuco; Recife PE Brazil
- Department of Genetics; Federal University of Pernambuco; Recife PE Brazil
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20
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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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21
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Smith BD, Divol B. Brettanomyces bruxellensis, a survivalist prepared for the wine apocalypse and other beverages. Food Microbiol 2016; 59:161-75. [PMID: 27375257 DOI: 10.1016/j.fm.2016.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
Brettanomyces bruxellensis is a common red wine spoilage yeast. Yet, in addition to wine, it has been isolated from other ecological niches that are just as nutritionally deficient as wine. B. bruxellensis can therefore be regarded as a survivor, well adapted to colonise harsh environments not often inhabited by other yeasts. This review is focused on the nutritional requirements of B. bruxellensis and the relevance thereof for its adaptation to the different matrices within which it occurs. Furthermore, the environmental conditions necessary (e.g. aerobic or anaerobic conditions) for the assimilation of the carbon or nitrogenous sources are discussed in this review. From literature, several confusing inconsistencies, regarding nutritional sources necessary for B. bruxellensis survival, in these specialist ecological niches are evidenced. The main focus of this review is wine but other products and niches that B. bruxellensis inhabits namely beer, cider, fruit juices and bioethanol production plants are also considered. This review highlights the lack of knowledge regarding B. bruxellensis when considering its nutritional requirements in comparison to Saccharomyces cerevisiae. However, there is a large enough body of evidence showing that the nutritional needs of B. bruxellensis are meagre, explaining its ability to colonise harsh environments.
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Affiliation(s)
- Brendan D Smith
- Institute of Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Benoit Divol
- Institute of Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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22
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Moktaduzzaman M, Galafassi S, Capusoni C, Vigentini I, Ling Z, Piškur J, Compagno C. Galactose utilization sheds new light on sugar metabolism in the sequenced strain Dekkera bruxellensis CBS 2499. FEMS Yeast Res 2015; 15:fou009. [PMID: 25673757 DOI: 10.1093/femsyr/fou009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Dekkera bruxellensis and Saccharomyces cerevisiae are considered two phylogenetically distant relatives, but they share several industrial relevant traits such as the ability to produce ethanol under aerobic conditions (Crabtree effect), high tolerance towards ethanol and acids, and ability to grow without oxygen. Beside a huge adaptability, D. bruxellensis exhibits a broader spectrum in utilization of carbon and nitrogen sources in comparison to S. cerevisiae. With the aim to better characterize its carbon source metabolism and regulation, the usage of galactose and the role that glucose plays on sugar metabolism were investigated in D. bruxellensis CBS 2499. The results indicate that in this yeast galactose is a non-fermentable carbon source, in contrast to S. cerevisiae that can ferment it. In particular, its metabolism is affected by the nitrogen source. Interestingly, D. bruxellensis CBS 2499 exhibits the 'short-term Crabtree effect', and the expression of genes involved in galactose utilization and in respiratory metabolism is repressed by glucose, similarly to what occurs in S. cerevisiae.
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Affiliation(s)
- Md Moktaduzzaman
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Silvia Galafassi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Claudia Capusoni
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Zhihao Ling
- Department of Biology, Lund University, Box 117, 221 00 Lund, Sweden
| | - Jure Piškur
- Department of Biology, Lund University, Box 117, 221 00 Lund, Sweden
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
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23
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Improving conversion yield of fermentable sugars into fuel ethanol in 1st generation yeast-based production processes. Curr Opin Biotechnol 2015; 33:81-6. [DOI: 10.1016/j.copbio.2014.12.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 11/22/2022]
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24
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Blomqvist J, Passoth V. Dekkera bruxellensis--spoilage yeast with biotechnological potential, and a model for yeast evolution, physiology and competitiveness. FEMS Yeast Res 2015; 15:fov021. [PMID: 25956542 DOI: 10.1093/femsyr/fov021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2015] [Indexed: 02/04/2023] Open
Abstract
Dekkera bruxellensis is a non-conventional yeast normally considered a spoilage organism in wine (off-flavours) and in the bioethanol industry. But it also has potential as production yeast. The species diverged from Saccharomyces cerevisiae 200 mya, before the whole genome duplication. However, it displays similar characteristics such as being Crabtree- and petite positive, and the ability to grow anaerobically. Partial increases in ploidy and promoter rewiring may have enabled evolution of the fermentative lifestyle in D. bruxellensis. On the other hand, it has genes typical for respiratory yeasts, such as for complex I or the alternative oxidase AOX1. Dekkera bruxellensis grows more slowly than S. cerevisiae, but produces similar or greater amounts of ethanol, and very low amounts of glycerol. Glycerol production represents a loss of energy but also functions as a redox sink for NADH formed during synthesis of amino acids and other compounds. Accordingly, anaerobic growth required addition of certain amino acids. In spite of its slow growth, D. bruxellensis outcompeted S. cerevisiae in glucose-limited cultures, indicating a more efficient energy metabolism and/or higher affinity for glucose. This review tries to summarize the latest discoveries about evolution, physiology and metabolism, and biotechnological potential of D. bruxellensis.
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Affiliation(s)
- Johanna Blomqvist
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Volkmar Passoth
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
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25
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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: 142] [Impact Index Per Article: 15.8] [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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26
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Schifferdecker AJ, Dashko S, Ishchuk OP, Piškur J. The wine and beer yeast Dekkera bruxellensis. Yeast 2014; 31:323-32. [PMID: 24932634 PMCID: PMC4257070 DOI: 10.1002/yea.3023] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/19/2014] [Accepted: 06/02/2014] [Indexed: 11/26/2022] Open
Abstract
Recently, the non-conventional yeast Dekkera bruxellensis has been gaining more and more attention in the food industry and academic research. This yeast species is a distant relative of Saccharomyces cerevisiae and is especially known for two important characteristics: on the one hand, it is considered to be one of the main spoilage organisms in the wine and bioethanol industry; on the other hand, it is 'indispensable' as a contributor to the flavour profile of Belgium lambic and gueuze beers. Additionally, it adds to the characteristic aromatic properties of some red wines. Recently this yeast has also become a model for the study of yeast evolution. In this review we focus on the recently developed molecular and genetic tools, such as complete genome sequencing and transformation, to study and manipulate this yeast. We also focus on the areas that are particularly well explored in this yeast, such as the synthesis of off-flavours, yeast detection methods, carbon metabolism and evolutionary history. © 2014 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Neto AGB, Pestana-Calsa MC, de Morais MA, Calsa T. Proteome responses to nitrate in bioethanol production contaminant Dekkera bruxellensis. J Proteomics 2014; 104:104-11. [PMID: 24667144 DOI: 10.1016/j.jprot.2014.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/24/2014] [Accepted: 03/12/2014] [Indexed: 11/17/2022]
Abstract
UNLABELLED Dekkera bruxellensis is an industrially relevant yeast, especially in bioethanol production. The capacity of D. bruxellensis to assimilate nitrate can confer advantages of this yeast over Saccharomyces cerevisiae at industrial conditions. In the present work we present the consequences of nitrate assimilation, using ammonium as reference, to the proteomics of D. bruxellensis. Thirty-four protein spots were overproduced in nitrate medium and were identified by MS-TOF/TOF analysis and were putatively identified by using local Mascot software. Apart from the overexpression of genes of nitrate metabolism, ATP synthesis and PPP and TCA pathways previously reported, cultivation on nitrate induced overproduction of glycolytic enzymes, which corroborate the high energy demand and NADH availability for nitrate assimilation. Overproduction of alcohol dehydrogenase (Adh) protein was also observed. Proteomic profile of D. bruxellensis cultivated in nitrate and described in the present work agrees with the hypothesis of metabolic flux regulation, making available the energy in the form of NADH to support nitrate assimilation. This work contributes with an initial picture of proteins presenting differential accumulation in industrial contaminant yeast, in strict association with possible metabolic responses to nitrate as sole nitrogen source in cultivation medium. BIOLOGICAL SIGNIFICANCE The present study investigated the gene expression at translational level of yeast D. bruxellensis for nitrate assimilation. This study corroborated with biological models that consider the ability to assimilate this nitrogen source confers advantages on this yeast during the fermentation process industry. However, larger studies are needed in this way as our group is investigating new proteins under LC-MS/MS approach. Together, these studies will help in understanding the operation of networks and cellular regulation of the process of assimilation of nitrogen sources for the D. bruxellensis, unravelling new aspects of the physiology of this yeast by proteomic analysis. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Adauto Gomes Barbosa Neto
- Laboratory of Plant Genomics and Proteomics, Department of Genetics, Center for Biological Sciences, Universidade Federal de Pernambuco, Recife, Brazil
| | - Maria Clara Pestana-Calsa
- Laboratory of Plant Genomics and Proteomics, Department of Genetics, Center for Biological Sciences, Universidade Federal de Pernambuco, Recife, Brazil; Environmental Engineering Area, Universidade Maurício de Nassau, Recife, Brazil
| | - Marcos Antonio de Morais
- Laboratory of Microbial Genetics, Department of Genetics, Center for Biological Sciences, Universidade Federal de Pernambuco, Recife, Brazil
| | - Tercilio Calsa
- Laboratory of Plant Genomics and Proteomics, Department of Genetics, Center for Biological Sciences, Universidade Federal de Pernambuco, Recife, Brazil.
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Reis ALS, de Fátima Rodrigues de Souza R, Baptista Torres RRN, Leite FCB, Paiva PMG, Vidal EE, de Morais MA. Oxygen-limited cellobiose fermentation and the characterization of the cellobiase of an industrial Dekkera/Brettanomyces bruxellensis strain. SPRINGERPLUS 2014; 3:38. [PMID: 24498580 PMCID: PMC3909126 DOI: 10.1186/2193-1801-3-38] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/14/2014] [Indexed: 12/05/2022]
Abstract
The discovery of a novel yeast with a natural capacity to produce ethanol from lignocellulosic substrates (second-generation ethanol) is of great significance for bioethanol technology. While there are some yeast strains capable of assimilating cellobiose in aerobic laboratory conditions, the predominant sugar in the treatment of lignocellulosic material, little is known about this ability in real industrial conditions. Fermentations designed to simulate industrial conditions were conducted in synthetic medium with glucose, sucrose, cellobiose and hydrolyzed pre-treated cane bagasse as a different carbon source, with the aim of further characterizing the fermentation capacity of a promising Dekkera bruxellensis yeast strain, isolated from the bioethanol process in Brazil. As a result, it was found (for the first time in oxygen-limiting conditions) that the strain Dekkera bruxellensis GDB 248 could produce ethanol from cellobiose. Moreover, it was corroborated that the cellobiase activity characterizes the enzyme candidate in semi-purified extracts (β-glucosidase). In addition, it was demonstrated that GDB 248 strain had the capacity to produce a higher acetic acid concentration than ethanol and glycerol, which confirms the absence of the Custer effect with this strain in oxygen-limiting conditions. Moreover, it is also being suggested that D. bruxellensis could benefit Saccharomyces cerevisiae and outcompete it in the industrial environment. In this way, it was confirmed that D. bruxellensis GDB 248 has the potential to produce ethanol from cellobiose, and is a promising strain for the fermentation of lignocellulosic substrates.
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Affiliation(s)
- Alexandre Libanio Silva Reis
- Bioprocessing Laboratory, CETENE, 50740-540 Recife, PE, Brazil ; Centro de Tecnologias Estratégicas do Nordeste - CETENE, Av. Prof. Luiz Freire, 01, Cidade Universitária, 50740-540 Recife, PE, Brasil
| | | | | | | | | | | | - Marcos Antonio de Morais
- Bioprocessing Laboratory, CETENE, 50740-540 Recife, PE, Brazil ; Interdepartmental Research Group on Metabolic Engineering, Federal University of Pernambuco, 50670-901 Recife, PE, Brazil ; Department of Genetics, Federal University of Pernambuco, 50670-901 Recife, PE, Brazil ; Department of Biochemistry, Federal University of Pernambuco, 50670-901 Recife, PE, Brazil
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29
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Pereira LF, Lucatti E, Basso LC, de Morais MA. The fermentation of sugarcane molasses by Dekkera bruxellensis and the mobilization of reserve carbohydrates. Antonie van Leeuwenhoek 2013; 105:481-9. [PMID: 24370978 DOI: 10.1007/s10482-013-0100-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/12/2013] [Indexed: 01/13/2023]
Abstract
The yeast Dekkera bruxellensis is considered to be very well adapted to industrial environments, in Brazil, USA, Canada and European Countries, when different substrates are used in alcoholic fermentations. Our previous study described its fermentative profile with a sugarcane juice substrate. In this study, we have extended its physiological evaluation to fermentation situations by using sugarcane molasses as a substrate to replicate industrial working conditions. The results have confirmed the previous reports of the low capacity of D. bruxellensis cells to assimilate sucrose, which seems to be the main factor that can cause a bottleneck in its use as fermentative yeast. Furthermore, the cells of D. bruxellensis showed a tendency to deviate most of sugar available for biomass and organic acids (lactic and acetic) compared with Saccharomyces cerevisiae, when calculated on the basis of their respective yields. As well as this, the acetate production from molasses medium by both yeasts was in marked contrast with the previous data on sugarcane juice. Glycerol and ethanol production by D. bruxellensis cells achieved levels of 33 and 53 % of the S. cerevisiae, respectively. However, the ethanol yield was similar for both yeasts. It is worth noting that this yeast did not accumulate trehalose when the intracellular glycogen content was 30 % lower than in S. cerevisiae. The lack of trehalose did not affect yeast viability under fermentation conditions. Thus, the adaptive success of D. bruxellensis under industrial fermentation conditions seems to be unrelated to the production of these reserve carbohydrates.
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Affiliation(s)
- Luciana Filgueira Pereira
- Interdepartmental Research Group on Metabolic Engineering, Federal University of Pernambuco, Recife, Brazil
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30
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de Barros Pita W, Silva DC, Simões DA, Passoth V, de Morais MA. Physiology and gene expression profiles of Dekkera bruxellensis in response to carbon and nitrogen availability. Antonie van Leeuwenhoek 2013; 104:855-68. [DOI: 10.1007/s10482-013-9998-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/07/2013] [Indexed: 12/01/2022]
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31
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Meneghin MC, Bassi APG, Codato CB, Reis VR, Ceccato-Antonini SR. Fermentative and growth performances ofDekkera bruxellensisin different batch systems and the effect of initial low cell counts in co-cultures withSaccharomyces cerevisiae. Yeast 2013; 30:295-305. [DOI: 10.1002/yea.2959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/21/2013] [Accepted: 05/01/2013] [Indexed: 11/05/2022] Open
Affiliation(s)
- Maria Cristina Meneghin
- Departamento de Tecnologia Agroindustrial e Sócio-Economia Rural, Centro de Ciências Agrárias; Universidade Federal de São Carlos; Araras; São Paulo State; Brazil; 13600-970
| | - Ana Paula Guarnieri Bassi
- Departamento de Tecnologia Agroindustrial e Sócio-Economia Rural, Centro de Ciências Agrárias; Universidade Federal de São Carlos; Araras; São Paulo State; Brazil; 13600-970
| | - Carolina Brito Codato
- Departamento de Tecnologia Agroindustrial e Sócio-Economia Rural, Centro de Ciências Agrárias; Universidade Federal de São Carlos; Araras; São Paulo State; Brazil; 13600-970
| | - Vanda Renata Reis
- Departamento de Tecnologia Agroindustrial e Sócio-Economia Rural, Centro de Ciências Agrárias; Universidade Federal de São Carlos; Araras; São Paulo State; Brazil; 13600-970
| | - Sandra Regina Ceccato-Antonini
- Departamento de Tecnologia Agroindustrial e Sócio-Economia Rural, Centro de Ciências Agrárias; Universidade Federal de São Carlos; Araras; São Paulo State; Brazil; 13600-970
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de Barros Pita W, Tiukova I, Leite FCB, Passoth V, Simões DA, de Morais MA. The influence of nitrate on the physiology of the yeast Dekkera bruxellensis grown under oxygen limitation. Yeast 2013; 30:111-7. [PMID: 23440690 DOI: 10.1002/yea.2945] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/30/2013] [Indexed: 11/07/2022] Open
Abstract
A previous study showed that the use of nitrate by Dekkera bruxellensis might be an advantageous trait when ammonium is limited in sugarcane substrate for ethanol fermentation. The aim of the present work was to evaluate the influence of nitrate on the yeast physiology during cell growth in different carbon sources under oxygen limitation. If nitrate was the sole source of nitrogen, D. bruxellensis cells presented slower growth, diminished sugar consumption and growth-associated ethanol production, when compared to ammonium. These results were corroborated by the increased expression of genes involved in the pentose phosphate (PP) pathway, the tricarboxylic acid (TCA) cycle and ATP synthesis. The presence of ammonium in the mixed medium restored most parameters to the standard conditions. This work may open up a line of investigation to establish the connection between nitrate assimilation and energetic metabolism in D. bruxellensis and their influence on its fermentative capacity in oxygen-limited or oxygen-depleted conditions.
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Affiliation(s)
- Will de Barros Pita
- Interdepartmental Research Group on Metabolic Engineering, Federal University of Pernambuco, Recife, PE, Brazil
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