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Marcos Antonio Morais - One of the best experts on this subject based on the ideXlab platform.

  • biological diversity of carbon assimilation among isolates of the yeast Dekkera bruxellensis from wine and fuel ethanol industrial processes
    Fems Yeast Research, 2019
    Co-Authors: Jackeline Maria Da Silva, Patricia Valente, Diogo Ardaillon Simões, Fernanda Cristina Bezerra Leite, Denise Castro Parente, Gilberto Henrique Teles Gomes Da Silva, Carolina S Silva, Angelica Ganga, Marcos Antonio Morais
    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.

  • second generation ethanol from sugarcane and sweet sorghum bagasses using the yeast Dekkera bruxellensis
    Industrial Crops and Products, 2016
    Co-Authors: Alexandre Libanio Silva Reis, Emmanuel Dutra Damilano, Romulo Simoes Cezer Menezes, Marcos Antonio Morais
    Abstract:

    Abstract In previous work we showed that the yeast Dekkera bruxellensis (strain GDB 248) is capable of assimilating cellobiose and converting this sugar to ethanol, a characteristic that may help in reducing the cost of biomass hydrolysis with commercial enzyme. In the present work we tested the efficiency of ethanol production by this yeast from bagasse of sugarcane (SCB) and sweet sorghum (SSB) after alkaline H 2 O 2 pretreatment and enzymatic hydrolysis treatment. SSB contained less lignin and ashes and more waxes than SCB, resulting in more efficient pretreatment and enzyme hydrolysis, as evidenced by chemical and physical analysis. Glucose and cellobiose were released from cellulose, as well as xylose from the remaining hemicellulose. The hexoses were completely consumed with final yields of 0.42 (±0.04) g/g for SCB and 0.44 (±0.03) g/g for SSB. Acetate was not produced, which indicated that the fermentations were carried out under anaerobic condition. This yeast was capable of metabolising cellobiose for ethanol production, which therefore proves to be a promising industrial microorganism for the production of second-generation ethanol.

  • production of sensory compounds by means of the yeast Dekkera bruxellensis in different nitrogen sources with the prospect of producing cachaca
    Yeast, 2014
    Co-Authors: Denise Castro Parente, Will De Barros Pita, Fernanda Cristina Bezerra Leite, Esteban Espinosa Vidal, Marcos Antonio Morais
    Abstract:

    The distilled spirit made from sugar cane juice, also known as cachaca, is a traditional Brazilian beverage that in recent years has increased its market share among international distilled beverages. Several volatile compounds produced by yeast cells during the fermentation process are responsible for the unique taste and aroma of this drink. The yeast Dekkera bruxellensis has acquired increasing importance in the fermented beverage production, as the different metabolites produced by this yeast may be either beneficial or harmful to the end-product. Since D. bruxellensis is often found in the fermentation processes carried out in ethanol fuel distillation in Brazil, we employed this yeast to analyse the physiological profile and production of aromatic compounds and to examine whether it is feasible to regard it as a cachaca-producing microorganism. The assays were performed on a small scale and simulated the conditions for the production of handmade cachaca. The results showed that the presence of aromatic and branched-chain amino acids in the medium has a strong influence on the metabolism and production of flavours by D. bruxellensis. The assimilation of these alternative nitrogen sources led to different fermentation yields and the production of flavouring compounds. The influence of the nitrogen source on the metabolism of fusel alcohols and esters in D. bruxellensis highlights the need for further studies of the nitrogen requirements to obtain the desired level of sensory compounds in the fermentation. Our results suggest that D. bruxellensis has the potential to play a role in the production of cachaca. Copyright © 2014 John Wiley & Sons, Ltd.

  • proteome responses to nitrate in bioethanol production contaminant Dekkera bruxellensis
    Journal of Proteomics, 2014
    Co-Authors: Adauto Gomes Barbosa Neto, Marcos Antonio Morais, Maria Clara Pestanacalsa, Tercilio Calsa
    Abstract:

    Abstract 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.

  • oxygen limited cellobiose fermentation and the characterization of the cellobiase of an industrial Dekkera brettanomyces bruxellensis strain
    SpringerPlus, 2014
    Co-Authors: Alexandre Libanio Silva Reis, Raquel Fátima Rodrigues De Souza, Fernanda Cristina Bezerra Leite, Esteban Espinosa Vidal, Rochane Regina Neves Baptista Torres, Patricia Maria Guedes Paiva, Marcos Antonio Morais
    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.

Anne Friedrich - One of the best experts on this subject based on the ideXlab platform.

  • high quality de novo genome assembly of the Dekkera bruxellensis yeast using nanopore minion sequencing
    G3: Genes Genomes Genetics, 2017
    Co-Authors: Teo Fournier, Jeansebastien Gounot, Kelle C Freel, Corinne Cruaud, Arnaud Lemainque, Jeanmarc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich
    Abstract:

    Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any nonmodel organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is to obtain the complete sequence and high-quality assembly of a reference genome. Here, we sequenced and assembled a reference genome of the nonconventional Dekkera bruxellensis yeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting that D. bruxellensis genome is very dynamic. The whole genome of the D. bruxellensis UMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguous de novo assembly of D. bruxellensis to date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.

  • high quality de novo genome assembly of the Dekkera bruxellensis umy321 yeast isolate using nanopore minion sequencing
    bioRxiv, 2017
    Co-Authors: Teo Fournier, Jeansebastien Gounot, Kelle C Freel, Corinne Cruaud, Arnaud Lemainque, Jeanmarc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich
    Abstract:

    Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is evidently to obtain the complete sequence and high quality assembly of a reference genome. Here, we completely sequenced and assembled a reference genome of the non-conventional Dekkera bruxellensis yeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting that D. bruxellensis genome is very dynamic. The whole genome of the D. bruxellensis UMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguous de novo assembly of D. bruxellensis to date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.

Jackeline Maria Da Silva - One of the best experts on this subject based on the ideXlab platform.

  • The biotechnological potential of the yeast Dekkera bruxellensis
    World Journal of Microbiology and Biotechnology, 2019
    Co-Authors: Will De Barros Pita, Irina Charlot Peña-moreno, Karol Cristianne Ribeiro, Gilberto Henrique Teles, Jackeline Maria Da Silva, Marcos Antonio De Morais Junior
    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.

  • biological diversity of carbon assimilation among isolates of the yeast Dekkera bruxellensis from wine and fuel ethanol industrial processes
    Fems Yeast Research, 2019
    Co-Authors: Jackeline Maria Da Silva, Patricia Valente, Diogo Ardaillon Simões, Fernanda Cristina Bezerra Leite, Denise Castro Parente, Gilberto Henrique Teles Gomes Da Silva, Carolina S Silva, Angelica Ganga, Marcos Antonio Morais
    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.

  • Nitrate boosts anaerobic ethanol production in an acetate-dependent manner in the yeast Dekkera bruxellensis
    Journal of Industrial Microbiology & Biotechnology, 2019
    Co-Authors: Irina Charlot Peña-moreno, Denise Castro Parente, Allyson Andrade Mendonça, Lino Angel Valcarcel Rojas, Jackeline Maria Da Silva, Marcos Antonio De Morais Junior, Will De Barros Pita
    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.

  • First aspects on acetate metabolism in the yeast Dekkera bruxellensis: a few keys for improving ethanol fermentation.
    Yeast, 2018
    Co-Authors: Gilberto Henrique Teles, Jackeline Maria Da Silva, Allyson Andrade Mendonça, Marcos Antonio De Morais Junior, Will De Barros Pita
    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.

  • Diversidade da assimilação de fontes de carbono em isolados industriais de Dekkera bruxellensis
    'Revista Brasileira de Hematologia e Hemoterapia (RBHH)', 2017
    Co-Authors: Jackeline Maria Da Silva
    Abstract:

    FACEPEDekkera bruxellensis pertence à família Saccharomycetaceae e é considerado um parente distante de Saccharomyces cerevisiae. Esta levedura, principalmente na sua forma anamorfa Brettanomyces bruxellensis, é um importante contaminante da produção de vinho. O objetivo deste estudo foi comparar a fisiologia de linhagens da levedura Dekkera bruxellensis isoladas da produção de vinho e de álcool combustível quanto ao metabolismo de diferentes açúcares potencialmente utilizados como substrato industrial. Para isso, 30 isolados de Dekkera bruxellensis foram avaliados quanto à habilidade de assimilação respiratória e fermentativa de monossacarídeos e dissacarídeos, a diversidade fenotípica relacionada à repressão catabólica pela glicose, e a assimilação de diferentes açúcares, tais como glicose, sacarose e celobiose sob condição anaeróbica. Diferenças entre os perfis de assimilação respiratória foram observadas para cada isolado. As mais altas velocidades de crescimento foram encontradas em meio com glicose, frutose e sacarose 0,32 h⁻¹, 0,30 h⁻¹ e 0,30 h⁻¹, respectivamente, em aerobiose pelos isolados de destilaria. Em maltose e galactose, as maiores taxas de crescimento foram respectivamente, 0,21 h⁻¹ e 0,27 h⁻¹, alcançadas por isolados de destilaria e de vinícola, e em celobiose e lactose, as maiores taxas foram respectivamente, 0,20 h⁻¹e 0,15 h⁻¹, alcançados pelos isolados de destilaria. A presença do repressor catabólico 2-deoxiglicose no meio com galactose e maltose inibiu o crescimento de todos os isolados de vinho, diferentemente de alguns isolados de etanol que apresentaram resistência a este composto. A adição de Antimicina A nos meios de cultura alterou o crescimento apenas dos isolados de vinícola. Em anaerobiose estrita, os isolados de destilaria alcançaram velocidades de crescimento iguais a 0,44 h⁻¹; 0,40 h⁻¹e 0,26 h⁻¹ em glicose, sacarose e celobiose, respectivamente. A capacidade de assimilação de diferentes açúcares pelos isolados de D. bruxellensis frente às diversas condições testadas mostram a diversidade fenotípica encontrada dentro desta espécie. Além disso, os dados podem colaborar para explicação da capacidade adaptativa dessa espécie em diferentes ambientes industriais cujas fontes alternativas de carbono estejam presentes. Do ponto de vista biotecnológico, estudos com isolados de D. bruxellensis podem ser voltados para a produção de etanol de segunda geração, cujo um dos substratos é a celobiose, açúcar dos quais linhagens selvagens de S. cerevisiae não são capazes de assimilar.Dekkera bruxellensis belongs to the family Saccharomycetaceae and is considered a distant relative of Saccharomyces cerevisiae. This yeast, mainly in its anamorphic form Brettanomyces bruxellensis, is an important contaminant of wine production. The aim of this study was to compare the physiology of strains Dekkera bruxellensis yeast isolated from wine production and ethanol on the metabolism of different sugars potentially used as industrial substrate. To this, 30 isolates of Dekkera bruxellensis were assessed for fermentative and respiratory assimilation ability monosaccharides and disaccharides, phenotypic diversity related to catabolite repression by glucose and the assimilation of different sugars, such as glucose, sucrose and cellobiose under anaerobic conditions. Differences between the profiles of respiratory assimilation were observed for each isolate. The highest growth rates were found in glucose, fructose and sucrose 0.32 h⁻¹, 0.30 h⁻¹and 0.30 h⁻¹, respectively, in aerobiosis by distillery isolates. In maltose and galactose, the highest growth rates were respectively 0.21 h⁻¹ and 0.27 h ⁻¹, reached by distillery and wine isolates, and in cellobiose and lactose, the highest rates were 0, 20 h⁻¹ and 0.15 h⁻¹, reached by distillery isolates. The presence of the 2-deoxyglucose catabolic repressor in the medium with galactose and maltose inhibited the growth of all the wine isolates, unlike some ethanol isolates were resistant to this compound. The addition of Antimycin A in the culture media altered the growth of only the wine isolates. In strict anaerobiosis the isolates of distillery reached growth rates equal to 0.44 h ⁻¹; 0.40 h ⁻¹ and 0.26 h ⁻¹ in glucose, sucrose and cellobiose, respectively. The capacity of assimilation of different sugars by D. bruxellensis isolates against the different conditions tested shows the phenotypic diversity found within this species. Moreover, the data can corroborate to explain the adaptive capacity of this species in different industrial environments whose alternative carbon sources are present. In biotechnological point of view, studies with isolated D. bruxellensis may be facing a second-generation ethanol, which one of the substrates is a cellobiose, sugar from which wild strains of S. cerevisiae are not able to assimilat

Volkmar Passoth - One of the best experts on this subject based on the ideXlab platform.

  • De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping
    GigaScience, 2015
    Co-Authors: Remi-andre Olsen, Volkmar Passoth, Ievgeniia A. Tiukova, Ignas Bunikis, Olga Vinnere Pettersson, Kicki Holmberg, Britta Lötstedt, Max Käller, Francesco Vezzi
    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.

  • Interaction of Lactobacillus vini with the ethanol-producing yeasts Dekkera bruxellensis and Saccharomyces cerevisiae
    Biotechnology and applied biochemistry, 2014
    Co-Authors: Ievgeniia A. Tiukova, Thomas Eberhard, Volkmar Passoth
    Abstract:

    Lactobacillus vini was recently described as a contaminant in industrial ethanol fermentations and its co-occurrence with Dekkera bruxellensis was noted. We investigated the growth characteristics of L. vini in cocultivation together with either Saccharomyces cerevisiae or D. bruxellensis. Lower cell numbers of both the yeasts and L. vini as well as a decrease in ethanol and lactate formation in mixed batch cultures compared with pure cultures were noted. L. vini formed cell aggregates (flocs) in all cultivation media with different shapes in Man–Rogosa–Sharpe and yeast extract–peptone–dextrose media. Flocs’ size and proportion of cells bound to flocs increased with increasing ethanol concentration. In coculture, formation of lactic acid bacteria–yeast cell aggregates consisting of a bacterial core with an outer layer of yeast cells was observed. L. vini–D. bruxellensis flocs had a bigger surface, due to cells protruding from the pseudomycelium. The involvement of mannose residues in the flocculation between L. vini and yeasts was tested. The presence of mannose induced deflocculation in a concentration-dependent manner. Less mannose was required for the deflocculation of D. bruxellensis as compared with S. cerevisiae.

  • adaptation of Dekkera bruxellensis to lignocellulose based substrate
    Biotechnology and Applied Biochemistry, 2014
    Co-Authors: Ievgeniia A. Tiukova, Jerry Stahlberg, Majid Haddad Momeni, Will De Barros Pita, Svein J. Horn, Marcos Antonio Morais, David Sundell, Volkmar Passoth
    Abstract:

    Adaptation of Dekkera bruxellensis to lignocellulose hydrolysate was investigated. Cells of D. bruxellensis were grown for 72 and 192H in batch and continuous culture, respectively (adapted cells). ...

  • physiology and gene expression profiles of Dekkera bruxellensis in response to carbon and nitrogen availability
    Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2013
    Co-Authors: Will De Barros Pita, Volkmar Passoth, Diogo Ardaillon Simões, Denise Castro Silva, Marcos Antonio Morais
    Abstract:

    The assimilation of nitrate, a nitrogenous compound, was previously described as an important factor favoring Dekkera bruxellensis in the competition with Saccharomyces cerevisiae for the industrial sugarcane substrate. In this substrate, nitrogen sources are limited and diverse, and a recent report showed that amino acids enable D. bruxellensis to grow anaerobically. Thus, understanding the regulation of nitrogen metabolism is one fundamental aspect to comprehend the competiveness of D. bruxellensis in the fermentation environment. In the present study, we evaluated the physiological and transcriptional profiles of D. bruxellensis in response to different carbon and nitrogen supplies to determine their influence on growth, sugar consumption, and ethanol production. Besides, the expression of genes coding for nitrogen permeases and enzymes involved in the biosynthesis of glutamate and energetic metabolism were investigated under these conditions. Our data revealed that genes related to nitrogen uptake in D. bruxellensis are under the control of nitrogen catabolite repression. Moreover, we provide indications that glutamate dehydrogenase and glutamate synthase may switch roles as the major pathway for glutamate biosynthesis in D. bruxellensis. Finally, our data showed that in nonoptimal growth conditions, D. bruxellensis leans toward the respiratory metabolism. The results presented herein show that D. bruxellensis and S. cerevisiae share similar regulation of GDH–GOGAT pathway, while D. bruxellensis converts less glucose to ethanol than S. cerevisiae do when nitrogen is limited. The consequence of this particularity to the industrial process is discussed.

  • transcriptome of the alternative ethanol production strain Dekkera bruxellensis cbs 11270 in sugar limited low oxygen cultivation
    PLOS ONE, 2013
    Co-Authors: Ievgeniia A. Tiukova, Thomas Eberhard, Mats E Petterson, Christian Tellgrenroth, Ignas Bunikis, Olga Vinnere Pettersson, Volkmar Passoth
    Abstract:

    Dekkera bruxellensis can outcompete Saccharomyces cerevisiae in environments with low sugar concentrations. It is usually regarded as a spoilage yeast but has lately been identified as an alternative ethanol production organism. In this study, global gene expression in the industrial isolate D. bruxellensis CBS 11270 under oxygen and glucose limitation was investigated by whole transcriptome sequencing using the AB SOLiD technology. Among other observations, we noted expression of respiratory complex I NADH-ubiquinone reductase although D. bruxellensis is a Crabtree positive yeast. The observed higher expression of NADH-generating enzymes compared to NAD+-generating enzymes might be the reason for the previously observed NADH imbalance and resulting Custer effect in D. bruxellensis. Low expression of genes involved in glycerol production is probably the molecular basis for high efficiency of D. bruxellensis metabolism under nutrient limitation. No D. bruxellensis homologs to the genes involved in the final reactions of glycerol biosynthesis were detected. A high number of expressed sugar transporter genes is consistent with the hypothesis that the competitiveness of D. bruxellensis is due to a higher affinity for the limiting substrate.

Concetta Compagno - One of the best experts on this subject based on the ideXlab platform.

  • cloning the putative gene of vinyl phenol reductase of Dekkera bruxellensis in saccharomyces cerevisiae
    Food Microbiology, 2017
    Co-Authors: Diego Romano, Silvia Galafassi, Concetta Compagno, Paolo Zambelli, Roberto Foschino, F Valdetara, Valerio De Vitis, Francesco Molinari, Ileana Vigentini
    Abstract:

    Vinylphenol reductase of Dekkera bruxellensis, the characteristic enzyme liable for “Brett” sensory modification of wine, has been recently recognized to belong to the short chain dehydrogenases/reductases family. Indeed, a preliminary biochemical characterisation has conferred to the purified protein a dual significance acting as superoxide dismutase and as a NADH-dependent reductase. The present study aimed for providing a certain identification of the enzyme by cloning the VPR gene in S. cerevisiae, a species not producing ethyl phenols. Transformed clones of S. cerevisiae resulted capable of expressing a biologically active form of the heterologous protein, proving its role in the conversion of 4-vinyl guaiacol to 4-ethyl guaiacol. A VPR specific protein activity of 9 ± 0.6 mU/mg was found in crude extracts of S. cerevisiae recombinant strain. This result was confirmed in activity trials carried out with the protein purified from transformant cells of S. cerevisiae by a his-tag purification approach; in particular, VPR-enriched fractions showed a specific activity of 1.83 ± 0.03 U/mg at pH 6.0. Furthermore, in agreement with literature, the purified protein behaves like a SOD, with a calculated specific activity of approximatively 3.41 U/mg. The comparative genetic analysis of the partial VPR gene sequences from 17 different D. bruxellesis strains suggested that the observed polymorphism (2.3%) and the allelic heterozygosity state of the gene do not justify the well described strain-dependent character in producing volatile phenols of this species. Actually, no correlation exists between genotype membership of the analysed strains and their capability to release off-flavours. This work adds valuable knowledge to the study of D. bruxellensis wine spoilage and prepare the ground for interesting future industrial applications.

  • Investigation of the SO2 stress response in Brettanomyces/Dekkera bruxellensis using RNA-seq
    2017
    Co-Authors: F Valdetara, Concetta Compagno, Roberto Foschino, M. Louw, M. &#352, D. Fracassetti, U. Petrovi&#269, M. Du Toit, B. Divol, Ileana Vigentini
    Abstract:

    Sulphur dioxide (SO2) is the most common additive worldwide used to prevent and/or control the microbial contamination in wine. Its use should be limited due to the detrimental effect to human health and the intolerance shown by a number of wine consumers. Brettanomyces/Dekkera bruxellensis, the main spoilage yeast of wine, is able to growth and produce volatile phenols even when SO2 is present. The SO2 resistance is a strain-dependent characteristic that needs to be further investigated. The two completely sequenced strains of B./D. bruxellensis, AWRI1499 (Curtin et al., 2012) and CBS2499 (Pi\u161kur et al., 2012), were used for batch fermentations carried out in synthetic wine medium. When cells reached the exponential phase of growth, SO2 was added (0.35 mg/L as molecular SO2). Samples for transcriptomic analysis were collected before SO2 pulse (T0), 5 hours after the addition (T5h) and at cell growth recovery (Tr). The results showed that more genes were significantly differentially expressed within the comparison Tr-vs-T0 than in the T5h-vs-T0 in both strains, thus indicating that mainly an adaptive response is activated. Among genes affected by SO2 addition and shared by the two strains, upregulated genes participating to carbohydrate, acyl-CoA and monocarboxylic acid metabolism were found. Interestingly, AWRI1499-0080, the gene homolog to SSU1, encoding the enzyme involved in the main mechanism of sulphite detoxification in Saccharomyces cerevisiae, increased its expression in the long term response up to 4 and 47 folds in CBS2499 and AWRI1499, respectively, thus highlighting the importance of this detoxification mechanism in B./D. bruxellensis as well. This study confirms the great ability of B./D. bruxellensis yeasts to survive and growth in extreme environmental conditions. In conclusion, due to the capacity of this yeast to counteract the stress induced by the addition of SO2, a proper management of the winemaking, including a deep cleaning of the winery equipment, is advisable for preventing, or at least minimizing the Brett contamination in wine

  • Effects of oxygen availability on acetic acid tolerance and intracellular pH in Dekkera bruxellensis
    Applied and environmental microbiology, 2016
    Co-Authors: Claudia Capusoni, Md Moktaduzzaman, Stefania Arioli, Paolo Zambelli, Diego Mora, Concetta Compagno
    Abstract:

    ABSTRACT The yeast Dekkera bruxellensis, associated with wine and beer production, has recently received attention, because its high ethanol and acid tolerance enables it to compete with Saccharomyces cerevisiae in distilleries that produce fuel ethanol. We investigated how different cultivation conditions affect the acetic acid tolerance of D. bruxellensis. We analyzed the ability of two strains (CBS 98 and CBS 4482) exhibiting different degrees of tolerance to grow in the presence of acetic acid under aerobic and oxygen-limited conditions. We found that the concomitant presence of acetic acid and oxygen had a negative effect on D. bruxellensis growth. In contrast, incubation under oxygen-limited conditions resulted in reproducible growth kinetics that exhibited a shorter adaptive phase and higher growth rates than those with cultivation under aerobic conditions. This positive effect was more pronounced in CBS 98, the more-sensitive strain. Cultivation of CBS 98 cells under oxygen-limited conditions improved their ability to restore their intracellular pH upon acetic acid exposure and to reduce the oxidative damage to intracellular macromolecules caused by the presence of acetic acid. This study reveals an important role of oxidative stress in acetic acid tolerance in D. bruxellensis, indicating that reduced oxygen availability can protect against the damage caused by the presence of acetic acid. This aspect is important for optimizing industrial processes performed in the presence of acetic acid. IMPORTANCE This study reveals an important role of oxidative stress in acetic acid tolerance in D. bruxellensis, indicating that reduced oxygen availability can have a protective role against the damage caused by the presence of acetic acid. This aspect is important for the optimization of industrial processes performed in the presence of acetic acid.

  • Unravelling SO2 stress response in Brettanomyces/Dekkera bruxellensis using RNA-seq
    2016
    Co-Authors: F Valdetara, Concetta Compagno, Roberto Foschino, M. Louw, M. &#352, D. Fracassetti, U. Petrovi&#269, M. Du Toit, B. Divol, Ileana Vigentini
    Abstract:

    Wine spoilage by Brettanomyces/Dekkera bruxellensis has increased in frequency because of the use of less-severe processing conditions, the great variety of diverse vinification tecniques and the tendency to reduce the use of preservatives, such as sulphur dioxide. Due to its antioxidant and antimicrobial effect, SO2 is a very common additive in many foods; however, it is also known for increased allergic reactions in humans and therefore consumer pressure to reduce the levels. The capability of B./D. bruxellensis to survive and to grow in wine can be partially ascribed to its high resistance to SO2, but no data are available on mechanisms involved in this metabolic trait.Triplicate batch fermentations were conducted in a wine-like medium using D. bruxellensis AWRI1499. Cells in exponential phase of growth were exposed to a molecular SO2 concentration of 0.35 mg/L and samples were collected for RNA-Seq analysis: i) before the SO2 pulse; ii) 5h thereafter; and iii) at cell growth recovery. Of the 4861 genes submitted to the gene set enrichment analysis (GSEA), 720 gene sets resulted upregulated. In particular, two distinct groups of gene sets resulted significantly enriched (p<0.01) in conditions ii) and iii), respectively. This result indicates that an early- and late response can be actuated by the yeast as a sequential strategy occurring under SO2 stress. Interestingly, SSU1, the main mechanism of sulphite detoxification in Saccharomyces cerevisiae, increased its expression during the late response up to 50 times. On the other hand, the data show that a long-term response, involving the carbohydrate biosynthesis and the sulphur compound metabolism, is activated and maintained by the yeast to counteract SO2 exposure

  • Effects of oxygen availability on acetic acid tolerance and intracellular pH in Dekkera bruxellensis
    'American Society for Microbiology', 2016
    Co-Authors: Claudia Capusoni, Md Moktaduzzaman, Stefania Arioli, Paolo Zambelli, Diego Mora, Concetta Compagno
    Abstract:

    The yeast Dekkera bruxellensis, associated with wine and beer production, has recently received attention, because its high ethanol and acid tolerance enables it to compete with Saccharomyces cerevisiae in distilleries that produce fuel ethanol. We investigated how different cultivation conditions affect the acetic acid tolerance of D. bruxellensis. We analyzed the ability of two strains (CBS 98 and CBS 4482) exhibiting different degrees of tolerance to grow in the presence of acetic acid under aerobic and oxygen-limited conditions. We found that the concomitant presence of acetic acid and oxygen had a negative effect on D. bruxellensis growth. In contrast, incubation under oxygen-limited conditions resulted in reproducible growth kinetics that exhibited a shorter adaptive phase and higher growth rates than those with cultivation under aerobic conditions. This positive effect was more pronounced in CBS 98, the more-sensitive strain. Cultivation of CBS 98 cells under oxygen-limited conditions improved their ability to restore their intracellular pH upon acetic acid exposure and to reduce the oxidative damage to intracellular macromolecules caused by the presence of acetic acid. This study reveals an important role of oxidative stress in acetic acid tolerance in D. bruxellensis, indicating that reduced oxygen availability can protect against the damage caused by the presence of acetic acid. This aspect is important for optimizing industrial processes performed in the presence of acetic acid