Genome Survey Sequencing of the Wine Spoilage Yeast Dekkera (Brettanomyces) bruxellensis

ABSTRACT The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4× coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.

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Anopheles stephensi Dual Oxidase Silencing Activates the Thioester-Containing Protein 1 Pathway to Suppress Plasmodium Development

Journal of Innate Immunity ◽

10.1159/000497417 ◽

2019 ◽

Vol 11 (6) ◽

pp. 496-505 ◽

Cited By ~ 2

Author(s):

Parik Kakani ◽

Mithilesh Kajla ◽

Tania Pal Choudhury ◽

Lalita Gupta ◽

Sanjeev Kumar

Keyword(s):

Amino Acid ◽

Calcium Binding ◽

Anopheles Stephensi ◽

Developmental Stages ◽

Transmembrane Protein ◽

Phylogenetic Analyses ◽

Amino Acid Identity ◽

Infected Mosquito ◽

Parasite Development ◽

Dual Oxidase

We characterized the dual oxidase (Duox) gene in the major Indian malaria vector Anopheles stephensi, which regulates the generation of reactive oxygen species. The AsDuox gene encodes for a 1,475-amino-acid transmembrane protein that contains an N-terminal noncytoplasmic heme peroxidase domain, a calcium-binding domain, seven transmembrane domains, and a C-terminal cytoplasmic NADPH domain. Phylogenetic analyses revealed that A. stephensi Duox protein is highly conserved and shares 97–100% amino acid identity with other anopheline Duoxes. AsDuox is expressed in all the developmental stages of A. stephensi and the pupal stages revealed relatively higher expressions. The Duox gene is induced in Plasmodium-infected mosquito midguts, and RNA interference-mediated silencing of this gene suppressed parasite development through activation of the thioester-containing protein 1 pathway. We propose that this highly conserved anopheline Duox, being a Plasmodium agonist, is an excellent target to control malaria parasite development inside the insect host.

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Comparative Genomics and Environmental Distribution of Large dsDNA viruses in the family Asfarviridae

10.1101/2021.01.29.428683 ◽

2021 ◽

Author(s):

Sangita Karki ◽

Mohammad Moniruzzaman ◽

Frank O. Aylward

Keyword(s):

Amino Acid ◽

African Swine Fever Virus ◽

Phylogenetic Analyses ◽

African Swine Fever ◽

Amino Acid Identity ◽

Metagenomic Data ◽

Genome Comparison ◽

Marker Genes ◽

Environmental Distribution ◽

Acid Identity

AbstractThe Asfarviridae is a family of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) of which African swine fever virus (ASFV) is the most well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and different eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with >95% amino acid identity to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a near-complete genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.

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New insights on the features of the vinyl phenol reductase from the wine-spoilage yeast Dekkera/Brettanomyces bruxellensis

Annals of Microbiology ◽

10.1007/s13213-014-0864-5 ◽

2014 ◽

Vol 65 (1) ◽

pp. 321-329 ◽

Cited By ~ 17

Author(s):

Tiziana Mariarita Granato ◽

Diego Romano ◽

Ileana Vigentini ◽

Roberto Carmine Foschino ◽

Daniela Monti ◽

...

Keyword(s):

Brettanomyces Bruxellensis ◽

Spoilage Yeast ◽

Wine Spoilage ◽

Vinyl Phenol

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Molecular characterisation of the wine spoilage yeast ? Dekkera (Brettanomyces) bruxellensis

Microbiology Australia ◽

10.1071/ma07076 ◽

2007 ◽

Vol 28 (2) ◽

pp. 76 ◽

Cited By ~ 4

Author(s):

Paul Henschke ◽

Chris Curtin ◽

Paul Grbin

Keyword(s):

Red Wine ◽

Yeast Species ◽

Sensory Characteristics ◽

Molecular Characterisation ◽

Dekkera Bruxellensis ◽

Brettanomyces Bruxellensis ◽

Spoilage Yeast ◽

Wine Spoilage ◽

Special Occasion

How would you react if, upon opening that expensive bottle of red wine you had been saving for a special occasion, all you could smell was a box of Band-aid medical plasters. ?Band-aid?, or ?medicinal? aroma in red wine is but one spectrum of the (generally) negative sensory characteristics that have become synonymous with wine ?spoiled? by the yeast species Dekkera bruxellensis, and its non-sporulating form Brettanomyces bruxellensis.

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Effect of Candida intermedia LAMAP1790 Antimicrobial Peptides against Wine-Spoilage Yeasts Brettanomyces bruxellensis and Pichia guilliermondii

Fermentation ◽

10.3390/fermentation6030065 ◽

2020 ◽

Vol 6 (3) ◽

pp. 65 ◽

Cited By ~ 1

Author(s):

Rubén Peña ◽

Jeniffer Vílches ◽

Camila G.-Poblete ◽

María Angélica Ganga

Keyword(s):

Antimicrobial Peptides ◽

Membrane Damage ◽

Pichia Guilliermondii ◽

Yeast Saccharomyces Cerevisiae ◽

Brettanomyces Bruxellensis ◽

Candida Intermedia ◽

Spoilage Yeast ◽

Spoilage Yeasts ◽

Wine Spoilage ◽

Fungicide Activity

Wine spoilage yeasts are one of the main issues in the winemaking industry, and the control of the Brettanomyces and Pichia genus is an important goal to reduce economic loses from undesired aromatic profiles. Previous studies have demonstrated that Candida intermedia LAMAP1790 produces antimicrobial peptides of molecular mass under 10 kDa with fungicide activity against Brettanomyces bruxellensis, without affecting the yeast Saccharomyces cerevisiae. So far, it has not been determined whether these peptides show biocontroller effect in this yeast or other spoilage yeasts, such as Pichia guilliermondii. In this work, we determined that the exposure of B. bruxellensis to the low-mass peptides contained in the culture supernatant of C. intermedia LAMAP1790 produces a continuous rise of reactive oxygen species (ROS) in this yeast, without presenting a significant effect on membrane damage. These observations can give an approach to the antifungal mechanism. In addition, we described a fungicide activity of these peptides fraction against two strains of P. guilliermondii in a laboratory medium. However, carrying out assays on synthetic must, peptides must show an effect on the growth of B. bruxellensis. Moreover, these results can be considered as a start to develop new strategies for the biocontrol of spoilage yeast.

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Characterization and Complete Nucleotide Sequence of an Unusual Reptilian Retrovirus Recovered from the Order Crocodylia

Journal of Virology ◽

10.1128/jvi.76.9.4651-4654.2002 ◽

2002 ◽

Vol 76 (9) ◽

pp. 4651-4654 ◽

Cited By ~ 10

Author(s):

Joanne Martin ◽

Peter Kabat ◽

Elisabeth Herniou ◽

Michael Tristem

Keyword(s):

Amino Acid ◽

Nucleotide Sequence ◽

Complete Nucleotide Sequence ◽

Phylogenetic Analyses ◽

Amino Acid Identity ◽

Acid Identity ◽

Conserved Regions

ABSTRACT A novel group of retroviruses found within the order Crocodylia are described. Phylogenetic analyses demonstrate that they are probably the most divergent members of the Retroviridae described to date; even the most conserved regions of Pol show an average of only 23% amino acid identity when compared to other retroviruses.

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Assessing the Biofilm Formation Capacity of the Wine Spoilage Yeast Brettanomyces bruxellensis through FTIR Spectroscopy

Microorganisms ◽

10.3390/microorganisms9030587 ◽

2021 ◽

Vol 9 (3) ◽

pp. 587

Author(s):

Maria Dimopoulou ◽

Vasiliki Kefalloniti ◽

Panagiotis Tsakanikas ◽

Seraphim Papanikolaou ◽

George-John E. Nychas

Keyword(s):

Biofilm Formation ◽

Classification Model ◽

Invasive Technique ◽

Cell Phenotype ◽

Brettanomyces Bruxellensis ◽

Spoilage Yeast ◽

Phenotype Class ◽

Metabolic Fingerprint ◽

Wine Spoilage ◽

Chemical Groups

Brettanomyces bruxellensis is a wine spoilage yeast known to colonize and persist in production cellars. However, knowledge on the biofilm formation capacity of B. bruxellensis remains limited. The present study investigated the biofilm formation of 11 B. bruxellensis strains on stainless steel coupons after 3 h of incubation in an aqueous solution. FTIR analysis was performed for both planktonic and attached cells, while comparison of the obtained spectra revealed chemical groups implicated in the biofilm formation process. The increased region corresponding to polysaccharides and lipids clearly discriminated the obtained spectra, while the absorption peaks at the specific wavenumbers possibly reveal the presence of β-glucans, mannas and ergosterol. Unsupervised clustering and supervised classification were employed to identify the important wavenumbers of the whole spectra. The fact that all the metabolic fingerprints of the attached versus the planktonic cells were similar within the same cell phenotype class and different between the two phenotypes, implies a clear separation of the cell phenotype; supported by the results of the developed classification model. This study represents the first to succeed at applying a non-invasive technique to reveal the metabolic fingerprint implicated in the biofilm formation capacity of B. bruxellensis, underlying the homogenous mechanism within the yeast species.

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Triticum mosaic virus: A Distinct Member of the Family Potyviridae with an Unusually Long Leader Sequence

Phytopathology ◽

10.1094/phyto-99-8-0943 ◽

2009 ◽

Vol 99 (8) ◽

pp. 943-950 ◽

Cited By ~ 63

Author(s):

Satyanarayana Tatineni ◽

Amy D. Ziems ◽

Stephen N. Wegulo ◽

Roy French

Keyword(s):

Amino Acid ◽

Mosaic Virus ◽

Phylogenetic Analyses ◽

Amino Acid Identity ◽

Recent Common Ancestor ◽

Acid Identity ◽

Most Recent Common Ancestor ◽

Nontranslated Region ◽

The Family ◽

Distinct Member

The complete genome sequence of Triticum mosaic virus (TriMV), a member in the family Potyviridae, has been determined to be 10,266 nucleotides (nt) excluding the 3′ polyadenylated tail. The genome encodes a large polyprotein of 3,112 amino acids with the “hall-mark proteins” of potyviruses, including a small overlapping gene, PIPO, in the P3 cistron. The genome of TriMV has an unusually long 5′ nontranslated region of 739 nt with 12 translation initiation codons and three small open reading frames, which resemble those of the internal ribosome entry site containing 5′ leader sequences of the members of Picornaviridae. Pairwise comparison of 10 putative mature proteins of TriMV with those of representative members of genera in the family Potyviridae revealed 33 to 44% amino acid identity within the highly conserved NIb protein sequence and 15 to 29% amino acid identity within the least conserved P1 protein, suggesting that TriMV is a distinct member in the family Potyviridae. In contrast, TriMV displayed 47 to 65% amino acid sequence identity with available sequences of mature proteins of Sugarcane streak mosaic virus (SCSMV), an unassigned member of the Potyviridae. Phylogenetic analyses of the complete polyprotein, NIa-Pro, NIb, and coat protein sequences of representative species of six genera and unassigned members of the family Potyviridae suggested that TriMV and SCSMV are sister taxa and share a most recent common ancestor with tritimoviruses or ipomoviruses. These results suggest that TriMV and SCSMV should be classified in a new genus, and we propose the genus Poacevirus in the family Potyviridae, with TriMV as the type member.

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Molecular cloning and overexpression of a glutathione transferase gene from Proteus mirabilis

Biochemical Journal ◽

10.1042/bj3180157 ◽

1996 ◽

Vol 318 (1) ◽

pp. 157-162 ◽

Cited By ~ 36

Author(s):

Brunella PERITO ◽

Nerino ALLOCATI ◽

Enrico CASALONE ◽

Michele MASULLI ◽

Beatrice DRAGANI ◽

...

Keyword(s):

Amino Acid ◽

Proteus Mirabilis ◽

Burkholderia Cepacia ◽

Glutathione Transferase ◽

Amino Acid Identity ◽

Amino Acid Residues ◽

Reading Frame ◽

Promoter Sequences ◽

E Coli ◽

Cloned Gene

The structural gene of the Proteus mirabilis glutathione transferase GSTB1-1 (gstB) has been isolated from genomic DNA. A nucleotide sequence determination of gstB predicted a translational product of 203 amino acid residues, perfectly matching the sequence of the previously purified protein [Mignogna, Allocati, Aceto, Piccolomini, Di Ilio, Barra and Martini (1993) Eur. J. Biochem. 211, 421–425]. The P. mirabilis GST sequence revealed 56% identity with the Escherichia coli GST at DNA level and 54% amino acid identity. Similarity has been revealed also with the translation products of the recently cloned gene bphH from Haemophilus influenzae (28% identity) and ORF3 of Burkholderia cepacia (27% identity). Putative promoter sequences with high similarity to the E. coli σ70 consensus promoter and to promoters of P. mirabiliscat and glnA genes preceded the ATG of the gstB open reading frame (ORF). gstB was brought under control of the tac promoter and overexpressed in E. coli by induction with isopropyl-β-d-thiogalactopyranoside and growth at 37 °C. The physicochemical and catalytic properties of overexpressed protein were indistinguishable from those of the enzyme purified from P. mirabilis extract. Unlike the GST belonging to Mu and Theta classes, GSTB1-1 was unable to metabolize dichloromethane. The study of the interaction of cloned GSTB1-1 with a number of antibiotics indicates that this enzyme actively participates in the binding of tetracyclines and rifamycin.

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Microbiological, biochemical, physicochemical surface properties and biofilm forming ability of Brettanomyces bruxellensis

10.1101/579144 ◽

2019 ◽

Author(s):

Maria Dimopoulou ◽

Margareth Renault ◽

Marguerite Dols-Lafargue ◽

Warren Albertin-Leguay ◽

Jean-Marie Herry ◽

...

Keyword(s):

Surface Properties ◽

Biofilm Formation ◽

Yeast Species ◽

Economic Loss ◽

Wine Industry ◽

Yeast Cells ◽

Volatile Phenols ◽

Brettanomyces Bruxellensis ◽

Wine Spoilage ◽

Strain Dependent

AbstractBrettanomyces bruxellensis is a serious source of concern for winemakers. The production of volatile phenols by the yeast species confers to wine unpleasant sensory characteristics which are unacceptable by the consumers and inevitably provoke economic loss for the wine industry. This ubiquitous yeast is able to adapt to all winemaking steps and to withstand various environmental conditions. Moreover, the ability of B. bruxellensis to adhere and colonize inert materials can be the cause of the yeast persistence in the cellars and thus recurrent wine spoilage. We therefore investigated the surface properties, biofilm formation capacity and the factors which may affect the attachment of the yeast cells to surfaces with eight strains representative of the genetic diversity of the species. Our results show that the biofilm formation ability is strain-dependent and suggest a possible link between the physicochemical properties of the studied strains and their corresponding genetic group.

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