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1.
BMC Bioinformatics ; 21(1): 500, 2020 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-33148180

RESUMO

BACKGROUND: High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of protein-protein interaction (PPI) networks of different species reveals important insights which may help in disease analysis and drug design. The study of PPI network alignment can also helps in understanding the different biological systems of different species. It can also be used in transfer of knowledge across different species. Different aligners have been introduced in the last decade but developing an accurate and scalable global alignment algorithm that can ensures the biological significance alignment is still challenging. RESULTS: This paper presents a novel global pairwise network alignment algorithm, SAlign, which uses topological and biological information in the alignment process. The proposed algorithm incorporates sequence and structural information for computing biological scores, whereas previous algorithms only use sequence information. The alignment based on the proposed technique shows that the combined effect of structure and sequence results in significantly better pairwise alignments. We have compared SAlign with state-of-art algorithms on the basis of semantic similarity of alignment and the number of aligned nodes on multiple PPI network pairs. The results of SAlign on the network pairs which have high percentage of proteins with available structure are 3-63% semantically better than all existing techniques. Furthermore, it also aligns 5-14% more nodes of these network pairs as compared to existing aligners. The results of SAlign on other PPI network pairs are comparable or better than all existing techniques. We also introduce [Formula: see text], a Monte Carlo based alignment algorithm, that produces multiple network alignments with similar semantic similarity. This helps the user to pick biologically meaningful alignments. CONCLUSION: The proposed algorithm has the ability to find the alignments that are more biologically significant/relevant as compared to the alignments of existing aligners. Furthermore, the proposed method is able to generate alternate alignments that help in studying different genes/proteins of the specie.


Assuntos
Algoritmos , Mapas de Interação de Proteínas , Proteínas/metabolismo , Animais , Bases de Dados de Proteínas , Humanos , Camundongos , Método de Monte Carlo , Proteínas/química , Leveduras/metabolismo
2.
Int J Food Microbiol ; 333: 108796, 2020 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-32771820

RESUMO

The objective of this study was to investigate the role of yeasts in the wet fermentation of coffee beans and their contribution to coffee quality using a novel approach. Natamycin (300 ppm) was added to the fermentation mass to suppress yeast growth and their metabolic activities, and the resultant microbial ecology, bean chemistry and sensory quality were analyzed and compared to non-treated spontaneous fermentation we reported previously. The yeast community was dominated by Hanseniaspora uvarum and Pichia kudriavzevii and grew to a maximum population of about 5.5 log CFU/g in the absence of Natamycin, while when Natamycin was added yeasts were suppressed. The major bacterial species in both the spontaneous and yeast-suppressed fermentations included the lactic acid bacteria Leuconostoc mesenteroides and Lactococcus lactis, the acetic acid bacteria Gluconobacter cerinus and Acetobacter persici and the Enterobacteriaceae Enterobacter, Citrobacter and Erwinia. For both fermentations, the mucilage layers were completely degraded by the end of the process and the absence of yeast activities had no significant impact on mucilage degradation. During fermentation, reducing sugars were consumed while lactic acid was accumulated inside the beans, and its concentration was significantly higher in the spontaneous fermentation (3 times) than that where yeasts were suppressed by Natamycin. Glycerol was detected with a concentration of 0.08% in the absence of Natamycin and was not identified when Natamycin was added. Green beans fermented with yeast growth contained a higher amount of isoamyl alcohol (21 times), ethanol (3.7 times), acetaldehyde (8 times), and ethyl acetate (25 times) compared to beans fermented in the absence of yeast activities, which remained higher in the former after roasting. Beans fermented without yeast activities had a mild fruity aroma, and lower sensory scores of fragrances (7.0), flavor (6.5), acidity (6.3), body (7.0) and overall score (6.5) compared to the former. These findings demonstrated the crucial roles of yeasts in wet fermentation of coffee beans and for producing high quality coffee.


Assuntos
Bactérias/metabolismo , Café/metabolismo , Fermentação/fisiologia , Hanseniaspora/metabolismo , Pichia/metabolismo , Leveduras/metabolismo , Acetaldeído/metabolismo , Acetatos/metabolismo , Ácido Acético/metabolismo , Anti-Infecciosos/farmacologia , Bactérias/classificação , Reatores Biológicos/microbiologia , Café/microbiologia , Etanol/metabolismo , Ácido Láctico/metabolismo , Natamicina/farmacologia , Odorantes/análise , Pentanóis/metabolismo , Paladar
3.
J Food Sci ; 85(7): 2069-2079, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32602125

RESUMO

Triggered by the development of lactic acid bacteria (LAB) during the production of Scotch whisky, this study examined the influence of yeast and LAB inoculation on whisky flavor. Four new spirits were produced using the same process. LAB were added as a form of a Greek yogurt's live culture. In each category (barley and rye), one sample was fermented with Greek yogurt while the other was fermented without it. The spirits were matured and analyzed at five different points. Results from gas chromatography-mass spectrometry (GC-MS) analysis showed basic volatile compounds, along with some important extra compounds with yogurt culture. The most obvious differences were observed in the concentration of butanoic acid, a characteristic acid in spirits undergoing lactic acid fermentation: to identify esters such as ethyl butanoate, ethyl isobutanoate, isoamyl butanoate, and 2-phenylethyl butanoate, they are not typical compounds in whisky.


Assuntos
Bebidas Alcoólicas/análise , Aromatizantes/química , Manipulação de Alimentos/métodos , Iogurte/análise , Bebidas Alcoólicas/microbiologia , Meios de Cultura/análise , Meios de Cultura/metabolismo , Fermentação , Aromatizantes/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Hordeum/metabolismo , Hordeum/microbiologia , Humanos , Lactobacillales/metabolismo , Odorantes/análise , Secale/metabolismo , Secale/microbiologia , Paladar , Compostos Orgânicos Voláteis/química , Compostos Orgânicos Voláteis/metabolismo , Leveduras/metabolismo , Iogurte/microbiologia
4.
Int J Food Microbiol ; 327: 108652, 2020 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-32442778

RESUMO

Food-grade waste and side streams should be strictly kept in food use in order to achieve sustainable food systems. At present, the baking industry creates food-grade waste as excess and deformed products that are mainly utilized for non-food uses, such as bioethanol production. The purpose of this study was therefore to explore the potential of waste wheat bread recycling for fresh wheat bread production. Waste bread recycling was assessed without further processing or after tailored fermentation with lactic acid bacteria producing either dextran or ß-glucan exopolysaccharides. When non-treated waste bread slurry was added to new bread dough, bread quality (specific volume and softness) decreased with increasing content of waste bread addition. In situ EPS-production (dextran and microbial ß-glucan) significantly increased waste bread slurry viscosity and yielded residual fructose or glucose that could effectively replace the sugar added for yeast leavening. Furthermore, fermentation acidified waste bread matrix, thus improving the hygienic safety of the process. Bread containing dextran synthesized in situ by Weissella confusa A16 showed good technological quality. The produced dextran compensated the adverse effect of recycled bread on new bread quality attributes by 12% increase in bread specific volume and 37% decrease in crumb hardness. In this study, a positive technological outcome of the bread containing microbial ß-glucan was not detected. The waste bread fermented by W. confusa A16 containing dextran appears to enable safe bread recycling with low acidity and minimal quality loss.


Assuntos
Pão/microbiologia , Pão/normas , Fermentação , Indústria Alimentícia , Resíduos Industriais , Reciclagem/métodos , Triticum/microbiologia , Dextranos/metabolismo , Ácido Láctico/metabolismo , Weissella/metabolismo , Leveduras/metabolismo , beta-Glucanas/metabolismo
5.
Food Chem ; 328: 127110, 2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-32464557

RESUMO

In the present work we aimed to demonstrate the influence of inoculum starter in support high quality fermentation. Cocoa fermentations were performed in wooden boxes and eight yeasts strains were used in separated fermentations of fine cocoa, type Scavina, as starter inoculum. Temperature, pH, titirable acidity, reducing sugar and free amino acids were evaluated during or after fermentation. The influence of starters yeasts on the decrease of acidity, sugar concentration and free amino acids was significant. The strains Candida parapsilosis, Torulaspora delbrueckii and Pichia kluyveri showed greater changes in the reducing sugar and free amino acids in fermented cocoa beans. These results indicate the ability of yeast used as inoculum starter to modify the end condition and further enhance the quality of fine cocoa beans.


Assuntos
Cacau , Microbiologia de Alimentos/métodos , Leveduras , Aminoácidos/análise , Aminoácidos/metabolismo , Cacau/química , Cacau/metabolismo , Candida parapsilosis/genética , Candida parapsilosis/metabolismo , Chocolate , Fermentação , Concentração de Íons de Hidrogênio , Pichia/genética , Pichia/metabolismo , Sementes/química , Sementes/microbiologia , Temperatura , Torulaspora/genética , Torulaspora/metabolismo , Leveduras/genética , Leveduras/metabolismo
6.
J Appl Microbiol ; 129(5): 1163-1172, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32392369

RESUMO

AIMS: This study evaluated the effects of exogenous lactic acid bacteria (LAB) on silage fermentation and bacterial community of reed canary grass (RCG) straw. METHODS AND RESULTS: The leaf, stem and whole crop of RCG straw were separately ensiled in small bag silos, without (control) or with inoculation of two exogenous LAB (LP, Lactobacillus plantarum; LB, Lactobacillus buchneri), and stored at ambient temperature of <20°C. Inoculation of exogenous LAB decreased (P < 0·05) bacterial alpha diversity and shifted (P < 0·05) bacterial community compositions, but did not change (P> 0·05) the relative abundance of Lactobacillus. Particularly, inoculation of LB increased (P < 0·05) acetic acid and propionic acid contents, decreased (P < 0·05) butyric acid (BA) and ammonia-N contents, separated (P < 0·05) the bacterial community in silage. However, the exogenous LAB inoculated silages were characterized by main distribution of yeasts, presence of undesirable bacterial genera such as Clostridium and high levels of BA and ammonia-N. CONCLUSION: Inoculation of exogenous LAB exerted a limited influence on the silage fermentation and bacterial community compositions of RCG straw on the Qinghai-Tibetan Plateau. SIGNIFICANCE AND IMPACT OF THE STUDY: Commercial LAB inoculants are not always efficient on enhancing silage quality and stability. Thus, an alternative additive for inhibiting undesirable microbes during storage is important to improve RCG silage quality on the Qinghai-Tibetan Plateau.


Assuntos
Lactobacillales/fisiologia , Microbiota , Phalaris/microbiologia , Silagem/microbiologia , Amônia/análise , Amônia/metabolismo , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Ácidos Graxos Voláteis/análise , Ácidos Graxos Voláteis/metabolismo , Fermentação , Lactobacillales/metabolismo , Phalaris/química , Silagem/análise , Tibet , Leveduras/classificação , Leveduras/crescimento & desenvolvimento , Leveduras/metabolismo
7.
J Biosci Bioeng ; 130(1): 63-70, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32265130

RESUMO

Japanese sake production involves three processes: rice koji fermentation, seed mash fermentation, and main mash fermentation. Traditional seed mash (kimoto) production utilizes natural lactic acid produced by lactic acid bacteria for pure cultures of only sake yeast, preventing the growth of wild yeast and other unwanted bacteria. Recently, because kimoto production requires substantial time and labor, sake yeast mass-cultured in usual liquid medium has been used as a seed mash alternative. Sake quality is highly similar to that of kimoto, suggesting that they share similar component profiles. However, comparative component analyses of sake brewed with kimoto and sake brewed with cultured yeast are lacking. In this study, a time-course analysis of hydrophilic compounds in the main mash brewed with kimoto and with cultured yeast as well as a sensory evaluation of the products were performed. As a result, differences in various compounds and in umami taste level between sake brewed with kimoto and cultured yeast were detected. This is the first comparative analysis of changes in the component profile during sake main mash brewing using kimoto seed mash and cultured sake yeast; our results clarify the effects of kimoto seed mash on main mash brewing and sake quality.


Assuntos
Bebidas Alcoólicas/análise , Aromatizantes/química , Leveduras/metabolismo , Bebidas Alcoólicas/microbiologia , Fermentação , Aromatizantes/metabolismo , Humanos , Ácido Láctico/análise , Ácido Láctico/metabolismo , Lactobacillales/metabolismo , Oryza/química , Oryza/metabolismo , Oryza/microbiologia , Sementes/química , Sementes/metabolismo , Sementes/microbiologia , Paladar
8.
Food Chem ; 322: 126710, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32283363

RESUMO

Sourdough fermentation influences several properties of leavened baked goods also because Lactic acid bacteria (LAB) and yeasts produce bioactive peptides with a positive effect on human health. In an early study, three Lactobacilli strains (L. farciminis H3 and A11 and L. sanfranciscensis I4) possessing different proteolytic activities were used to produce sourdoughs containing peptides equipped with anti-inflammatory and/or antioxidant properties. This work was aimed to assess whether these properties could be retained after cooking. The selected LABs were used to produce breads from which low molecular weight (LMW-) peptides were extracted. The results provide solid proofs of keeping both antioxidant and anti-inflammatory activities of peptides from cooked products. Sequences of LMW-peptides either from doughs and breads were determined by mass spectrometry: differences have been noticed in amino acidic composition and in sequences, however, all the strains produce peptides equipped with antioxidant and anti-inflammatory activities.


Assuntos
Anti-Inflamatórios/análise , Antioxidantes/análise , Pão/análise , Pão/microbiologia , Lactobacillus/metabolismo , Anti-Inflamatórios/metabolismo , Antioxidantes/metabolismo , Fermentação , Farinha/análise , Microbiologia de Alimentos , Humanos , Peptídeos/análise , Peptídeos/metabolismo , Leveduras/metabolismo
9.
Nat Microbiol ; 5(7): 943-954, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32313201

RESUMO

The conventional view is that high temperatures cause microorganisms to replicate slowly or die. In this view, microorganisms autonomously combat heat-induced damages. However, microorganisms co-exist with each other, which raises the underexplored and timely question of whether microorganisms can cooperatively combat heat-induced damages at high temperatures. Here, we use the budding yeast Saccharomyces cerevisiae to show that cells can help each other and their future generations to survive and replicate at high temperatures. As a consequence, even at the same temperature, a yeast population can exponentially grow, never grow or grow after unpredictable durations (hours to days) of stasis, depending on its population density. Through the same mechanism, yeasts collectively delay and can eventually stop their approach to extinction, with higher population densities stopping faster. These features arise from yeasts secreting and extracellularly accumulating glutathione-a ubiquitous heat-damage-preventing antioxidant. We show that the secretion of glutathione, which eliminates harmful extracellular chemicals, is both necessary and sufficient for yeasts to collectively survive at high temperatures. A mathematical model, which is generally applicable to any cells that cooperatively replicate by secreting molecules, recapitulates all of these features. Our study demonstrates how organisms can cooperatively define and extend the boundaries of life-permitting temperatures.


Assuntos
Glutationa/biossíntese , Temperatura , Leveduras/metabolismo , Transporte Biológico , Proliferação de Células , Ecossistema , Regulação Fúngica da Expressão Gênica , Genes Fúngicos , Modelos Teóricos
10.
Int J Food Microbiol ; 323: 108610, 2020 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-32240882

RESUMO

Gioddu, also known as "Miciuratu", "Mezzoraddu" or "Latte ischidu" (literally meaning acidulous milk), is the sole variety of traditional Italian fermented milk. The aim of the present study was to elucidate the microbiota and the mycobiota occurring in artisan Gioddu sampled from three Sardinian producers by combining the results of viable counting on selective culture media and high-throughput sequencing. Physico-chemical parameters were also measured. The overall low pH values (3.80-4.22) recorded in the analyzed Gioddu samples attested the strong acidifying activity carried out by lactic acid bacteria during fermentation. Viable counts revealed the presence of presumptive lactococci, presumptive lactobacilli and non-Saccharomyces yeasts. A complex (kefir-like) microbiota of bacteria and yeasts was unveiled through sequencing. In more detail, Lactobacillus delbrueckii was found to dominate in Gioddu together with Streptococcus thermophilus, thus suggesting the establishment of a yogurt-like protocooperation. Unexpectedly, in all the three analyzed batches from two out of the three producers Lactobacillus kefiri was also detected, thus representing an absolute novelty, which suggests the presence of bioactive compounds (e.g. exopolysaccharides) similar to those characterizing milk kefir beverage. Mycobiota population, studied for the very first time in Gioddu, revealed a more complex composition, with Kluyveromyces marxianus, Galactomyces candidum and Geotrichum galactomyces constituting the core species. Further research is needed to disclose the eventual occurence in Gioddu of probiotic cultures and bioactive compounds (e.g. exopolysaccharides, angiotensin-converting enzyme inhibitory peptides and antimicrobial compounds) with potential health-benefits for the consumers.


Assuntos
Produtos Fermentados do Leite/microbiologia , Fermentação , Microbiologia de Alimentos , Lactobacillus/classificação , Leveduras/classificação , Animais , Produtos Fermentados do Leite/análise , Itália , Lactobacillus/isolamento & purificação , Lactobacillus/metabolismo , Probióticos/classificação , Probióticos/isolamento & purificação , Probióticos/metabolismo , Streptococcus thermophilus/isolamento & purificação , Streptococcus thermophilus/metabolismo , Leveduras/isolamento & purificação , Leveduras/metabolismo , Iogurte/microbiologia
11.
Science ; 368(6486): 78-84, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32241946

RESUMO

The design of modular protein logic for regulating protein function at the posttranscriptional level is a challenge for synthetic biology. Here, we describe the design of two-input AND, OR, NAND, NOR, XNOR, and NOT gates built from de novo-designed proteins. These gates regulate the association of arbitrary protein units ranging from split enzymes to transcriptional machinery in vitro, in yeast and in primary human T cells, where they control the expression of the TIM3 gene related to T cell exhaustion. Designed binding interaction cooperativity, confirmed by native mass spectrometry, makes the gates largely insensitive to stoichiometric imbalances in the inputs, and the modularity of the approach enables ready extension to three-input OR, AND, and disjunctive normal form gates. The modularity and cooperativity of the control elements, coupled with the ability to de novo design an essentially unlimited number of protein components, should enable the design of sophisticated posttranslational control logic over a wide range of biological functions.


Assuntos
Receptor Celular 2 do Vírus da Hepatite A/química , Engenharia de Proteínas , Mapas de Interação de Proteínas , Processamento de Proteína Pós-Traducional , Receptor Celular 2 do Vírus da Hepatite A/genética , Humanos , Lógica , Espectrometria de Massas , Biologia Sintética , Linfócitos T/metabolismo , Transcrição Genética , Leveduras/metabolismo
12.
Nucleic Acids Res ; 48(8): 4115-4138, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32182340

RESUMO

Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and crotonylation on histones H3 and H4 during mouse spermatogenesis. Lysine crotonylation appeared to be of significant abundance compared to acetylation, particularly on Lys27 of histone H3 (H3K27cr) that accumulates in sperm in a cleaved form of H3. We identified the genomic localization of H3K27cr and studied its effects on transcription compared to the classical active mark H3K27ac at promoters and distal enhancers. The presence of both marks was strongly associated with highest gene expression. Assessment of their co-localization with transcription regulators (SLY, SOX30) and chromatin-binding proteins (BRD4, BRDT, BORIS and CTCF) indicated systematic highest binding when both active marks were present and different selective binding when present alone at chromatin. H3K27cr and H3K27ac finally mark the building of some sperm super-enhancers. This integrated analysis of omics data provides an unprecedented level of understanding of gene expression regulation by H3K27cr in comparison to H3K27ac, and reveals both synergistic and specific actions of each histone modification.


Assuntos
Elementos Facilitadores Genéticos , Epigênese Genética , Código das Histonas , Regiões Promotoras Genéticas , Espermatogênese/genética , Acetilcoenzima A/metabolismo , Acetilação , Acil Coenzima A/metabolismo , Animais , Evolução Biológica , Crotonatos/metabolismo , Genômica , Histonas/química , Histonas/metabolismo , Lisina/metabolismo , Masculino , Metabolômica , Camundongos Endogâmicos C57BL , Proteômica , Transcrição Genética , Leveduras/metabolismo , Leveduras/fisiologia
13.
Nat Chem Biol ; 16(6): 653-659, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32152544

RESUMO

Defining the biologically active structures of proteins in their cellular environments remains challenging for proteins with multiple conformations and functions, where only a minor conformer might be associated with a given function. Here, we use deep mutational scanning to probe the structure and dynamics of α-synuclein, a protein known to adopt disordered, helical and amyloid conformations. We examined the effects of 2,600 single-residue substitutions on the ability of intracellularly expressed α-synuclein to slow the growth of yeast. Computational analysis of the data showed that the conformation responsible for this phenotype is a long, uninterrupted, amphiphilic helix with increasing dynamics toward the C terminus. Deep mutational scanning can therefore determine biologically active conformations in cellular environments, even for a highly dynamic multi-conformational protein.


Assuntos
Proteínas Mutantes/química , Proteínas Mutantes/genética , Mutação , alfa-Sinucleína/química , alfa-Sinucleína/genética , Sequência de Aminoácidos , Amiloide/química , Biblioteca Genômica , Modelos Moleculares , Fenótipo , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade , Leveduras/metabolismo
14.
Nucleic Acids Res ; 48(7): 3692-3707, 2020 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-32133535

RESUMO

Alkylation is one of the most ubiquitous forms of DNA lesions. However, the motif preferences and substrates for the activity of the major types of alkylating agents defined by their nucleophilic substitution reactions (SN1 and SN2) are still unclear. Utilizing yeast strains engineered for large-scale production of single-stranded DNA (ssDNA), we probed the substrate specificity, mutation spectra and signatures associated with DNA alkylating agents. We determined that SN1-type agents preferably mutagenize double-stranded DNA (dsDNA), and the mutation signature characteristic of the activity of SN1-type agents was conserved across yeast, mice and human cancers. Conversely, SN2-type agents preferably mutagenize ssDNA in yeast. Moreover, the spectra and signatures derived from yeast were detectable in lung cancers, head and neck cancers and tumors from patients exposed to SN2-type alkylating chemicals. The estimates of mutation loads associated with the SN2-type alkylation signature were higher in lung tumors from smokers than never-smokers, pointing toward the mutagenic activity of the SN2-type alkylating carcinogens in cigarettes. In summary, our analysis of mutations in yeast strains treated with alkylating agents, as well as in whole-exome and whole-genome-sequenced tumors identified signatures highly specific to alkylation mutagenesis and indicate the pervasive nature of alkylation-induced mutagenesis in cancers.


Assuntos
Alquilantes/toxicidade , Mutagênese , Mutação , Neoplasias/genética , Adenina/química , Animais , DNA Glicosilases/metabolismo , DNA Fúngico/química , DNA de Cadeia Simples/química , Humanos , Camundongos , Leveduras/efeitos dos fármacos , Leveduras/genética , Leveduras/metabolismo
15.
Enzyme Microb Technol ; 135: 109490, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32146936

RESUMO

Bioproducts production using monomeric sugars derived from lignocellulosic biomass presents several challenges, such as to require a physicochemical pretreatment to improve its conversion yields. Hydrothermal lignocellulose pretreatment has several advantages and results in solid and liquid streams. The former is called hemicellulosic hydrolysate (HH), which contains inhibitory phenolic compounds and sugar degradation products that hinder microbial fermentation products from pentose sugars. Here, we developed and applied a novel enzyme process to detoxify HH. Initially, the design of experiments with different redox activities enzymes was carried out. The enzyme mixture containing the peroxidase (from Armoracia rusticana) together with superoxide dismutase (from Coptotermes gestroi) are the most effective to detoxify HH derived from sugarcane bagasse. Butanol fermentation by the bacteria Clostridium saccharoperbutylacetonicum and ethanol production by the yeast Scheffersomyces stipitis increased by 24.0× and 2.4×, respectively, relative to the untreated hemicellulosic hydrolysates. Detoxified HH was analyzed by chromatographic and spectrometric methods elucidating the mechanisms of phenolic compound modifications by enzymatic treatment. The enzyme mixture degraded and reduced the hydroxyphenyl- and feruloyl-derived units and polymerized the lignin fragments. This strategy uses biocatalysts under environmentally friendly conditions and could be applied in the fuel, food, and chemical industries.


Assuntos
Clostridium/metabolismo , Peroxidase/química , Polissacarídeos/química , Saccharum/química , Superóxido Dismutase/química , Leveduras/metabolismo , Biocatálise , Butanóis/metabolismo , Celulose/química , Celulose/metabolismo , Fermentação , Microbiologia Industrial , Peroxidase/metabolismo , Polissacarídeos/metabolismo , Saccharum/microbiologia , Superóxido Dismutase/metabolismo
16.
Int J Food Microbiol ; 321: 108544, 2020 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-32086129

RESUMO

The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.


Assuntos
Coffea/microbiologia , Manipulação de Alimentos/métodos , Microbiota , Austrália , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Bactérias/isolamento & purificação , Bactérias/metabolismo , Coffea/química , Café/química , Fermentação , Microbiologia de Alimentos , Microbiota/genética , Sementes/química , Sementes/microbiologia , Leveduras/classificação , Leveduras/crescimento & desenvolvimento , Leveduras/isolamento & purificação , Leveduras/metabolismo
17.
OMICS ; 24(2): 96-109, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31895625

RESUMO

Ribosomopathies result in various cancers, neurodegenerative and viral diseases, and other pathologies such as Diamond-Blackfan anemia and Shwachman-Diamond syndrome. Their pathophysiology at a proteome and functional level remains to be determined. Protein networks and highly connected hub proteins for ribosome biogenesis in Saccharomyces cerevisiae offer a potential as a model system to inform future therapeutic innovation in ribosomopathies. In this context, we report a ribosome biogenesis protein-protein interaction network in S. cerevisiae, created with 1772 proteins and 22,185 physical interactions connecting them. Moreover, by network decomposition analysis, we determined the linear pathways between the transcription factors and target proteins with a view to drug repurposing. While considering only the paths containing the three C/D box proteins (Nop56, Nop58, and Nop1), the most frequently encountered proteins were Aft1, Htz1, Ssa1, Ssb1, Ssb2, Gcn5, Cka1, Tef1, Nop1, Cdc28, Act1, Krr1, Rpl8B, and Tor1, which were then identified as potential drug targets. For drug repurposing, these candidate proteins were further searched in the DrugBank to find other diseases associated with them, as well as the drugs used to treat these diseases. To support the computational results, an experimental study was conducted using in-house manufactured microfluidic bioreactor platform, while the effect of the drug temsirolimus, Tor1 inhibitor, on yeast cells was investigated by following Nop56 protein expression. In conclusion, these results inform the ways in which ribosomopathies and associated common complex human diseases materialize and how drug repurposing might accelerate therapeutic innovation through bioinformatic studies of yeast.


Assuntos
Reposicionamento de Medicamentos , Mapeamento de Interação de Proteínas , Mapas de Interação de Proteínas/efeitos dos fármacos , Ribossomos/efeitos dos fármacos , Ribossomos/metabolismo , Leveduras/efeitos dos fármacos , Leveduras/metabolismo , Biologia Computacional/métodos , Descoberta de Drogas , Ontologia Genética , Humanos , Modelos Teóricos , Anotação de Sequência Molecular , Mapeamento de Interação de Proteínas/métodos , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/metabolismo
18.
Food Microbiol ; 87: 103398, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31948610

RESUMO

Melatonin is an indole amine that interacts with some proteins in mammals, such as calreticulin, calmodulin or sirtuins. In yeast, melatonin is synthetized and interacts with glycolytic proteins during alcoholic fermentation in Saccharomyces cerevisiae. Due to its importance as an antioxidant molecule in both Saccharomyces and non-Saccharomyces yeasts, the aim of this study was to determine the intracellular and extracellular synthesis profiles of melatonin in four non-Saccharomyces strains (Torulaspora delbrueckii, Hanseniaspora uvarum, Starmeralla bacillaris and Metschnikowia pulcherrima) and to confirm whether glycolytic enzymes can also interact with this molecule in non-conventional yeast cells. Melatonin from fermentation samples was analyzed by liquid chromatography mass spectrometry, and proteins bound to melatonin were immunopurified by melatonin-IgG-Dynabeads. Melatonin was produced in a similar pattern in all non-Saccharomyces yeast, with M. pulcherrima and S. bacillaris being the highest producers. However, melatonin only bound to proteins in two non-conventional yeasts, S. bacillaris and T. delbrueckii, which specifically had higher fermentative capacities. Sequence analysis showed that most proteins shared high levels of homology with glycolytic enzymes, but an RNA-binding protein, the elongation alpha factor, which is related to mitochondria, was also identified. This study reports for the first time the interaction of melatonin with proteins inside non-Saccharomyces yeast cells. These results reinforce the possible role of melatonin as a signal molecule, likely related to fermentation metabolism and provide a new perspective for understanding its role in yeast.


Assuntos
Proteínas Fúngicas/metabolismo , Melatonina/metabolismo , Leveduras/enzimologia , Fermentação , Proteínas Fúngicas/genética , Glicólise , Ligação Proteica , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Leveduras/genética , Leveduras/metabolismo
19.
Biochem J ; 477(1): 243-258, 2020 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-31951000

RESUMO

Physiological membrane vesicles are built to separate reaction spaces in a stable manner, even when they accidentally collide or are kept in apposition by spatial constraints in the cell. This requires a natural resistance to fusion and mixing of their content, which originates from substantial energetic barriers to membrane fusion [1]. To facilitate intracellular membrane fusion reactions in a controlled manner, proteinaceous fusion machineries have evolved. An important open question is whether protein fusion machineries actively pull the fusion reaction over the present free energy barriers, or whether they rather catalyze fusion by lowering those barriers. At first sight, fusion proteins such as SNARE complexes and viral fusion proteins appear to act as nano-machines, which mechanically transduce force to the membranes and thereby overcome the free energy barriers [2,3]. Whether fusion proteins additionally alter the free energy landscape of the fusion reaction via catalytic roles is less obvious. This is a question that we shall discuss in this review, with particular focus on the influence of the eukaryotic SNARE-dependent fusion machinery on the final step of the reaction, the formation and expansion of the fusion pore.


Assuntos
Membranas Intracelulares/metabolismo , Fusão de Membrana/fisiologia , Proteínas SNARE , Vacúolos/metabolismo , Proteínas SNARE/química , Proteínas SNARE/metabolismo , Leveduras/metabolismo
20.
J Food Sci ; 85(2): 455-464, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31957879

RESUMO

Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.


Assuntos
Bactérias/isolamento & purificação , Bebidas/microbiologia , Alimentos e Bebidas Fermentados/microbiologia , Microbiota , Leveduras/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Fermentação , Metagenoma , Metagenômica , Análise de Sequência de DNA , Leveduras/classificação , Leveduras/genética , Leveduras/metabolismo
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