Caracterização do papel de Nop53 na montagem da subunidade ribossomal maior em Saccharomyces cerevisiae / Characterization of the role of Nop53 in the assembly of the large ribosomal subunit in Saccharomyces cerevisiae

Os ribossomos são complexos ribonucleoproteicos conservados formados por duas subunidades assimétricas (40S e 60S em eucariotos) responsáveis pela tradução da informação genética e catálise da síntese proteica. A montagem destes complexos em eucariotos é mais bem descrita em S. cerevisiae, constituindo um processo celular energeticamente dispendioso e com múltiplas etapas. Ela tem origem no nucléolo com a transcrição do pré-rRNA 35S e requer o recrutamento hierárquico e transiente de cerca de 200 fatores de montagem para garantir a formação correta dos centros funcionais aptos à tradução. Neste processo, que se estende no núcleo e citoplasma, 79 proteínas ribossomais associam-se gradativamente à medida que o prérRNA é dobrado, modificado e processado. O processamento do pré-rRNA 35S consiste na remoção progressiva de espaçadores internos (ITS1 e ITS2) e externos (5ETS e 3ETS), que separam e flanqueiam os rRNAs maduros componentes de ambas subunidades ribossomais. A clivagem do ITS1 separa as vias de maturação do pré-60S e do pré-40S. O ITS2, que, em associação a fatores de montagem, forma uma estrutura denominada ITS2-foot, é o último espaçador do pré-60S a ser removido. A composição do ITS2-foot permanece inalterada no nucléolo até a transição entre o estado E nucleolar e a formação da partícula Nog2 nuclear. Nesta etapa, a liberação do fator Erb1 permite o recrutamento do fator de montagem conservado e essencial Nop53. Na base do ITS2-foot, Nop53 recruta o exossomo via RNA helicase Mtr4 para a clivagem 3-5 exonucleolítica de parte do ITS2 levando à desmontagem do ITS2-foot. O fato de Nop53 atuar como ponte entre dois grandes complexos e apresentar uma estrutura flexível e estendida nos levou a aprofundar a caracterização de seu papel durante a maturação do pré60S. Neste trabalho, usando análise proteômica quantitativa label-free baseada em espectrometria de massas, caracterizou-se o interactoma de Nop53, e avaliou-se o impacto da depleção de Nop53 no interactoma da subunidade catalítica do exossomo Rrp6 e na composição de pré-ribossomos representativos de quase todas as etapas de maturação do pré-60S. Em paralelo, foram caracterizados mutantes truncados de Nop53 e avaliada por pull-down a interação de Nop53 com componentes do exossomo. Os resultados obtidos mostraram que Nop53 é capaz de interagir com o cofator do exossomo Mpp6, sugerindo pontos adicionais de interação durante o recrutamento do exossomo ao pré-60S. A análise do interactoma de Rrp6 mostrou uma associação precoce do exossomo aos intermediários pré-ribossomais nucleolares mais iniciais, anteriores aos previamente descritos. Mudanças na composição dos intermediários pré-60S revelaram que a depleção de Nop53 afeta a transição entre o estado E e a partícula Nog2, afetando eventos tardios de maturação como o recrutamento de Yvh1. Comparando-se o efeito da depleção de Nop53 com o de mutantes nop53 desprovidos da região de recrutamento do exossomo, obtivemos evidências bioquímicas do papel estrutural de Nop53 na base do ITS2- foot. Em conjunto, estas observações, à luz de estruturas de intermediários pré-ribossomais recentemente descritas, nos permitiram concluir que o recrutamento de Nop53 ao pré-60S contribui para a estabilização de eventos de remodelamento do rRNA que antecedem a formação da partícula Nog2

Ribosomes are conserved ribonucleoprotein complexes formed by two asymmetric subunits (the 40S and the 60S in eukaryotes) responsible for translating the genetic information and catalyzing protein synthesis. The assembly of these complexes in eukaryotes is best described in S. cerevisiae. It is an energetically demanding, multi-step cellular process, that starts in the nucleolus with the transcription of the 35S pre-rRNA. It requires the hierarchical and transient recruitment of about 200 assembly factors to ensure the correct formation of the functional centers suitable for translation. In this process, which extends into the nucleus and cytoplasm, 79 ribosomal proteins gradually associate as the pre-rRNA is folded, modified, and processed. The 35S pre-rRNA processing happens with the progressive removal of internal (ITS1 and ITS2) and external (5'ETS and 3'ETS) transcribed spacers, which separate and flank the mature rRNA components of both ribosomal subunits. The cleavage at the ITS1 separates the pre-60S and pre40S maturation pathways. The ITS2, which in association with assembly factors constitutes a structure called ITS2-foot, is the last pre-60S spacer to be removed. The composition of the ITS2- foot remains unchanged in the nucleolus until the transition between the nucleolar state E and the nuclear Nog2 particle. At this stage, the release of Erb1 allows the recruitment of the conserved and essential assembly factor Nop53. At the base of the ITS2-foot, Nop53 recruits the exosome via the RNA helicase Mtr4 for the ITS2 3'-5' exonucleolytic cleavage leading to the ITS2-foot disassembly. The fact that Nop53 acts as a bridge between these two large complexes and exhibits a flexible and extended structure led us to further characterize its role in the pre-60S maturation. In this work, using mass spectrometry-based label-free quantitative proteomics, we characterized the interactome of Nop53, as well as the impact of the depletion of Nop53 on the interactome of the exosome catalytic subunit Rrp6 and on the composition of pre-ribosomes representative of almost all pre-60S maturation stages. In parallel, we characterized nop53 truncated mutants and evaluated the interaction of Nop53 with exosome components by pulldown assays. The results showed that Nop53 can interact with the exosome cofactor Mpp6, suggesting the contribution of additional points of interaction during the exosome recruitment to the pre-60S. The analysis of the Rrp6 interactome revealed an early association of the exosome with pre-ribosomal intermediates at very early nucleolar stages, before those previously described. Changes in the composition of pre-60S intermediates revealed that Nop53 depletion affects the transition between the state E and the Nog2 particle, affecting late pre-60S maturation events, such as the Yvh1 recruitment. Comparing the effect of Nop53 depletion with that of nop53 mutants lacking the exosome interacting region, we obtained biochemical evidence of the structural role of Nop53 at the base of the ITS2-foot. Altogether, and in light of recently described structures of pre-ribosomal intermediates, these observations allowed us to conclude that the recruitment of Nop53 to the pre-60S contributes to the stabilization of rRNA remodeling events that precede the formation of the Nog2 particle

Saccharomyces cerevisiae populations and other yeasts associated with indigenous beers (chicha) of Ecuador

ABSTRACT Chicha, a type of beer made mainly with maize or cassava, is a traditional fermented beverage of the Andean region. There have only been a few studies on yeasts associated with chicha fermentation, and the species diversity occurring during the production of this beverage is not known. The objective of this study was to determine the biodiversity of yeasts in chicha, and to characterize the Saccharomyces cerevisiae populations associated with the production of chicha de jora, seven-grain chicha, chicha de yuca, and chicha de morocho in Ecuador. The molecular diversity of S. cerevisiae populations was determined by restriction polymorphism mitochondrial profiles. The beverages were characterized based on their physicochemical parameters. Twenty-six species were identified, and the most prevalent species were S. cerevisiae and Torulaspora delbrueckii. Other yeast species were isolated at low frequencies. Among 121 isolates of S. cerevisiae, 68 different mtDNA molecular profiles were identified. These results showed that chichas are fermented by a high number of different strains of S. cerevisiae. Some other species provided a minor contribution to the fermentation process. The chicha presented generally similar physicochemical parameters to those observed for other traditional fermented beverages, and can be considered as an acid fermented beverage.

Bioethanol strains of Saccharomyces cerevisiae characterised by microsatellite and stress resistance

Abstract Strains of Saccharomyces cerevisiae may display characteristics that are typical of rough-type colonies, made up of cells clustered in pseudohyphal structures and comprised of daughter buds that do not separate from the mother cell post-mitosis. These strains are known to occur frequently in fermentation tanks with significant lower ethanol yield when compared to fermentations carried out by smooth strains of S. cerevisiae that are composed of dispersed cells. In an attempt to delineate genetic and phenotypic differences underlying the two phenotypes, this study analysed 10 microsatellite loci of 22 S. cerevisiae strains as well as stress resistance towards high concentrations of ethanol and glucose, low pH and cell sedimentation rates. The results obtained from the phenotypic tests by Principal-Component Analysis revealed that unlike the smooth colonies, the rough colonies of S. cerevisiae exhibit an enhanced resistance to stressful conditions resulting from the presence of excessive glucose and ethanol and high sedimentation rate. The microsatellite analysis was not successful to distinguish between the colony phenotypes as phenotypic assays. The relevant industrial strain PE-2 was observed in close genetic proximity to rough-colony although it does not display this colony morphology. A unique genetic pattern specific to a particular phenotype remains elusive.

Biologia molecular de leveduras e sua aplicação biotecnológica para estudo de mecanismos celulares do câncer e seu tratamento / Molecular biology of yeast and its biotechnological application to study the cellular mechanisms of cancer and its treatment

A levedura Saccharomyces cerevisiae é o eucarioto mais bem caracterizado quanto às vias metabólicas, celulares e funções de genes. Calcula-se que dos 6.000 genes codificadores de proteínas, pelo menos 3.000 tenham homologia com genes humanos. Além disso, mesmo quando não há homologia direta, os mecanismos moleculares são conservados e em ensaios de complementação de função é possível caracterizar funções análogas em humanos. Leveduras apresentam além de mecanismos conservados, diversas semelhanças metabólicas com células tumorais; talvez a mais marcante delas seja a repressão catabólica por glicose. Esse fenômeno causa uma superativação da via glicolítica e inibição da cadeia respiratória, o que lembra muito o efeito Warburg apresentado pelas células tumorais. Esse comportamento metabólico tem relação estreita com a homeostase redox celular. Estes fatores mostram o quanto à caracterização dessas células fúngicas pode ser aplicada ao entendimento e tratamento do câncer. Mesmo assim, 20 anos após o término do sequenciamento do genoma de S. cerevisiae, mais de 1.000 genes continuam anotados como não caracterizados. Além disso, as leveduras têm papel fundamental na produção biotecnológica de insumos farmacêuticos. Nesse texto sistematizado relato as contribuições dos meus estudos, juntamente com os resultados do meu grupo de pesquisa, usando a biologia molecular das leveduras, para responder questões aplicadas à compreensão de funções celulares (com destaque à resposta antioxidante), mecanismos moleculares de resposta aos antitumorais e produção de biofármacos. Além de modelo celular, as leveduras representam excelentes plataformas para expressão heteróloga de proteínas de interesse Biotecnológico-Farmacêutico

The yeast Saccharomyces cerevisiae is the most well characterized eukaryote for metabolic, cellular and gene functions. It is estimated that of the 6,000 protein-encoding genes, at least 3,000 have homology to human genes. Moreover, even when there is no direct homology, the molecular mechanisms are conserved and through function complementation assays it is possible to characterize analogous functions in humans. Yeasts present, in addition to conserved mechanisms, diverse metabolic similarities with tumor cells; perhaps the most remarkable of them is the catabolic repression by glucose. This phenomenon causes an over activation of the glycolytic pathway and inhibition of the respiratory chain, which strongly resembles the Warburg effect presented by tumor cells. This metabolic behavior is closely related to cellular redox homeostasis. These factors show how much the characterization of these fungal cells can be applied to the understanding and treatment of cancer. Even so, 20 years after the end of the sequencing of the S. cerevisiae genome, more than 1,000 genes remain annotated as uncharacterized. In addition, yeasts play a key role in the biotechnological production of pharmaceutical inputs. In this systematized text I show the contributions of my studies, together with the results of my research group, using molecular biology of yeast to answer questions applied to understanding cellular functions (with emphasis on the antioxidant response), molecular response mechanisms to antitumor drugs and biopharmaceutical production. In addition to cellular model, yeasts represent excellent platforms for the heterologous expression of proteins of Biotechnological-Pharmaceutical interes

Isolation, identification and characterization of regional indigenous Saccharomyces cerevisiae strains

Abstract In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir) were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic) wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typing were employed to differentiate among indigenous S. cerevisiae strains. This combination of the methods provides a rapid and relatively simple approach for identification of yeast of S. cerevisiae at strain level. In total, 120 isolates were identified and grouped by molecular approaches and 45 of the representative strains were tested for selected important oenological properties including ethanol, sulfur dioxide and osmotic stress tolerance, intensity of flocculation and desirable enzymatic activities. Their ability to produce and utilize acetic/malic acid was examined as well; in addition, H2S production as an undesirable property was screened. The oenological characteristics of indigenous isolates were compared to a commercially available S. cerevisiae BS6 strain, which is commonly used as the starter culture. Finally, some indigenous strains coming from organically treated grape berries were chosen for their promising oenological properties and these strains will be used as the starter culture, because application of a selected indigenous S. cerevisiae strain can enhance the regional character of the wines.

Influence of fermentation time on characteristics of sourdough bread

Sourdough is used in the manufacture of numerous baked products. The microorganisms used in this preparation of sourdoughs included two strains from the Lactobacillus paracasei (1 and 2) and two strains from the Saccharomyces cerevisiae group (1 and 2). Samples of raw dough were analyzed for pH, titratable acidity and plate counts and samples of resulting bread were analyzed for pH, titratable acidity and specific volume. The samples were analyzed every 2 h, between 4 and 10 h of fermentation. After 10 hours of fermentation, the lowest values of pH were for dough with LC2 and bread with SC1. Titratable acidity values increased over time, with the highest levels of acidity were found in the dough and bread with yeasts. Lactic acid bacteria showed the highest microbial counts over time. With the exception of SC2, the greatest microbial increases occurred at 10 hours of fermentation. LC1 showed the lowest volume across all time points (p < 0.05). The largest volumes were found in breads after 6 hours of fermentation. SC1 showed the best specific volume values across all times tested.

O fermento natural é usado no processamento de vários produtos de panificação. Os micro-organimos usados no preparo dos fermentos foram duas cepas de Lactobacillus paracasei (1 e 2) e duas cepas de Saccharomyces cerevisiae (1 e 2). Das amostras de massa crua, foi analisado o pH, a acidez titulável e a contagem em placas e das amostras do pão, foi analisado o pH, a acidez titulável e o volume específico. As amostras foram analisadas num intervalo de 2 h, entre 4 e 10 h de fermentação. Ao final, os menores valores de pH foram para a massa crua com LC2 e o pão com SC1. Os valores de acidez titulável aumentaram ao longo do tempo, apresentando os maiores teores de acidez a massa e o pão com leveduras. As bactérias láticas apresentaram as maiores contagens microbiológicas ao longo do tempo. Com exceção de SC2, os maiores crescimentos microbianos foram com 10 h de fermentação. LC1 apresentou menor volume em todas as horas (p < 0.05). Os maiores volumes encontrados nos pães foram com 6 h de fermentação. SC1 apresentou os melhores resultados de volume específico durante todo o período.

Fate of ochratoxin A content in Argentinean red wine during a pilot scale vinification / Evolución del contenido de ocratoxina A en vinos tintos argentinos durante el proceso de vinificación a escala piloto

The aim of this work was to evaluate the fate of ochratoxin A (OTA) content from must to wine during the red wine making process in a pilot scale vinification. The study was done using musts obtained from two red grape varieties (Bonarda and Tempranillo) artificially contaminated with two OTA levels. A duplicate set of tanks of 100 l each was established for each must (Bonarda and Tempranillo). The fermentations were initiated by inoculation of two Saccharomyces spp. strains having different fermentation performance. The must from the Tempranillo variety was spiked with 6 μg/l of OTA while that from the Bonarda variety with 0.3 μg/l of the toxin. Samples were collected at different stages of the process. Performance of the alcoholic and malolactic fermentations was monitored. Titratable and volatile acidity, pH, ethanol, sugar and SO2 concentrations were determined following standard methods proposed by the Office International de la Vigne et du Vin (OIV). OTA analysis was done by HPLC. Detection and quantification limits were 0.01 and 0.1 ng/ml, respectively. The OTA levels during the vinification trials dropped to an average of about 86.5%. The type of Saccharomyces strains used showed no effect on toxin reduction.

El objetivo del presente trabajo fue evaluar la evolución del contenido de ocratoxina A (OTA) en mostos durante un proceso de vinificación a escala piloto. Se utilizaron mostos de dos variedades de uvas tintas (Bonarda y Tempranillo) contaminados artificialmente con dos niveles distintos de OTA. El ensayo fue llevado a cabo por duplicado en tanques de fermentación de 100 l cada uno. La fermentación se inició mediante la inoculación de dos cepas de Saccharomyces spp. con diferentes características fermentativas. El mosto de la variedad Tempranillo fue contaminado con 6 μg/l de OTA y el mosto de la variedad Bonarda con 0,3 μg/l de la toxina. Se colectaron muestras durante los diferentes estadios del proceso de vinificación. Se estableció el avance de dicho proceso sobre la base de la evolución de las fermentaciones alcohólica y maloláctica. Se determinó la acidez total y volátil, el pH y el contenido de etanol, de azúcar y de SO2 siguiendo los protocolos estándares propuestos por la Oficina Internacional de la Vid y el Vino (OIV). El contenido de OTA se evaluó por HPLC. Los límites de detección y cuantificación fueron 0,01 y 0,1 ng/ml, respectivamente. Los niveles de OTA disminuyeron alrededor del 86,5% al final del proceso de vinificación. El tipo de cepa de Saccharomyces spp. utilizada no tuvo efecto sobre la reducción de OTA.

Identificación preliminar in vitro de propiedades probióticas en cepas de S. cerevisiae / In vitro preliminary identification of probiotic properties of S. cerevisiae strains

Objetivo. Evaluar preliminarmente in vitro algunas propiedades probióticas de dos cepas nativas de S.cerevisiae. Materiales y métodos. Las cepas fueron utilizadas en ensayos de tolerancia a sales biliares, pH, temperatura, adherencia a Salmonella spp., E.coli y Shigella spp., y antagonismo. Se realizó un diseño factorial 33 x 3, con tres niveles de cada factor (cepa, pH y concentración inicial de sustrato) por triplicado, para establecer las condiciones de cultivo de cada cepa. Como control se empleó una cepa comercial (B). La cepa seleccionada se empleó para la producción en biorreactor de 2L; la biomasa fue sometida a secado por temperatura; al producto resultante se le determinó concentración de N2 y la viabilidad celular. Resultados. La cepa A (obtenida de caña de azúcar), toleró pH 3 ± 0.2, 0.3% (p/v) de sales biliares y 42oC. El ANOVA del diseño factorial reportó diferencias significativas entre los 27 ensayos (p≤0.05), el análisis de superficies reportó que la interacción entre los factores cepa y Sustrato (S0) son significativos, sugiriendo para la optimización la cepa A y concentraciones crecientes de S0. Los resultados se reprodujeron en biorreactor con mx 0.31h-1, td 2.18h y Y(x/s) 0.126g/g; la biomasa seca obtenida fue viable y reportó entre 6.3 y 6.9% N2/g. Conclusiones. Se identificaron levaduras nativas con propiedades probióticas como tolerancia a pH, sales biliares, temperatura y adherencia a Salmonella spp., E.coli y Shigella spp.

Comportamiento de una cepa salvaje de Saccharomyces cerevisiae killer y su isogénica sensible respecto de diferentes fuentes de nitrógeno en cultivos mixtos / Behaviour of a wild Saccharomyces cerevisiae killer yeast and its isogenic sensitive one with respect to different nitrogen sources in mixed cultures

La composición química del vino constituye el fundamento de la posterior respuesta sensorial del producto y está determinada por varios factores, como las relaciones levadura-levadura. Se denomina fenómeno killer a la secreción por parte de ciertas cepas de levadura de una proteína tóxica que mata a células denominadas sensibles. El conocimiento del comportamiento en condición aeróbica de cultivos mixtos killer-sensible es útil para relacionarlo con la primera fase de la fermentación enológica, ya que en ella puede definirse la prevalencia o no de la cepa killer. Además, el empleo de mutantes con el plásmido curado permite comparaciones más precisas. El objetivo fue analizar el mecanismo de competencia por sustrato en levaduras killer de Saccharomyces cerevisiae y su mutante sensible con el plásmido curado, empleando distintas fuentes de nitrógeno. Si las muestras se incuban a temperatura de inactivación de la toxina, se evita la infraestimación de células sensibles. Los resultados del co-cultivo de las cepas en proporciones iguales muestran el rol desempeñado por la fuente de nitrógeno en la actividad killer. Cuando el inóculo es 10%K-90%S, el modelo de exclusión competitiva planteado para levaduras killer deja paso a otras variables de competencia.

Wine chemical composition is the outcome of complex chemosensory interactions that are difficult to predict because of the influences of many variables, like as yeast-yeast interactions. Killer phenomenon implicates the secretion of a toxic protein by some yeasts, that kill other yeasts called sensitive. The knowledge of the behaviour of killer-sensitive mixed cultures in aerobic conditions is useful to be related with the first stages of oenological fermentation. In these stages it can be defined the killer prevalence in the medium. Also, the use of cured plasmid mutants allows better comparisons. The objective was to analyse the mechanism of substrate competition in Saccharomyces cerevisiae killer strains and its sensitive cured plasmid mutant, using different nitrogen sources. When samples were incubated at the toxin inactivation temperature, the infraestimation of sensitive cells is avoided. Results obtained in co-cultures (50%K-50%S) show the role of the nitrogen source in killer activity. Results obtained with 10%K-90%S inoculum, show that there are another competence variables than the competitive exclusion model for killer yeasts.

Contribución al estudio del lúpulo / Lupulus humuls study

Tiene como finalidad contribuir a la motivación del cultivo de lupulo en el Perú, ya que es imprescindible e insustituible en la fabricación de cerveza ya que aporta características importantes como sabor y aroma e influye en el proceso de fabricación. Se brinda información sobre los cuidados en el cultivo, características del suelo, clima, temperatura, en las diferentes etapas del desarrollo de la planta y técnicas de cosechas así como preparados de las diferentes presentaciones que favorecen el transporte y su manipuleo en el momento de la aplicación. Esta planta se está adaptando a diferentes zonas geográficas de nuestro continente por lo que cremos que debido a las condiciones climaticas existen en los valles de Urubamba (Cuzco), Curahuasi (Apurimac). La Campiña (Arequipa), Mantaro (Junín), San Marcos y San Juan (Cajamarca), seria viable su adaptación y cultivo en el país. Se realizó análisis de humedad por el método de destilación directa y de resinas (alfa y beta ácidos) por el método espectrofotométrico de 10 muestras de pellets y 16 muestras de extractos de lupulo de diferentes procedencias obteniéndose los muestras de extractos de lupulo de diferentes procedencias obteniéndose los siguientes resultados:muestra de pellets: por ciento humedad (3,90-9,06), por ciento Ó-ácidos (4,50-10.90), por ciento ß-ácidos (3,50-8,10). Muestra de extractos de lupulo: por ciento humedad (1,57-5,20), por ciento Ó-ácidos (23,90-42.60), por ciento ß-ácidos (19.80-31,70).