Los autores agradecen a René Scriwanek para la asistencia en la preparación de la figura. FR es apoyada por ECHO (700.59.003), Programa ALW abierta (821.02.017 y 822.02.014), la cooperación DFG-NWO (DN82-303) y ZonMW VICI (016.130.606) subvenciones.

1. Preparación Esferoplasto <ol><li> Incubar la levadura durante la noche a 30 ° C en 10 ml del medio apropiado determinado por el diseño del experimento. </li><li> El día después, medir la densidad óptica del cultivo a 600 nm (OD 600) usando un fotómetro, Diluir las células en el mismo medio de cultivo hasta una DO 600 de 0,2-0,4 y crecer a una fase de crecimiento exponencial a menos que el diseño de la experimento requiere una condición diferente. Las células se encuentran en la fase exponencial cuando la cultura tiene un OD 600 de 1-2. </li><li> Recoger 10 OD 600 equivalentes de células por centrifugación a 3500 xg durante 5 min en un tubo de 50 ml. Después de la centrifugación, desechar el sobrenadante. </li><li> Resuspender el sedimento de células en 5 ml de tubos de 100 mM (pH 9,6), ditiotreitol 10 mM y se incubaron a 30 ° C durante 10 min. </li><li> Recoger de nuevo las células por centrifugación a 3500 xg durante 5 min. Eliminar el sobrenadante. </li><li> Resuspender las células in 5 ml de medio (determinado por el diseño del experimento) que contiene 1 M de sorbitol y 5 mg de enzima lítica, e incubar la mezcla a 30 ° C con agitación suave durante 30 min. </li><li> Centrifugar la suspensión de células a 300 xg durante 5 min para recoger la fracción de sedimento, que se corresponde con los esferoplastos. Eliminar el sobrenadante. </li><li> Resuspender los esferoplastos en 960 l de hielo frío medios (medio determinado por el diseño del experimento) que contiene 1 M de sorbitol y transferir la mezcla en un frío de hielo 2 ml tubo de microcentrífuga. </li></ol> 2. Nanogold captación <ol><li> Con una pipeta, mezclar suavemente el esferoplasto con 4 nmol de partículas con carga positiva Nanogold resuspendieron en 40 l de agua. El volumen final de la mezcla tiene que ser de 1 ml. </li><li> Coloque la suspensión celular obtenida en hielo durante 15 min. </li><li> Transferir la suspensión a temperatura ambiente y se incuba durante el tiempo necesario para permitir la internalización nanogold por correondocytosis. NOTA: A la recaptación de 5 min dirigirá principalmente al etiquetado de vesículas endocítica y endosomal compartimentos tempranos, mientras que la absorción de 15 minutos permitirá a marcar todo el sistema endosomal (a principios y finales de endosomes). Tiempos de incubación más largos (más de 30 min) también permitirá etiquetar la vacuola. NOTA: los experimentos de pulso-caza de etiquetado no se pueden realizar con este método. Por lo tanto, cuando el etiquetado para el análisis de LE, nanogold también puede encontrar en el PM y el INEE. </li></ol> 3. La fijación y seccionamiento <ol><li> Detener la absorción nanogold mediante la adición de 1 ml de fijador doble fuerza [4% de paraformaldehído (PFA), 0,4% de glutaraldehído (GA) en tampón PHEM 0,1 M (TUBOS 20 mM, HEPES 50 mM, pH 6,9, 20 mM de EGTA, 4 mM de MgCl 2)] que contiene 1 M de sorbitol a la suspensión celular. Se mantuvo el tubo a temperatura ambiente. </li><li> Invertir suavemente manualmente los tubos micocentrifuge varias veces durante 30 min (esto permitirá mantener los esferoplastos ensuspensión) y centrifugar dos veces a 1.700 xg durante 25 s. </li><li> Reemplazar el fijador descartando el sobrenadante y mediante la adición de 1 ml de fijador estándar de la fuerza fresco (2% de PFA, 0.2% GA en tampón PHEM 0,1 M) que contiene 1 M de sorbitol y se incuba durante 2 horas a temperatura ambiente en una rueda que gira lentamente. </li><li> Procesar las células para la crio-seccionamiento como se describe anteriormente 6. NOTA: Para los procedimientos de mejora de captación nanogold y plata, no tiene que realizarse el tratamiento con ácido periódico describe en el protocolo indicado. El tratamiento con ácido periódico es mejor para permeabilizar la pared de la célula 26, pero esta estructura ha sido eliminado durante la generación de esferoplastos. </li><li> Cortar 50 cryosections delgadas nm a -120 ° C con un cuchillo de diamante en seco utilizando un ultramicrotomo UCT como se describió previamente 8 y colocarlos en carbono Formvar recubierto 50 mallas de rejillas de níquel. </li></ol> 4. Silver Enhancement para Nanogold partículas Visualización NOTA: El procedimiento para preparar las mezclas de reacción es, básicamente, la indicada por el fabricante. Adaptaciones prácticas que utilizan este protocolo, hace que el procedimiento de mejora de la plata eficaz y fiable sobre cryosections. <ol><li> Retire el kit de mejora de la plata del congelador y descongele en un 37 ° C incubadora o baño de agua. Cuando descongelado, coloque el kit en una incubadora de 24 ° C se coloca en un cuarto oscuro hasta su uso (ver 4.7). </li><li> Coloque la placa de calefacción en la habitación oscura y deje que se caliente a la temperatura final de 24 ° C. </li><li> Cubra la parte superior de la placa de calentamiento con el protector de la superficie, el lado brillante hacia arriba, y seguro que con una cinta. </li><li> Coloque el Parafilm sobre la Benchkote y marcar los bordes con un marcador negro para poder ver los bordes de Parafilm en la oscuridad. </li><li> Cinta de un termómetro en la parte superior de la Benchkote para controlar la temperatura de la placa de calentamiento. Poco a poco ajustar la temperatura si no es 24 ° C. </li><li> PlaCE El tubo de 50 ml con agua bidestilada y el kit de mejora de plata dentro. </li><li> Llene las pequeñas cajas de Petri con agua doblemente destilada, previamente calentada a 37 ° C. Coloque las rejillas en el agua, espécimen lado de abajo, durante 30 minutos. </li><li> Repita este paso 4.7 una vez más. </li><li> Transfiera las rejillas en la caja de almacenamiento y llevarlos a la sala oscura. </li><li> Enjuague las rejillas de nuevo pasándolos (con el lado de la muestra hacia abajo) en varias gotas de agua doble destilada a 24 ° C colocados en el Parafilm que se ha fijado en la placa de calentamiento. </li><li> Asegúrese de que 9 gotas de agua destilada dobles adicionales están dispuestos en el Parafilm, para el enjuague después de la reacción mejora plata. </li><li> Apaga la luz y asegúrese de que todas las luces están apagadas. Encienda la luz roja. </li><li> Sacar las soluciones A y B del kit de mejora de la plata de la incubadora 24 ° C. </li><li> Ponga primero 6 gotas de la solución A y luego 6 gotas de la solución B en un 1,5 mtubo de microcentrífuga de L, y mezclar bien con una pipeta Pasteur de vidrio evitando para hacer burbujas. La solución es bastante gruesa y tiene que ser mezclada manualmente con una pipeta antes de que finalmente vórtex brevemente. </li><li> Poner las soluciones A y B de nuevo en la incubadora de 24 ° C y retirar la solución C. </li><li> Añadir 6 gotas de la solución C a la mezcla A / B. A continuación, mezclar de nuevo en primer lugar con una pipeta Pasteur y luego por agitación, evite hacer burbujas. </li><li> Utilizar inmediatamente la mezcla final mediante la colocación de gotas (~ 20 l / gota) en el Parafilm. </li><li> Con unas pinzas limpias, anti-magnético, colocar las rejillas en la mezcla (por ejemplo., Reacción mejorar plata) para 6 a 15 min dependiendo de la mejora (es decir. Tamaño de las partículas de oro) deseado a obtener. </li><li> Retire las rejillas de la mezcla y pasarlos en la parte superior del agua doblemente destilada cae a 24 ° C para el lavado. En primer lugar, el uso en la sucesión rápida 6 gotas y luego 3 gotas con 7 min tiempo de incubación por gota, Antes de encender las luces. </li><li> Continúe con el siguiente paso, ya sea etiquetado inmuno-oro o tinción de la membrana 27 con el fin de visualizar el resultado de una investigación de EM. </li></ol>

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The authors have nothing to disclose.

Inmuno-microscopía electrónica es una técnica que permite la combinación de localización de las proteínas con la resolución ultraestructural de los portadores y orgánulos donde residen estas proteínas. Esto es especialmente importante cuando se estudia el sistema endosomal levadura porque sus compartimentos aparecen como estructuras puntiformes en la microscopía de fluorescencia. Por lo tanto, es difícil distinguirlas. Por esta razón el uso de una sonda detectable por EM y de entrar en la ruta endocítica de...

El sistema endosomal es un aparato de clasificación de membrana importante que desempeña múltiples funciones celulares importantes, incluyendo el tráfico de la enzima lisosomal receptores de clasificación y el reciclaje de la membrana plasmática (PM), los receptores 1,2. Endosomes se dividen en tres compartimentos diferentes, es decir. los endosomas tempranos (EE), a finales de los endosomas (LE) y los endosomas de reciclaje. Esta clasificación se basa en el tiempo que toma para el material endocytosed para llegar a ellos, en las proteínas marcadoras específicas y en su morfología. Las membranas, es decir, proteínas y lípidos bicapa, interiorizadas del PM pueden o bien ser entregados a través de endosomas lisosomas para la degradación o se reciclan de nuevo. Las membranas también son transportados a los endosomas de el aparato de Golgi y de manera similar, ya sea seguir a los lisosomas o ser recuperada de nuevo a los de Golgi. Además, las proteínas se pueden clasificar en vesículas luminales en ciernes hacia el interior de la membrana endosomal limitación, un proceso que conduce a la formación deuna subcategoría de LE, los cuerpos multivesiculares. El sistema endosomal levadura es relativamente menos compleja que la de las células eucariotas altos. Endosomas levadura se dividen en EE y LE. En contraste con las células de mamífero que no contienen los endosomas de reciclaje, sino también orgánulos relacionados con los lisosomas-específicos de tejido. En consecuencia, tienen una red de menor complejidad de las rutas de tráfico endosomal 3,4. Por lo tanto, la levadura ha representado y sigue representando un sistema experimental ventajosa para estudiar algunos de los principios del tráfico de membrana subyacente en el sistema endosomal. Esta ventaja se acentúa por el hecho de que numerosos genes implicados en las vías de endosomal se han aislado inicialmente con pantallas genéticas en la levadura 5. Mientras que el sistema endosomal levadura en las células de tipo salvaje y mutantes se ha estudiado ampliamente el uso de enfoques de microscopía de fluorescencia y bioquímicos, su investigación en el nivel ultraestructural sólo ha sidomínimo. Los análisis morfológicos son particularmente relevantes en la levadura porque la mayoría de los orgánulos endosomales son detectados como estructuras puntiformes por microscopía de fluorescencia, lo que hace difícil su identificación inequívoca 6. Desgraciadamente, sólo un número limitado de antisueros reconocimiento de los marcadores de proteínas endosomal levadura está trabajando en inmuno-microscopía electrónica (IEM) preparaciones 7-10. Para algunas proteínas, este problema se ha eludido por el etiquetado endógena del gen de interés y el uso de un anticuerpo que reconoce la etiqueta para detectar que 7,11,12. A menudo, sin embargo, las proteínas son indetectables por IEM debido a sus bajos niveles de expresión. Su sobreexpresión no es una solución, porque este enfoque puede inducir mis-localizaciones y / o alteraciones en los orgánulos morfología / funciones. Así, el etiquetado de los compartimentos endocítica con una sonda detectable por microscopía electrónica de EM es una opción efectiva. Esta es una solución óptima sobre todo si la PRobe está entrando en la ruta endocítica de una manera dependiente del tiempo, lo que permite saber cuándo va a marcar un orgánulo específico 6. La captación de nanogold cargado positivamente por esferoplastos de levadura (es decir. De levadura donde la pared celular se ha eliminado enzimáticamente) con éxito ha sido utilizado para identificar el endosomal levadura compartimentos 10. Estas partículas se unen fuertemente a los lípidos cargados negativamente que componen las membranas biológicas. Por lo tanto los asociados Nanogold cargados positivamente con la PM, penetra en la célula por endocitosis y pasa a través de la EE y LE antes de llegar a la vacuola. Estas pequeñas partículas de oro, sin embargo, no tienen un tamaño adecuado para ser visto por EM. Para hacerlos visibles, su tamaño se puede ampliar por reacciones químicas que conducen a la deposición de plata o de oro alrededor de la sonda de oro 13-15. Hemos desarrollado y aplicado con éxito un enfoque IEM basado en el método Tokuyasu para realizar subcelularlocalización estudia 8,16. Este método permite realizar inmunomarcaje sobre los preparativos de la levadura con una excelente resolución de la morfología 8,17-24. También hemos establecido un procedimiento que combina este protocolo IEM con el etiquetado nanogold del sistema endosomal levadura compartimentos 6. Con este enfoque hemos caracterizado morfológicamente diferentes subclases de endosomas y ultraestructuralmente examinado mutantes con un tráfico endosomal defecto 6,25. Por otra parte, hemos demostrado que este etiquetado nanogold se puede combinar con marcajes de inmunomarcaje proporcionar la posibilidad de explorar la distribución de una proteína de interés en las diferentes subpoblaciones endosoma. Aquí presentamos cómo se realiza prácticamente el etiquetado del sistema endosomal levadura con nanogold cargado positivamente.

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nanogold labeling of the yeast endosomal system for ultrastructural analyses

Los endosomas son uno de los principales puntos de control de clasificación de membrana en células eucariotas y regulan el reciclado o la destrucción de la mayoría de las proteínas de la membrana plasmática y el aparato de Golgi. Como resultado, el sistema endosomal juega un papel central en el mantenimiento de la homeostasis celular, y las mutaciones en los genes que pertenecen a esta red de orgánulos interconectados por el transporte vesicular, causan patologías graves como el cáncer y trastornos neurobiológicos. Por lo tanto, de primordial importancia es entender los mecanismos subyacentes a la biogénesis y la organización del sistema endosomal. La levadura Saccharomyces cerevisiae ha sido fundamental en esta tarea. Para etiquetar y analizar a nivel ultraestructural el sistema endosomal de este organismo modelo en concreto, presentamos aquí un protocolo detallado para la captación nanogold cargado positivamente por esferoplastos seguido de la visualización de estas partículas a través de una reacción en la mejora de plata. Este método es también una valiosa demasiadol para el examen morfológico de mutantes con defectos en el tráfico endosomal. Por otra parte, no sólo es aplicable para los exámenes ultraestructurales pero también se puede combinar con marcajes de inmunomarcaje para investigaciones de localización de proteínas.

De acuerdo con el protocolo presentado, la morfología del sistema endosoma de la levadura puede ser el acceso por EM de transmisión. Figura 1 muestra diferentes tipos de compartimientos endosomal que han sido alcanzados y por lo tanto marcadas con nanogold. El nanogold mejorada de plata se puede ver claramente como partículas densas de electrones. Los ajustes óptimos establecidos para la reacción mejora la plata permite tener partículas de oro en un intervalo de tamaño homogéneo entre 5 y 15 nm,...

Watch this Scientific Journal Video about Nanogold Labeling of the Yeast Endosomal System for Ultrastructural Analyses at JoVE.com

Nanogold Labeling of the Yeast Endosomal System for Ultrastructural Analyses

La levadura, Saccharomyces cerevisiae, ha sido un modelo de organismo clave para identificar y estudiar los genes que regulan la biogénesis y funciones del sistema endosomal. Aquí se presenta un protocolo detallado para el etiquetado específico de los compartimentos endosomal para estudios ultraestructurales.

Nanogold Etiquetado del Sistema Endosomal Levadura de análisis ultraestructurales

Endosomes are one of the major membrane sorting checkpoints in eukaryotic cells and they regulate recycling or destruction of proteins mostly from the ...

nanogold-labeling-yeast-endosomal-system-for-ultrastructural

Research

JoVE Journal

Biology

10.2K vistas.  University Medical Center Utrecht.  La levadura, Saccharomyces cerevisiae, ha sido un modelo de organismo clave para identificar y estudiar los genes que regulan la biogénesis y funciones del sistema endosomal. Aquí se presenta un protocolo detallado para el etiquetado específico de los compartimentos endosomal para estudios ultraestructurales. 

Video: Nanogold Labeling of the Yeast Endosomal System for Ultrastructural Analyses

A Rapid Technique for the Visualization of Live Immobilized Yeast Cells

We present here a simple, rapid, and extremely flexible technique for the immobilization and visualization of growing yeast cells by epifluorescence microscopy. The technique is equally suited for visualization of static yeast populations, or time courses experiments up to ten hours in length. My microscopy investigates epigenetic inheritance at the silent mating loci in S. cerevisiae. There are two silent mating loci, HML and HMR, which are normally not expressed as they are packaged in heterochromatin. In the sir1 mutant background silencing is weakened such that each locus can either be in the expressed or silenced epigenetic state, so in the population as a whole there is a mix of cells of different epigenetic states for both HML and HMR. My microscopy demonstrated that there is no relationship between the epigenetic state of HML and HMR in an individual cell. sir1 cells stochastically switch epigenetic states, establishing silencing at a previously expressed locus or expressing a previously silenced locus. My time course microscopy tracked individual sir1 cells and their offspring to score the frequency of each of the four possible epigenetic switches, and thus the stability of each of the epigenetic states in sir1 cells. See also  Xu et al., Mol. Cell 2006.

A rapid technique for the visualization of growing immobilized yeast cells, here applied to fluorescent reporters at the silent mating loci HML and HMR

Una técnica rápida para la visualización en vivo de las células de levadura inmovilizada

We present here a simple, rapid, and extremely flexible technique for the immobilization and visualization of growing yeast cells by epifluorescence ...

Investigación

Biología

Bioelectric Analyses of an Osseointegrated Intelligent Implant Design System for Amputees

The projected number of American amputees is expected to rise to 3.6 million by 2050.  Many of these individuals depend on artificial limbs to perform routine activities, but prosthetic suspensions using traditional socket technology can prove to be cumbersome and uncomfortable for a person with limb loss.  Moreover, for those with high proximal amputations, limited residual limb length may prevent exoprosthesis attachment all together. Osseointegrated implant technology is a novel operative procedure which allows firm skeletal attachment between the host bone and an implant. Preliminary results in European amputees with osseointegrated implants have shown improved clinical outcomes by allowing direct transfer of loads to the bone-implant interface.  Despite the apparent advantages of osseointegration over socket technology, the current rehabilitation procedures require long periods of restrictive load bearing prior which may be reduced with expedited skeletal attachment via electrical stimulation.  The goal of the osseointegrated intelligent implant design (OIID) system is to make the implant part of an electrical system to accelerate skeletal attachment and help prevent periprosthetic infection. To determine optimal electrode size and placement, we initiated proof of concept with computational modeling of the electric fields and current densities that arise during electrical stimulation of amputee residual limbs.  In order to provide insure patient safety, subjects with retrospective computed tomography scans were selected and three dimensional reconstructions were created using customized software programs to ensure anatomical accuracy (Seg3D and SCIRun) in an IRB and HIPAA approved study.  These software packages supported the development of patient specific models and allowed for interactive manipulation of electrode position and size. Preliminary results indicate that electric fields and current densities can be generated at the implant interface to achieve the homogenous electric field distributions   required to induce osteoblast migration, enhance skeletal fixation and may help prevent periprosthetic infections.  Based on the electrode configurations experimented with in the model, an external two band configuration will be advocated in the future.

There is a need to develop alternative prosthesis attachment due to limb loss attributed to vascular occlusive diseases and trauma. The goal of the work is to introduce an osseointegrated intelligent implant design system to increase skeletal fixation and reduce periprosthetic infection rates for patients needing osseointegrated technology.

Los análisis bioeléctricos de una osteointegrados Sistema Inteligente diseño de los implantes para Amputados

The projected number of American amputees is expected to rise to 3.6 million by 2050.  Many of these individuals depend on artificial limbs to perform ...

Fluorescent Labeling of Drosophila Heart Structures

The Drosophila melanogaster dorsal vessel, or heart, is a tubular structure comprised of a single layer of contractile cardiomyocytes, pericardial cells that align along each side of the heart wall, supportive alary muscles and, in adults, a layer of ventral longitudinal muscle cells. The contractile fibers house conserved constituents of the muscle cytoarchitecture including densely packed bundles of myofibrils and cytoskeletal/submembranous protein complexes, which interact with homologous components of the extracellular matrix. Here we describe a protocol for the fixation and the fluorescent labeling of particular myocardial elements from the hearts of dissected larvae and semi-intact adult Drosophila. Specifically, we demonstrate the labeling of sarcomeric F-actin and of &alpha;-actinin in larval hearts. Additionally, we perform labeling of F-actin and &alpha;-actinin in myosin-GFP expressing adult flies and of &alpha;-actinin and pericardin, a type IV extracellular matrix collagen, in wild type adult hearts. Particular attention is given to a mounting strategy for semi-intact adult hearts that minimizes handling and optimizes the opportunity for maintaining the integrity of the cardiac tubes and the associated tissues. These preparations are suitable for imaging via fluorescent and confocal microscopy. Overall, this procedure allows for careful and detailed analysis of the structural characteristics of the heart from a powerful genetically tractable model system.

Fluorescent Labeling of Drosophila Heart Structures

Here we describe a basic protocol for fluorescent labeling of different elements of heart tubes from larva and adult Drosophila melanogaster. These specimens are well-suited for imaging via fluorescent or confocal microscopy. This technique permits detailed structural analysis of the features of the hearts from a powerful model organism.

Marcaje fluorescente de Drosophila Estructuras del Corazón

The Drosophila melanogaster dorsal vessel, or heart, is a tubular structure comprised of a single layer of contractile cardiomyocytes, pericardial cells ...

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System 

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers. Genetic studies in mammalian systems have been limited due to the lack of readily available tools including defined mutant genetic cell lines, regulatory expression systems, and appropriate selectable markers. To circumvent these difficulties, model genetic systems in lower eukaryotes have become an attractive choice for the study of functionally conserved DNA repair proteins and pathways. We have developed a model yeast system to study the poorly defined genetic functions of the Werner syndrome helicase-nuclease (WRN) in nucleic acid metabolism. Cellular phenotypes associated with defined genetic mutant backgrounds can be investigated to clarify the cellular and molecular functions of WRN through its catalytic activities and protein interactions. The human WRN gene and associated variants, cloned into DNA plasmids for expression in yeast, can be placed under the control of a regulatory plasmid element. The expression construct can then be transformed into the appropriate yeast mutant background, and genetic function assayed by a variety of methodologies. Using this approach, we determined that WRN, like its related RecQ family members BLM and Sgs1, operates in a Top3-dependent pathway that is likely to be important for genomic stability. This is described in our recent publication [1] at <a href="http://www.impactaging.com">www.impactaging.com</a>. Detailed methods of specific assays for genetic complementation studies in yeast are provided in this paper.

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

Genetic studies in yeast can be employed to investigate the molecular and cellular functions of human genes in cellular DNA metabolism. Methods are described for the genetic characterization of the human WRN gene product defective in the premature aging disorder Werner syndrome in functionally conserved pathways using yeast as a tractable model system.

Los estudios genéticos de proteínas humanas de reparación del ADN utilizando la levadura como un sistema modelo

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers.  Genetic studies in mammalian ...

Split-Ubiquitin Based Membrane Yeast Two-Hybrid (MYTH) System: A Powerful Tool For Identifying Protein-Protein Interactions

The fundamental biological and clinical importance of integral membrane proteins prompted the development of a yeast-based system for the high-throughput identification of protein-protein interactions (PPI) for full-length transmembrane proteins. To this end, our lab developed the split-ubiquitin based Membrane Yeast Two-Hybrid (MYTH) system. This technology allows for the sensitive detection of transient and stable protein interactions using Saccharomyces cerevisiae as a host organism. MYTH takes advantage of the observation that ubiquitin can be separated into two stable moieties: the C-terminal half of yeast ubiquitin (Cub) and the N-terminal half of the ubiquitin moiety (Nub). In MYTH, this principle is adapted for use as a 'sensor' of protein-protein interactions. Briefly, the integral membrane bait protein is fused to Cub which is linked to an artificial transcription factor. Prey proteins, either in individual or library format, are fused to the Nub moiety. Protein interaction between the bait and prey leads to reconstitution of the ubiquitin moieties, forming a full-length 'pseudo-ubiquitin' molecule. This molecule is in turn recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor, and subsequent induction of reporter gene expression. The system is highly adaptable, and is particularly well-suited to high-throughput screening. It has been successfully employed to investigate interactions using integral membrane proteins from both yeast and other organisms.

Split-Ubiquitin Based Membrane Yeast Two-Hybrid MYTH System: A Powerful Tool For Identifying Protein-Protein Interactions

MYTH allows the sensitive detection of transient and stable interactions between proteins that are expressed in the model organism Saccharomyces cerevisiae. It has been successfully applied to study exogenous and yeast integral membrane proteins in order to identify their interacting partners in a high throughput manner.

Split-ubiquitina levadura membrana base de dos híbridos (MITO) del sistema: Una poderosa herramienta para identificar interacciones proteína-proteína

The fundamental biological and clinical importance of integral membrane proteins prompted the development of a yeast-based system for the high-throughput ...

Modified Yeast-Two-Hybrid System to Identify Proteins Interacting with the Growth Factor Progranulin

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role in a variety of physiologic and disease processes, including early embryogenesis, wound healing 1, inflammation 2, 3, and host defense 4. PGRN also functions as a neurotrophic factor 5, and mutations in the PGRN gene resulting in partial loss of the PGRN protein cause frontotemporal dementia 6, 7. Our recent studies have led to the isolation of PGRN as an important regulator of cartilage development and degradation 8-11. Although PGRN, discovered nearly two decades ago, plays crucial roles in multiple physiological and pathological conditions, efforts to exploit the actions of PGRN and understand the mechanisms involved have been significantly hampered by our inability to identify its binding receptor(s). To address this issue, we developed a modified yeast two-hybrid (MY2H) approach based on the most commonly used GAL4 based 2-hybrid system. Compared with the conventional yeast two-hybrid screen, MY2H dramatically shortens the screen process and reduces the number of false positive clones. In addition, this approach is reproducible and reliable, and we have successfully employed this system in isolating the binding proteins of various baits, including ion channel 12, extracellular matrix protein 10, 13, and growth factor14. In this paper, we describe this MY2H experimental procedure in detail using PGRN as an example that led to the identification of TNFR2 as the first known PGRN-associated receptor 14, 15.

We have modified the conventional yeast two-hybrid screening, an effective genetic tool in identifying protein interaction. This modification markedly shortens the process, reduces the workload, and most importantly, reduces the number of false positives. In addition, this approach is reproducible and reliable.

Modificado levadura sistema híbrido de dos para identificar proteínas que interactúan con el factor de crecimiento progranulina

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role ...

The Green Monster Process for the Generation of Yeast Strains Carrying Multiple Gene Deletions

Phenotypes for a gene deletion are often revealed only when the mutation is tested in a particular genetic background or environmental condition1,2. There are examples where many genes need to be deleted to unmask hidden gene functions3,4. Despite the potential for important discoveries, genetic interactions involving three or more genes are largely unexplored. Exhaustive searches of multi-mutant interactions would be impractical due to the sheer number of possible combinations of deletions. However, studies of selected sets of genes, such as sets of paralogs with a greater a priori chance of sharing a common function, would be informative.
In the yeast Saccharomyces cerevisiae, gene knockout is accomplished by replacing a gene with a selectable marker via homologous recombination. Because the number of markers is limited, methods have been developed for removing and reusing the same marker5,6,7,8,9,10. However, sequentially engineering multiple mutations using these methods is time-consuming because the time required scales linearly with the number of deletions to be generated.
Here we describe the Green Monster method for routinely engineering multiple deletions in yeast11. In this method, a green fluorescent protein (GFP) reporter integrated into deletions is used to quantitatively label strains according to the number of deletions contained in each strain (Figure 1). Repeated rounds of assortment of GFP-marked deletions via yeast mating and meiosis coupled with flow-cytometric enrichment of strains carrying more of these deletions lead to the accumulation of deletions in strains (Figure 2). Performing multiple processes in parallel, with each process incorporating one or more deletions per round, reduces the time required for strain construction.
The first step is to prepare haploid single-mutants termed 'ProMonsters,' each of which carries a GFP reporter in a deleted locus and one of the 'toolkit' loci&#x2014;either Green Monster GMToolkit-a or GMToolkit-&alpha; at the can1&Delta; locus (Figure 3). Using strains from the yeast deletion collection12, GFP-marked deletions can be conveniently generated by replacing the common KanMX4 cassette existing in these strains with a universal GFP-URA3 fragment. Each GMToolkit contains: either the a- or &alpha;-mating-type-specific haploid selection marker1 and exactly one of the two markers that, when both GMToolkits are present, collectively allow for selection of diploids.
The second step is to carry out the sexual cycling through which deletion loci can be combined within a single cell by the random assortment and/or meiotic recombination that accompanies each cycle of mating and sporulation.

The Green Monster method enables the rapid assembly of multiple deletions marked with a reporter gene encoding green fluorescent protein. This method is based on driving yeast strains through repeated cycles of sexual assortment of deletions and fluorescence-based enrichment of cells carrying more deletions.

El Proceso de Monstruo Verde para la generación de cepas de levadura que llevan deleciones múltiples genes

Phenotypes  for a gene deletion are often revealed only when the mutation is tested in a  particular genetic background or environmental condition1,2. ...

Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously hard to disrupt. Here we describe the use of a bead mill homogenizer for the extraction of proteins into buffers optimized to maintain the functions, interactions and post-translational modifications of proteins. Logarithmically growing cells expressing the protein of interest are grown in a liquid growth media of choice. The growth media may be supplemented with reagents to induce protein expression from inducible promoters (e.g. galactose), synchronize cell cycle stage (e.g. nocodazole), or inhibit proteasome function (e.g. MG132). Cells are then pelleted and resuspended in a suitable buffer containing protease and/or phosphatase inhibitors and are either processed immediately or frozen in liquid nitrogen for later use. Homogenization is accomplished by six cycles of 20 sec&#160;bead-beating (5.5 m/sec), each followed by one minute incubation on ice. The resulting homogenate is cleared by centrifugation and small particulates can be removed by filtration. The resulting cleared whole cell extract (WCE) is precipitated using 20% TCA for direct analysis of total proteins by SDS-PAGE followed by Western blotting. Extracts are also suitable for affinity purification of specific proteins, the detection of post-translational modifications, or the analysis of co-purifying proteins. As is the case for most protein purification protocols, some enzymes and proteins may require unique conditions or buffer compositions for their purification and others may be unstable or insoluble under the conditions stated. In the latter case, the protocol presented may provide a useful starting point to empirically determine the best bead-beating strategy for protein extraction and purification. We show the extraction and purification of an epitope-tagged SUMO E3 ligase, Siz1, a cell cycle regulated protein that becomes both sumoylated and phosphorylated, as well as a SUMO-targeted ubiquitin ligase subunit, Slx5.

The preparation of high quality yeast cell extracts is a necessary first step in the analysis of individual proteins or entire proteomes. Here we describe a fast, efficient, and reliable homogenization protocol for budding yeast cells that has been optimized to preserve protein functions, interactions, and post-translational modifications.

Florecimiento extracción de proteínas de levadura y purificación para el Estudio de la función, las interacciones y modificaciones post-traduccionales

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously ...

Reverse Yeast Two-hybrid System to Identify Mammalian Nuclear Receptor Residues that Interact with Ligands and/or Antagonists

As a critical regulator of drug metabolism and inflammation, Pregnane X Receptor (PXR), plays an important role in disease pathophysiology linking metabolism and inflammation (e.g.&#160;hepatic steatosis)1,2. There has been much progress in the identification of agonist ligands for PXR, however, there are limited descriptions of drug-like antagonists and their binding sites on PXR3,4,5. A critical barrier has been the inability to efficiently purify full-length protein for structural studies with antagonists despite the fact that PXR was cloned and characterized in 1998. Our laboratory developed a novel high throughput yeast based two-hybrid assay to define an antagonist, ketoconazole&#39;s, binding residues on PXR6. Our method involves creating mutational libraries that would rescue the effect of single mutations on the AF-2 surface of PXR expected to interact with ketoconazole. Rescue or &#34;gain-of-function&#34; second mutations can be made such that conclusions regarding the genetic interaction of ketoconazole and the surface residue(s) on PXR are feasible. Thus, we developed a high throughput two-hybrid yeast screen of PXR mutants interacting with its coactivator, SRC-1. Using this approach, in which the yeast was modified to accommodate the study of the antifungal drug, ketoconazole, we could demonstrate specific mutations on PXR enriched in clones unable to bind to ketoconazole. By reverse logic, we conclude that the original residues are direct interaction residues with ketoconazole. This assay represents a novel, tractable genetic assay to screen for antagonist binding sites on nuclear receptor surfaces. This assay could be applied to any drug regardless of its cytotoxic potential to yeast as well as to cellular protein(s) that cannot be studied using standard structural biology or proteomic based methods. Potential pitfalls include interpretation of data (complementary methods useful), reliance on single Y2H method, expertise in handling yeast or performing yeast two-hybrid assays, and assay optimization.

Ketoconazole binds to and antagonizes Pregnane X Receptor (PXR) activation. Yeast high throughput screens of PXR mutants define a unique region for ketoconazole binding. This yeast-based genetic method discovers novel nuclear receptor interactions with ligands that associate with surface binding sites.

Invierta levadura de dos sistema híbrido para identificar mamíferos Receptor Nuclear Residuos que interactúan con ligandos y / o antagonistas

As a critical regulator of drug metabolism and inflammation, Pregnane X Receptor (PXR), plays an important role in disease pathophysiology linking ...

Applications of pHluorin for Quantitative, Kinetic and High-throughput Analysis of Endocytosis in Budding Yeast

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal remodeling and vesicular trafficking in living cells. Quantitative methodologies using chimeric GFP fusions have been developed for many applications; however, GFP is somewhat resistant to proteolysis, thus its fluorescence persists in the lysosome/vacuole, which can impede quantification of cargo trafficking in the endocytic pathway. An alternative method for quantifying endocytosis and post-endocytic trafficking events makes use of superecliptic pHluorin, a pH-sensitive variant of GFP that is quenched in acidic environments. Chimeric fusion of pHluorin to the cytoplasmic tail of transmembrane cargo proteins results in a dampening of fluorescence upon incorporation of the cargo into multivesicular bodies (MVBs) and delivery to the lysosome/vacuole lumen. Thus, quenching of vacuolar fluorescence facilitates quantification of endocytosis and early events in the endocytic pathway. This paper describes methods using pHluorin-tagged cargos for quantification of endocytosis via fluorescence microscopy, as well as population-based assays using flow cytometry.

Accurate quantification of vesicular trafficking events often provides key insights into roles for specific proteins and the effects of mutations. This paper presents methods for using superecliptic pHluorin, a pH-sensitive GFP variant, as a tool for quantification of endocytic events in living cells using quantitative fluorescence microscopy and flow cytometry.

Aplicaciones de pHluorin para cuantitativa, cinética y de alto rendimiento Análisis de la endocitosis de levadura en ciernes

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal ...