Rol de los cuerpos de preocesamiento (P-bodies) durante la apoptosis en Drosophila melanogaster

El objetivo del presente trabajo es estudiar el rol de los cuerpos de procesamiento en el control del inicio de la traducción de genes proapoptóticos en Drosophila melanogaster. Para ello nos planteamos los siguientes objetivos específicos: -determinar la composición de los mRNPs presentes en P-bodies y que regulan la expresión de genes proapoptóticos en Drosophila melanogaster. -estudiar las interacciones entre las proteínas integrantes de estos complejos. -conocer el rol que estas interacciones cumplen en la degradación y el silenciamiento del ARNm.Eje: BiotecnologíaCentro Regional de Estudios Genómico

Análisis de componentes de gránulos ribonucleoproteicos en <i>Drosophila</i>

La regulación de la expresión génica es un proceso altamente regulado, que controla qué genes son expresados en cada momento. Uno de los controles más dinámicos del proteoma celular es la regulación de la traducción. El control de la expresión de los mensajeros celulares se ha relacionado hace algunos años con dos estructuras de silenciamiento particulares, los PB (de processing bodies) y los SG (de stress granules). Ambas son formaciones citoplasmáticas que acumulan ARNm y proteínas. Los PB son estructuras constitutivas de las células mientras que los SG aparecen frente a estímulos de estrés celular. En la primera parte de esta tesis se realizó una caracterización de los PB en células S2 Drosophila melanogaster. Particularmente demostramos la presencia de las proteínas Lsm-1, Me31B y eIF4E en los PB. Durante estrés inducido por arsenito de sodio se encontró a eIF4E en SG. Se realizó un estudio más minucioso sobre eIF4E. El análisis de diversos mutantes demostró que el residuo W117, parte del dominio de unión a las 4E-BP, es el responsable de la ubicación de este factor en PB y SG. Mientras que los residuos que participan en la unión al cap de los mensajeros (W100 y W 146) no están involucrados en este proceso. Finalmente se realizó el estudio de interacciones entre estos componentes en PB de células S2 in vivo mediante FRET. Se demostró que las proteínas Lsm-1 y Me31B interaccionan con eIF4E. Sin embargo no pudo ser demostrada por este método la interacción entre Me31B y Lsm-1. Se realizó la predicción de posibles sitios de interacción entre eIF4E y Me31B mediante modelado por homología.Facultad de Ciencias Exacta

Cytoplasmic Ribonucleoprotein Foci in Eukaryotes: Hotspots of Bio(chemical)Diversity

The life of an mRNA from transcription to degradation offers multiple control check points that regulate gene expression. Transcription, splicing, and translation have been widely studied for many years; however, in recent years, new layers of posttranscriptional and posttranslational control have been uncovered. They involve the regulation of the metabolism of mRNA in cytoplasmic foci. They are collections of ribonucleoprotein complexes that, in most cases, remain still uncharacterized, except the processing bodies (PBs) and stress granules (SGs), which have been studied (and reviewed) in detail. A challenging prospective is to know how many different classes of foci exist, which functions they support, how are they formed, and how do they relate one to each other. Here, we present an update of the component of the different granules, a possible function, and hypothesis on their in vivo dynamics related to translational control

Time-course analysis of cyanobacterium transcriptome: detecting oscillatory genes

The microarray technique allows the simultaneous measurements of the expression levels of thousands of mRNAs. By mining these data one can identify the dynamics of the gene expression time series. The detection of genes that are periodically expressed is an important step that allows us to study the regulatory mechanisms associated with the circadian cycle. The problem of finding periodicity in biological time series poses many challenges. Such challenge occurs due to the fact that the observed time series usually exhibit non-idealities, such as noise, short length, outliers and unevenly sampled time points. Consequently, the method for finding periodicity should preferably be robust against such anomalies in the data. In this paper, we propose a general and robust procedure for identifying genes with a periodic signature at a given significance level. This identification method is based on autoregressive models and the information theory. By using simulated data we show that the suggested method is capable of identifying rhythmic profiles even in the presence of noise and when the number of data points is small. By recourse of our analysis, we uncover the circadian rhythmic patterns underlying the gene expression profiles from Cyanobacterium Synechocystis.Facultad de Ciencias Exacta

Abortive and propagating intracellular calcium waves: Analysis from a hybrid model

The functional properties of inositol(1,4,5)-triphosphate (IP3) receptors allow a variety of intracellular Ca2+ phenomena. In this way, global phenomena, such as propagating and abortive Ca2+ waves, as well as local events such as puffs, have been observed. Several experimental studies suggest that many features of global phenomena (e.g., frequency, amplitude, speed wave) depend on the interplay of biophysical processes such as diffusion, buffering, efflux and influx rates, which in turn depend on parameters such as buffer concentration, Ca2+ pump density, cytosolic IP3 level, and intercluster distance. Besides, it is known that cells are able to modify some of these parameters in order to regulate the Ca2+ signaling. By using a hybrid model, we analyzed different features of the hierarchy of calcium events as a function of two relevant parameters for the calcium signaling, the intercluster distance and the pump strength or intensity. In the space spanned by these two parameters, we found two modes of calcium dynamics, one dominated by abortive calcium waves and the other by propagating waves. Smaller distances between the release sites promote propagating calcium waves, while the increase of the efflux rate makes the transition from propagating to abortive waves occur at lower values of intercluster distance. We determined the frontier between these two modes, in the parameter space defined by the intercluster distance and the pump strength. Furthermore, we found that the velocity of simulated calcium waves accomplishes Luther's law, and that an effective rate constant for autocatalytic calcium production decays linearly with both the intercluster distance and the pump strength.Instituto de Física de Líquidos y Sistemas BiológicosCentro de Investigaciones CardiovascularesCentro Regional de Estudios Genómico

Cytoplasmic ribonucleoprotein foci in eukaryotes: hotspots of bio(chemical)diversity

The life of an mRNA from transcription to degradation offers multiple control check points that regulate gene expression. Transcription, splicing, and translation have been widely studied for many years; however, in recent years, new layers of posttranscriptional and posttranslational control have been uncovered. They involve the regulation of the metabolism of mRNA in cytoplasmic foci. They are collections of ribonucleoprotein complexes that, in most cases, remain still uncharacterized, except the processing bodies (PBs) and stress granules (SGs), which have been studied (and reviewed) in detail. A challenging prospective is to know how many different classes of foci exist, which functions they support, how are they formed, and how do they relate one to each other. Here, we present an update of the component of the different granules, a possible function, and hypothesis on their in vivo dynamics related to translational control.Facultad de Ciencias Exacta

Cap binding-independent recruitment of eIF4E to cytoplasmic foci

Eukaryotic translation initiation factor 4E (eIF4E) is required for cap-dependent initiation. In addition, eIF4E occurs in cytoplasmic foci such as processing bodies (PB) and stress granules (SG). We examined the role of key functional amino acid residues of eIF4E in the recruitment of this protein to cytoplasmic foci. We demonstrate that tryptophan residues required for mRNA cap recognition are not required for the recruitment of eIF4E to SG or PB. We show that a tryptophan residue required for protein-protein interactions is essential for the accumulation of eIF4E in granules. Moreover, we show, by the analysis of two Drosophila eIF4E isoforms, that the tryptophan residue is the common feature for eIF4E for the transfer of active mRNA from polysomes to other ribonucleoprotein particles in the cytoplasm. This residue resides in a putative interaction domain different than the eIF4E-BP domain. We conclude that protein-protein interactions rather than interactions with the mRNA are essential for the recruitment of eIF4E and for a putative nucleation function.Facultad de Ciencias Exacta

Abortive and propagating intracellular calcium waves: Analysis from a hybrid model

The functional properties of inositol(1,4,5)-triphosphate (IP3) receptors allow a variety of intracellular Ca2+ phenomena. In this way, global phenomena, such as propagating and abortive Ca2+ waves, as well as local events such as puffs, have been observed. Several experimental studies suggest that many features of global phenomena (e.g., frequency, amplitude, speed wave) depend on the interplay of biophysical processes such as diffusion, buffering, efflux and influx rates, which in turn depend on parameters such as buffer concentration, Ca2+ pump density, cytosolic IP3 level, and intercluster distance. Besides, it is known that cells are able to modify some of these parameters in order to regulate the Ca2+ signaling. By using a hybrid model, we analyzed different features of the hierarchy of calcium events as a function of two relevant parameters for the calcium signaling, the intercluster distance and the pump strength or intensity. In the space spanned by these two parameters, we found two modes of calcium dynamics, one dominated by abortive calcium waves and the other by propagating waves. Smaller distances between the release sites promote propagating calcium waves, while the increase of the efflux rate makes the transition from propagating to abortive waves occur at lower values of intercluster distance. We determined the frontier between these two modes, in the parameter space defined by the intercluster distance and the pump strength. Furthermore, we found that the velocity of simulated calcium waves accomplishes Luther's law, and that an effective rate constant for autocatalytic calcium production decays linearly with both the intercluster distance and the pump strength.Instituto de Física de Líquidos y Sistemas BiológicosCentro de Investigaciones CardiovascularesCentro Regional de Estudios Genómico

Distinct domains of Me31B interact with different eIF4E isoforms in the male germ line of <i>Drosophila melanogaster</i>

Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E isoforms, and the canonical isoform eIF4E-1 is a ubiquitous protein that plays a key role in mRNA translation. eIF4E-3 is specifically expressed in testis and controls translation during spermatogenesis. In eukaryotic cells, translational control and mRNA decay is highly regulated in different cytoplasmic ribonucleoprotein foci, which include the processing bodies (PBs). In this study, we show that Drosophila eIF4E-1 and eIF4E-3 occur in PBs where might play a role in mRNA storage and translational repression. We also demonstrate that the DEAD-box RNA helicase Me31B, a component of PBs, physically interacts with eIF4E-1 and eIF4E-3 both in the yeast two-hybrid system and FRET in Drosophila S2 cells. Moreover, truncated and point mutated Me31B proteins indicate that the binding sites of Me31B for eIF4E-1 and eIF4E-3 are located in different domains. Residues Y401-L407 (at the carboxy-terminal) are essential for interaction with eIF4E-1, whereas residues F63-L70 (at the amino-terminal) are critical for interaction with eIF4E-3. Thus, Me31B represents a novel type of eIF4E-interacting protein. Our observations suggest that Me31B might recognize different eIF4E isoforms in different tissues, which could be the key to silencing specific messengers. They provide further evidence that alternative forms of eIF4E and their interactions with various partners add complexity to the control of gene expression in eukaryotes.Centro Regional de Estudios Genómico

Cap binding-independent recruitment of eIF4E to cytoplasmic foci

Eukaryotic translation initiation factor 4E (eIF4E) is required for cap-dependent initiation. In addition, eIF4E occurs in cytoplasmic foci such as processing bodies (PB) and stress granules (SG). We examined the role of key functional amino acid residues of eIF4E in the recruitment of this protein to cytoplasmic foci. We demonstrate that tryptophan residues required for mRNA cap recognition are not required for the recruitment of eIF4E to SG or PB. We show that a tryptophan residue required for protein-protein interactions is essential for the accumulation of eIF4E in granules. Moreover, we show, by the analysis of two Drosophila eIF4E isoforms, that the tryptophan residue is the common feature for eIF4E for the transfer of active mRNA from polysomes to other ribonucleoprotein particles in the cytoplasm. This residue resides in a putative interaction domain different than the eIF4E-BP domain. We conclude that protein-protein interactions rather than interactions with the mRNA are essential for the recruitment of eIF4E and for a putative nucleation function.Facultad de Ciencias Exacta