Academic literature on the topic 'Large ribosomal subunit'

L'activité de traduction des ribosomes est portée directement par les ARN ribosomiques (ARNr) qui composent ses deux sous-unités. La grande sous-unité (60S) est formée par les ARNr 25S, 5.8S et 5S et la petite sous-unité (40S) est formée par l'ARNr 18S. Un des principaux buts de la biogenèse des ribosomes est de convertir les ARNr en molécules correctement repliées et donc actives. La production des sous-unités ribosomiques est le résultat d'étapes successives de maturation de particules précurseurs, les pré-60S et les pré-40S, précurseurs de la grande (60S) et la petite (40S) sous-unité ribosomique, respectivement. Des protéines ribosomiques, des facteurs d'assemblage (FA) et des petites particules ribonucléoprotéique (snoRNPs) sont impliquées dans ces étapes successives. Ces facteurs jouent des rôles importants dans l'organisation spatiale et le maintien de l'intégrité structurelle des ARNr. Les ARN hélicases forment le plus grand groupe des FA et peuvent moduler les interactions ARN-ARN et ARN-protéine. Elles forment des candidates potentielles du repliement tridimensionnelle des ARNr. Cependant, les mécanismes par lesquels ces enzymes participent à la production des ribosomes restent vagues. Dans cette étude, on se focalise sur la fonction de l'ARN hélicase à boîte DEAD Dbp6 dans la structuration précoce de l'ARNr de la grande sous-unité ribosomique (60S). Dbp6 est essentielle pour la production de la grande sous-unité ribosomique. En son absence la production de la première particule pré-60S est inhibée. Néanmoins, l'importance des activités enzymatiques de Dbp6 pour la production de la première particule pré-60S n'ont pas été évalué et ses substrats ARN n'ont pas été déterminé. Dans notre étude, nous avons démontré que Dbp6 montre les activités biochimiques attendues, tels que l'hydrolyse d'ATP et la liaison à l'ARN. Dbp6 n'a pas montré une activité de dissociation de brins d'ARN (hélicase) dans les conditions testées dans le laboratoire. Nous avons pu identifier et étudier une activité d'association de brins (annealing) qui est contrôlée par l'ATP. En étudiant des mutants de Dbp6 qui ciblent les motifs conservés du cœur hélicase, nous avons établi que l'hydrolyse ATP est importante mais pas essentielle pour la survie cellulaire. Cependant, l'activité d'annealing semble jouer un rôle clé dans la fonction moléculaire de l'enzyme. Nous avons ensuite identifié les substrats in vivo de Dbp6 par l'expérience de pontage aux UV et analyse de l'ADNc (CRAC). Cela a montré que Dbp6 interagie principalement avec des snoARN qui se lient dans la région 5' de l'ARNr 25S et parmi lesquels certains sont des snoARN orphelins qui ne guident pas de modifications chimiques de nucléotides. Ces résultats soutiennent la notion que Dbp6 pourrait participer à l'organisation spatiale de cette région de l'ARNr de la grande sous-unité par l'intermédiaire des snoARN chaperons<br>The translation activity of ribosomes is directly held by the ribosomal RNAs (rRNAs) composing its two subunits. The large ribosomal subunit (60S) is formed of the 25S, 5.8S and 5S rRNAs and the small ribosomal subunit (40S) of the 18S rRNA. One of the main goals of ribosome biogenesis is to turn the rRNAs into correctly folded and active molecules. The production of the ribosomal subunits is the result of successive processing and maturation steps of precursor particles, the pre-60S and the pre-40S particles, precursors of the large (60S) and small (40S) ribosomal subunits, respectively. Ribosomal proteins (RPs), assembly factors (AFs) and small ribonucleoprotein particles (snoRNPs) are implicated in these successive steps. These factors play important roles in the spatial organization and in maintaining the structural integrity of the rRNAs. RNA helicases form the largest group of AFs and can modulate RNA-RNA and RNA-protein interactions. They form potential candidates for the tridimensional folding of the rRNAs. However, the mechanisms by which these enzymes participate in ribosomal particles production remain vague. In this study, we focus on the DEAD-box RNA helicase Dbp6's function in the early structuring of rRNAs of the large ribosomal subunit (60S). Dbp6 is essential for the production of the large ribosomal subunits. In its absence the production of the first pre-60S particle is impaired. Nevertheless, Dbp6 enzymatic activities' importance for the first pre-60S particle production has not been assessed nor have its RNA substrates been determined. In our study, we demonstrated that Dbp6 displays expected biochemical activities, such as ATP hydrolysis and RNA binding. Dbp6 did not show any RNA strands dissociation activity (helicase activity) in the conditions tested in the laboratory. We were able to identify and study a strand association activity (annealing activity) that is controlled by ATP. By studying Dbp6's mutants targeting the conserved helicase core motifs, we established that ATP hydrolysis is important but not essential for cell survival. However, the annealing activity seems to play a key role in the molecular function of the enzyme. We then identified Dbp6 in vivo substrates by in vivo cross-linking and analysis of cDNA experiment (CRAC). This showed that Dbp6 mostly interacts with snoRNAs that bind the 5' region of the 25S rRNA of which several are orphan snoRNA that do not guide the chemical modification of nucleotides. These findings support the notion that Dbp6 might participate in the spatial organization of this region of the large subunit rRNA by the intermediate of chaperoning snoRNAs

The Crepidotaceae (Imai) Singer (Basidiomycetes: Agaricales) represents a proposed family of saprophytic fungi containing five agaricoid (Crepidotus, Tubaria, Melanomphalia, Simocybe, Pleurotellus) and four cyphelloid (Episphaeria, Phaeosolenia, Pellidiscus, Chromocyphella) genera. Several contemporary classification systems exist that delegate some or all of these genera to other agaric families. Phylogenetic relationships for the most prevalent genera in the Crepidotaceae were investigated using nuclear large subunit ribosomal DNA (LSU rDNA) sequences. Parsimony analysis of the molecular data supports the Singer classification of Crepidotus, Melanomphalia, and Simocybe as a single monophyletic unit within the Agaricales. The affinities of the genus Tubaria remain uncertain. Crepidotus (Fr.) Staude is the largest and most phenotypically variable genus in the Crepidotaceae. Sequencing of the LSU rDNA region for a cross-section of morphologically diverse species suggests that Crepidotus is not a monophyletic genus. Analysis of morphological characters for 23 Crepidotus taxa shows that characters traditionally applied for infrageneric classification of Crepidotus are homoplasic in origin, but that less commonly emphasized characters such as spore shape and ultrastructure of spore wall ornamentation may be indicative of monophyletic clades for this complex. A unique pattern of basidiospore dormancy and germination, unknown in any other species of agaric, is reported for 11 species of Crepidotus. Similar patterns were also encountered in species of Simocybe and Melanomphalia. In these species an endogenous period of spore dormancy of four to six months is followed by an activation period where the factors necessary for subsequent germination appear to involve a minimal nutritional component, water, and exposure to light.<br>Master of Science

Ribosome biogenesis in eukaryotes involves the transcription, folding, and processing of ribosomal RNA (rRNA), as well as the concomitant assembly of ribosomal proteins. Several hundred trans-acting assembly factors also play a role in the complex process of ribosome biogenesis. Investigations of the construction of ribosomes have focused primarily on the roles of these assembly factors. Little is understood about how ribosomal proteins (r-proteins) function in ribosomal subunit biogenesis in vivo, in either prokaryotes or eukaryotes. I began by focusing on a subset of r-proteins surrounding the polypeptide exit tunnel of the large ribosomal subunit in yeast. R-proteins in this neighborhood, namely L17, L26, L35, and L37, are of importance because they fail to assemble with preribosomes when early pre-rRNA processing steps are blocked. I showed that these rproteins are important for the next pre-rRNA processing, cleavage of the ITS2 spacer sequence in 27SB pre-rRNA. Interestingly, I showed that this biogenesis defect is not due to changes in structure of ITS2. Instead, these r-proteins are required for stable recruitment of key assembly factors that function in this event. I then carried out a global survey of the majority of r-proteins in the 60S subunit. I found that co-transcriptional binding of r-proteins influences post-transcriptional stabilization of 60S subunit structural neighborhoods. This led to a model wherein structural domains of eukaryotic large ribosomal subunits are constructed in a hierarchical fashion. Assembly begins at the convex solvent side, followed by the polypeptide exit tunnel, the intersubunit side, and finally the central protuberance. This hierarchy serves as an initial framework to further understand 60S assembly in vivo. I also showed that pre-ribosomes become more stable as assembly proceeds and that the final steps in 60S maturation occur around regions important for ribosome function. My results also support the hypothesis that the formation of the 3’ end of 27S pre-rRNA is important for early steps of 60S assembly occurring near the 5’ end of pre-rRNA. I also studied the functions of conserved and eukaryote-specific extensions of rproteins that are intrinsically disordered. This revealed distinct roles of extensions in 60S subunit biogenesis and supported a model for the sequential binding of globular and then extended domains of r-proteins during ribosome assembly. My surprising finding for a eukaryote-specific r-protein tail highlights the importance of understanding why several yeast r-proteins have evolved extra sequences that are conserved in higher eukaryotes. Together, these investigations revealed important principles governing ribosome assembly. Furthermore, striking similarities and differences between assembly of bacterial and eukaryotic large ribosomal subunits also emerged, providing insights into how these RNA–protein particles evolved.

Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.<br>Bizkaia:Talent and the European Union's Seventh Framework Program (Marie Curie Actions; COFUND; to S.C., A.S., T.K.); Marie Curie Actions Career Integration Grant (PCIG14-GA-2013-632072 to P.F.); Ministerio de Economía Y Competitividad (CTQ2014-55907-R to P.F., S.C.); FIRB Futuro in Ricerca from the Italian Ministero dell'Istruzione, dell'Universitá e della Ricerca (RBFR130VS5_001 to A.F.); Peruvian Programa Nacional de Innovación para la Competitividad y Productividad (382-PNICP-PIBA-2014 (to P.M. and A.F.)). Funding for open access charge: Institutional funding.<br>Revisión por pares