The roles of RNA helicases and other ribosome biogenesis factors during small subunit maturation

von Jimena Davila Gallesio
Dissertation
Datum der mündl. Prüfung:2019-08-27
Erschienen:2020-05-29
Betreuer:Prof. Dr. Markus Bohnsack
Gutachter:Prof. Dr. Jörg Enderlein
Gutachter:Prof. Dr. Gerhard Braus
Gutachter:Prof. Dr. Blanche Schwappach
Gutachter:Prof. Dr. Michael Meinecke
Gutachter:Prof. Dr. Michael Thumm
Gutachter:Prof. Dr. Ralf Ficner
Zum Verlinken/Zitieren: http://dx.doi.org/10.53846/goediss-8004

 

 

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Name:JDG-PhD Thesis.pdf
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Zusammenfassung

Englisch

RNA helicases are a highly conserved family of proteins that act as RNA-dependent NTPases. These proteins contain a conserved helicase core consisting of two RecA-like domains that are responsible for unwinding or annealing RNA duplexes and remodelling RNP complexes in an NTP-dependent manner. As most RNA helicases perform their unwinding activity in a sequence independent manner, protein-protein interactions with cofactors can modulate their activity or provide substrate specificity. In line with their molecular functions, these proteins are central players in important cellular processes involving RNA, including pre-mRNA splicing, translation and ribosome biogenesis. The production of mature eukaryotic ribosomes is a highly dynamic and energy-consuming process that involves four rRNAs, ~80 ribosomal proteins and more than 200 trans-acting factors. In the yeast S. cerevisiae, 21 RNA helicases are involved in the assembly steps of the small and large subunits (SSU and LSU respectively), where general roles have been attributed to RNA helicases in remodelling rRNAs and modulating the dynamics of small nucleolar (sno)RNPs on pre-ribosomes. In recent years, the identification of binding sites of different RNA helicases on the rRNA as well as structural analyses of preribosomal particles has facilitated a deeper understanding of how these proteins act in ribosome biogenesis. However, for other RNA helicases, the lack of information regarding their rRNA binding sites and their molecular targets has prevented further characterisation of their functions in ribosome biogenesis. This study focused on the uncharacterised DEAD-box helicase Fal1 and the MIF4G domain-containing protein Sgd1, which are both required for SSU maturation. Analyses of pre-rRNA processing upon protein depletion demonstrated that Fal1 and Sgd1 are both required for early pre-rRNA cleavages at sites A0, A1 and A2, and complementation experiments showed that the ATPase activity of the helicase is required for this function. Fal1 and Sgd1 were shown to associate in vivo, and in vitro analyses determined that the MIF4G domain of Sgd1 mediates the interaction with Fal1. Excitingly, the data suggest that the MIF4G domain of Sgd1 can stimulate the ATPase activity of Fal1 in vitro, suggesting a role of Sgd1 as an MIF4G domain-containing cofactor of Fal1. The UV crosslinking and analysis of cDNA (CRAC) approach allowed the identification of a Sgd1 binding site within the 18S rRNA sequence, which is in line with a suggested role in the early stages of pre-SSU assembly. Interestingly, expression of different Sgd1 truncations for in vivo crosslinking experiments highlighted the C-terminal region of Sgd1 as responsible for the association with RNA. Anisotropy experiments demonstrated that the C-terminal region of Sgd1 can bind RNA in vitro in a non-sequence specific manner, suggesting that Sgd1 can simultaneously bind Fal1 through the MIF4G domain and the rRNA through the C-terminal region. Altogether, these findings expand our understanding of the role of Fal1 and Sgd1 in ribosome biogenesis, and suggest a common function of these proteins in the early stages of ribosome assembly, likely as an RNA helicasecofactor complex.
Keywords: RNA; ribosome biogenesis; SSU; SSU processome
 
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