Xie, J.
Aiello, U.
Clement, Y.
Haidara, N.
Girbig, M.
Schmitzova, J.
Pena, V.
Müller, C.W.
Libri, D.
Porrua, O.
(2022). An integrated model for termination of RNA polymerase III transcription. ,
Vol.8
(28),
p. eabm9875.
show abstract
RNA polymerase III (RNAPIII) synthesizes essential and abundant noncoding RNAs such as transfer RNAs. Controlling RNAPIII span of activity by accurate and efficient termination is a challenging necessity to ensure robust gene expression and to prevent conflicts with other DNA-associated machineries. The mechanism of RNAPIII termination is believed to be simpler than that of other eukaryotic RNA polymerases, solely relying on the recognition of a T-tract in the nontemplate strand. Here, we combine high-resolution genome-wide analyses and in vitro transcription termination assays to revisit the mechanism of RNAPIII transcription termination in budding yeast. We show that T-tracts are necessary but not always sufficient for termination and that secondary structures of the nascent RNAs are important auxiliary cis-acting elements. Moreover, we show that the helicase Sen1 plays a key role in a fail-safe termination pathway. Our results provide a comprehensive model illustrating how multiple mechanisms cooperate to ensure efficient RNAPIII transcription termination..
Mieczkowski, M.
Steinmetzger, C.
Bessi, I.
Lenz, A.-.
Schmiedel, A.
Holzapfel, M.
Lambert, C.
Pena, V.
Höbartner, C.
(2021). Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine. Nature communications,
Vol.12
(1),
pp. 3549-?.
show abstract
Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO + and DMHBI + ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer..
Cretu, C.
Gee, P.
Liu, X.
Agrawal, A.
Nguyen, T.-.
Ghosh, A.K.
Cook, A.
Jurica, M.
Larsen, N.A.
Pena, V.
(2021). Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Nature communications,
Vol.12
(1).
show abstract
AbstractIntron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)—a complex chaperoning the selection of branch and 3′ splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept..
de Moura, T.R.
Mozaffari-Jovin, S.
Szabó, C.Z.
Schmitzová, J.
Dybkov, O.
Cretu, C.
Kachala, M.
Svergun, D.
Urlaub, H.
Lührmann, R.
Pena, V.
(2018). Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors. Molecular cell,
Vol.69
(6),
pp. 979-992.e6.
Cretu, C.
Agrawal, A.A.
Cook, A.
Will, C.L.
Fekkes, P.
Smith, P.G.
Lührmann, R.
Larsen, N.
Buonamici, S.
Pena, V.
(2018). Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Molecular cell,
Vol.70
(2),
pp. 265-273.e8.
Cretu, C.
Schmitzová, J.
Ponce-Salvatierra, A.
Dybkov, O.
De Laurentiis, E.I.
Sharma, K.
Will, C.L.
Urlaub, H.
Lührmann, R.
Pena, V.
(2016). Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations. Molecular cell,
Vol.64
(2),
pp. 307-319.
Ponce-Salvatierra, A.
Wawrzyniak-Turek, K.
Steuerwald, U.
Höbartner, C.
Pena, V.
(2016). Crystal structure of a DNA catalyst. Nature,
Vol.529
(7585),
pp. 231-234.
Rauhut, R.
Fabrizio, P.
Dybkov, O.
Hartmuth, K.
Pena, V.
Chari, A.
Kumar, V.
Lee, C.-.
Urlaub, H.
Kastner, B.
Stark, H.
Luhrmann, R.
(2016). Molecular architecture of the Saccharomyces cerevisiae activated spliceosome. Science,
Vol.353
(6306),
pp. 1399-1405.
De, I.
Bessonov, S.
Hofele, R.
dos Santos, K.
Will, C.L.
Urlaub, H.
Lührmann, R.
Pena, V.
(2015). The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes. Nature structural & molecular biology,
Vol.22
(2),
pp. 138-144.