Variants of U1 small nuclear RNA assemble into spliceosomal complexes - Pereira-Simon - 2004 - Insect Molecular Biology - Wiley Online Library
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In this study, the existence of additional U1 snRNA variants in the posterior silk gland of the Bombyx mori Nistari strain from India was investigated. Three new U1 variants were detected. One of the new isoforms (U1 SG1) was found to be preferentially assembled into high molecular weight spliceosomal complexes in comparison with the total cellular lysate RNA control. Structural and nucleotide differences were examined in these new isoforms and compared with the previously reported U1 variants. Free energy (&DG) values for the entire U1 snRNA secondary structures as well as the individual stem/loops (I, II, III and IV) domains of the isoforms were estimated to determine their structural stability.36 Assembleon feeder part
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aisn-detailSaccharomyces cerevisiae NineTeen Complex (NTC)-associated Factor Bud31/Ycr063w Assembles on Precatalytic Spliceosomes and
Improves First and Second Step Pre-mRNA Splicing Efficiency
From the ?Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India and
the §Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
1 To whom correspondence should be addressed. Tel.: 91-80-; E-mail: uvr{at}mcbl.iisc.ernet.in or uvr123{.
Background: Some yeast splicing factors, e.g. Bud31 in Cef1p subcomplex, are nonessential for cell viability.
Results: Bud31 occurs in precatalytic (B) and catalytic spliceosomes and stabilizes protein interactions with the pre-mRNA; its absence
affects the first and second step of splicing.
Conclusion: Bud31 aids both catalytic steps through its spliceosome interactions.
Significance: Nonessential factors have auxiliary roles in multiple steps of pre-mRNA splicing.
Pre-mRNA splicing occurs in spliceosomes whose assembly and activation are critical for splice site selection and catalysis.
The highly conserved NineTeen complex protein complex stabilizes various snRNA and protein interactions early in the spliceosome
assembly pathway. Among several NineTeen complex-associated proteins is the nonessential protein Bud31/Ycr063w, which is also
a component of the Cef1p subcomplex. A role for Bud31 in pre-mRNA splicing is implicated by virtue of its association with
splicing factors, but its specific functions and spliceosome interactions are uncharacterized. Here, using in vitro splicing assays with extracts from a strain lacking Bud31, we illustrate its role in efficient progression to the first catalytic
step and its requirement for the second catalytic step in reactions at higher temperatures. Immunoprecipitation of functional
epitope-tagged Bud31 from in vitro reactions showed that its earliest association is with precatalytic B complex and that the interaction continues in catalytically
active complexes with stably bound U2, U5, and U6 small nuclear ribonucleoproteins. In complementary experiments, wherein
precatalytic spliceosomes are selected from splicing reactions, we detect the occurrence of Bud31. Cross-linking of proteins
to pre-mRNAs with a site-specific 4-thio uridine residue at the -3 position of exon 1 was tested in reactions with WT and
bud31 null extracts. The data suggest an altered interaction between a ~25-kDa protein and this exonic residue of pre-mRNAs in
the arrested bud31 null spliceosomes. These results demonstrate the early spliceosomal association of Bud31 and provide plausible functions
for this factor in stabilizing protein interactions with the pre-mRNA.
* This work was supported by an infrastructure grant to the Indian Institute of Science (IISc) from the Department of Biotechnology
(to U. V.); by scholarships (to D. S. and P. K.) from the Council of Scientific and Industrial Research, Government of I
and by a short term travel fellowship by the International Relations Cell, IISc, and funding from the Biotechnology and Biological
Sciences Research Council (courtesy of The University of Manchester) for the stay in Manchester (to D. S.), which facilitated
the UV cross-linking experiments.
This article contains .
Received September 7, 2011.
Revision received December 13, 2011.
The Journal of Biological Chemistry
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You'll be in good company.Kiyoshi Nagai - MRC Laboratory of Molecular Biology
Kiyoshi Nagai
CryoEM, crystallographic and biochemical studies of the spliceosome
The removal of introns from nuclear pre-mRNA and splicing together of exons into a continuous translatable coding sequence is catalyzed by a large and dynamic RNA-protein machine known as the spliceosome. Five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs) and numerous non-snRNP factors assemble at each intron in the pre-mRNA to form a spliceosome. Subsequently the spliceosome undergoes extensive compositional and structural changes to become catalytically active. How does the spliceosome assemble and carry out its function? How did a molecular machine as immense and complex as the spliceosome evolve in the Eukaryotic lineage? Our project aims to answer these questions by solving structures of the whole spliceosome and its key components by crystallography and electron cryo-microscopy (cryoEM).
U1 snRNP binds to the 5’ splice site of pre-mRNA and initiates the assembly of the spliceosome. The human spliceosomal U1 snRNP consists of U1 small nuclear RNA (snRNA) and 10 proteins. We have determined the crystal structure of the functional core of human U1 snRNP revealing the architectural principle of the spliceosomal snRNPs and the structural basis of 5'-splice site recognition (Pomeranz Krummel et al., 2009; Kondo et al., 2015).
We determined the structure of yeast U4/U6.U5 tri-snRNP by cryoEM single-particle reconstruction first at 5.9 ? resolution (Nguyen et al., 2015) and then at 3.7 ? overall resolution (Nguyen et al., 2016). U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex, which represents a substantial part of the spliceosome prior to activation. We have been able to build a near complete atomic model of this complex comprising U5 snRNA, U4 snRNA, U6 snRNA and more than 30 proteins, including the key components Prp8 (Galej et al., 2013), Brr2 (Nguyen et al., 2013) and Snu114. It provided important insight into the active site and activation mechanism of the spliceosome.
Recently we have solved a high resolution cryo-EM structure of the whole spliceosome captured immediately after the first step of catalysis (Galej et al., 2016). We have built an atomic model for this nearly 2MDa complex composed of 44 subunits including proteins and RNAs. Most importantly, the data allowed them to visualise for the very first time the pre-mRNA substrate inside the active spliceosome and its interactions with the RNA catalytic core and surrounding proteins. This has provided important mechanistic insights into RNA-based catalysis. It has consolidated nearly three decades of biochemistry and genetics on the spliceosome and indicates new research directions to be explored.
Our work provides crucial insights into the structure and function of the spliceosome as well as the evolutionary origin of the spliceosome.
Selected Papers
Galej, W. P., Wilkinson, M. E., Fica, S. M., Oubridge, C., Newman, A. J. and Nagai, K. (2016)Nature, DOI: 10.1038/nature19316
Nguyen, T.H.D., Galej, W.P., Bai, X-C., Oubridge, C., Newman, A.J., Scheres, S.H.W. and Nagai, K.
(2016)Nature 530: 298-302
Nguyen, T.H.D., Galej, W.P., Bai, X-C., Savva, C.G., Newman, A.J., Scheres, S.H.W.
and Nagai, K. (2015)Nature 523: 47-52
Kondo, Y., Oubridge, C., van Roon, A.M. and Nagai, K. (2015)Elife 4: e04986
Nguyen, T.H., Li, J., Galej, W.P., Oshikane, H., Newman, A.J. and Nagai, K. (2013)Structure 21: 910-919.
Galej, W.P., Oubridge, C., Newman, A.J. and Nagai, K.
(2013)Nature 493: 638-643.
Leung, A.K.W., Nagai, K. and Li, J. (2011)Nature 473: 536-539.
Pomeranz Krummel, D.A., Oubridge, C., Leung, A.K.W., Li, J. and Nagai, K. (2009)Nature 458: 475-480.
Group Members
Christine Norman
Chris Oubridge
Andrew Newman
Pei-chun Lin
Sebastian Fica
Lisa Strittmatter
Max Wilkinson
Clemens Plaschka