scholarly journals Comprehensive database and evolutionary dynamics of U12-type introns

2020 ◽  
Author(s):  
Devlin C Moyer ◽  
Graham E Larue ◽  
Courtney E Hershberger ◽  
Scott W Roy ◽  
Richard A Padgett
Keyword(s):  
Rna Splicing ◽  
Evolutionary Dynamics ◽  
Messenger Rnas ◽  
Spliceosomal Introns ◽  
Conversion Model ◽  
Nuclear Maturation ◽  
Small Nuclear Ribonucleoprotein ◽  
Associated Proteins ◽  
Non Coding Rnas ◽  
Nuclear Ribonucleoprotein

Abstract During nuclear maturation of most eukaryotic pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing. Different classes of introns are excised by the U2-type or the U12-type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and associated proteins. We created intronIC, a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD). We then used the data in the IAOD to revisit several hypotheses concerning the evolution of the two classes of spliceosomal introns, finding support for the class conversion model explaining the low abundance of U12-type introns in modern genomes.

scholarly journals Updated Database and Evolutionary Dynamics of U12-Type Introns

2019 ◽  
Author(s):  
Devlin C. Moyer ◽  
Graham E. Larue ◽  
Courtney E. Hershberger ◽  
Scott W. Roy ◽  
Richard A. Padgett
Keyword(s):  
Rna Splicing ◽  
Evolutionary Dynamics ◽  
Messenger Rnas ◽  
Spliceosomal Introns ◽  
Conversion Model ◽  
Nuclear Maturation ◽  
Small Nuclear Ribonucleoprotein ◽  
Associated Proteins ◽  
Non Coding Rnas ◽  
Nuclear Ribonucleoprotein

ABSTRACTDuring nuclear maturation of most eukaryotic pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing. Different classes of introns are excised by the U2-type or the U12-type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and associated proteins. We created intronIC, a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD). We then used the data in the IAOD to revisit several hypotheses concerning the evolution of the two classes of spliceosomal introns, finding support for the class conversion model explaining the low abundance of U12-type introns in modern genomes.

Leucine periodicity of U2 small nuclear ribonucleoprotein particle (snRNP) A' protein is implicated in snRNP assembly via protein-protein interactions

1991 ◽  
Vol 11 (3) ◽  
pp. 1578-1589
Author(s):  
L D Fresco ◽  
D S Harper ◽  
J D Keene
Keyword(s):  
Protein Interactions ◽  
Leucine Zipper ◽  
Tandem Repeats ◽  
Mutational Analysis ◽  
Particle Density ◽  
Protein Protein Interactions ◽  
Small Nuclear Ribonucleoprotein ◽  
Cell Extracts ◽  
Associated Proteins ◽  
Nuclear Ribonucleoprotein

Recombinant A' protein could be reconstituted into U2 small nuclear ribonucleoprotein particles (snRNPs) upon addition to HeLa cell extracts as determined by coimmunoprecipitation and particle density; however, direct binding to U2 RNA could not be demonstrated except in the presence of the U2 snRNP B" protein. Mutational analysis indicated that a central core region of A' was required for particle reconstitution. This region consists of five tandem repeats of approximately 24 amino acids each that exhibit a periodicity of leucine and asparagine residues that is distinct from the leucine zipper. Similar leucine-rich (Leu-Leu motif) repeats are characteristic of a diverse array of soluble and membrane-associated proteins from yeasts to humans but have not been reported previously to reside in nuclear proteins. Several of these proteins, including Toll, chaoptin, RNase/angiogenin inhibitors, lutropin-choriogonadotropin receptor, carboxypeptidase N, adenylyl cyclase, CD14, and human immunodeficiency virus type 1 Rev, may be involved in protein-protein interactions. Our findings suggest that in cell extracts the Leu-Leu motif of A' is required for reconstitution with U2 snRNPs and perhaps with other components involved in splicing through protein-protein interactions.

Single-molecule fluorescence-based studies on the dynamics, assembly and catalytic mechanism of the spliceosome

2014 ◽  
Vol 42 (4) ◽  
pp. 1211-1218 ◽  
Author(s):  
Chandani Warnasooriya ◽  
David Rueda
Keyword(s):  
Single Molecule ◽  
Catalytic Mechanism ◽  
Cellular Gene ◽  
Small Nuclear Ribonucleoprotein ◽  
Assembly Kinetics ◽  
Associated Proteins ◽  
Conformational Rearrangements ◽  
Nuclear Ribonucleoprotein ◽  
Mrna Precursor ◽  
Precursor Mrna

Pre-mRNA (precursor mRNA) splicing is a key step in cellular gene expression where introns are excised and exons are ligated together to produce mature mRNA. This process is catalysed by the spliceosome, which consists of five snRNPs (small nuclear ribonucleoprotein particles) and numerous protein factors. Assembly of these snRNPs and associated proteins is a highly dynamic process, making it challenging to study the conformational rearrangements and spliceosome assembly kinetics in bulk studies. In the present review, we discuss recent studies utilizing techniques based on single-molecule detection that have helped overcome this challenge. These studies focus on the assembly dynamics and splicing kinetics in real-time, which help understanding of spliceosomal assembly and catalysis.

scholarly journals The pre-mRNA-splicing factor SF3a66 functions as a microtubule-binding and -bundling protein

2004 ◽  
Vol 382 (1) ◽  
pp. 223-230 ◽  
Author(s):  
Kei TAKENAKA ◽  
Hiroyuki NAKAGAWA ◽  
Shigeaki MIYAMOTO ◽  
Hiroaki MIKI
Keyword(s):  
Rna Splicing ◽  
Ectopic Expression ◽  
Neuroblastoma Cells ◽  
High Molecular Mass ◽  
Mrna Splicing ◽  
Splicing Factor ◽  
Canonical Function ◽  
High Affinity ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Ribonucleoprotein

SF3a (splicing factor 3a) complex is an essential component of U2 snRNPs (small nuclear ribonucleoprotein particles), which are involved in pre-mRNA splicing. This complex consists of three subunits: SF3a60, SF3a66 and SF3a120. Here, we report a possible non-canonical function of a well-characterized RNA-splicing factor, SF3a66. Ectopic expression experiments using each SF3a subunit in N1E 115 neuroblastoma cells reveals that SF3a66 alone can induce neurite extension, suggesting that SF3a66 functions in the regulation of cell morphology. A screen for proteins that bind to SF3a66 clarifies that SF3a66 binds to β-tubulin, and also to microtubules, with high affinity, indicating that SF3a66 is a novel MAP (microtubule-associated protein). Electron microscopy experiments show that SF3a66 can bundle microtubules, and that bundling of microtubules is due to cross-bridging of microtubules by high-molecular-mass complexes of oligomerized SF3a66. These results indicate that SF3a66 is likely to be a novel MAP, and can function as a microtubule-bundling protein independently of RNA splicing.

scholarly journals Splicing-independent recruitment of spliceosomal small nuclear RNPs to nascent RNA polymerase II transcripts

2007 ◽  
Vol 178 (6) ◽  
pp. 937-949 ◽  
Author(s):  
Snehal Bhikhu Patel ◽  
Natalya Novikova ◽  
Michel Bellini
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Messenger Rnas ◽  
Stem Loop ◽  
Small Nuclear Ribonucleoprotein ◽  
Small Nuclear Rnas ◽  
Transcriptional Units ◽  
Necessary And Sufficient ◽  
Nuclear Ribonucleoprotein ◽  
Nascent Transcripts

In amphibian oocytes, most lateral loops of the lampbrush chromosomes correspond to active transcriptional sites for RNA polymerase II. We show that newly assembled small nuclear ribonucleoprotein (RNP [snRNP]) particles, which are formed upon cytoplasmic injection of fluorescently labeled spliceosomal small nuclear RNAs (snRNAs), target the nascent transcripts of the chromosomal loops. With this new targeting assay, we demonstrate that nonfunctional forms of U1 and U2 snRNAs still associate with the active transcriptional units. In particular, we find that their association with nascent RNP fibrils is independent of their base pairing with pre–messenger RNAs. Additionally, stem loop I of the U1 snRNA is identified as a discrete domain that is both necessary and sufficient for association with nascent transcripts. Finally, in oocytes deficient in splicing, the recruitment of U1, U4, and U5 snRNPs to transcriptional units is not affected. Collectively, these data indicate that the recruitment of snRNPs to nascent transcripts and the assembly of the spliceosome are uncoupled events.

scholarly journals Leucine periodicity of U2 small nuclear ribonucleoprotein particle (snRNP) A' protein is implicated in snRNP assembly via protein-protein interactions.

1991 ◽  
Vol 11 (3) ◽  
pp. 1578-1589 ◽  
Author(s):  
L D Fresco ◽  
D S Harper ◽  
J D Keene
Keyword(s):  
Protein Interactions ◽  
Leucine Zipper ◽  
Tandem Repeats ◽  
Mutational Analysis ◽  
Particle Density ◽  
Protein Protein Interactions ◽  
Small Nuclear Ribonucleoprotein ◽  
Cell Extracts ◽  
Associated Proteins ◽  
Nuclear Ribonucleoprotein

Recombinant A' protein could be reconstituted into U2 small nuclear ribonucleoprotein particles (snRNPs) upon addition to HeLa cell extracts as determined by coimmunoprecipitation and particle density; however, direct binding to U2 RNA could not be demonstrated except in the presence of the U2 snRNP B" protein. Mutational analysis indicated that a central core region of A' was required for particle reconstitution. This region consists of five tandem repeats of approximately 24 amino acids each that exhibit a periodicity of leucine and asparagine residues that is distinct from the leucine zipper. Similar leucine-rich (Leu-Leu motif) repeats are characteristic of a diverse array of soluble and membrane-associated proteins from yeasts to humans but have not been reported previously to reside in nuclear proteins. Several of these proteins, including Toll, chaoptin, RNase/angiogenin inhibitors, lutropin-choriogonadotropin receptor, carboxypeptidase N, adenylyl cyclase, CD14, and human immunodeficiency virus type 1 Rev, may be involved in protein-protein interactions. Our findings suggest that in cell extracts the Leu-Leu motif of A' is required for reconstitution with U2 snRNPs and perhaps with other components involved in splicing through protein-protein interactions.

scholarly journals Dramatically reduced spliceosome in Cyanidioschyzon merolae

2015 ◽  
Vol 112 (11) ◽  
pp. E1191-E1200 ◽  
Author(s):  
Martha R. Stark ◽  
Elizabeth A. Dunn ◽  
William S. C. Dunn ◽  
Cameron J. Grisdale ◽  
Anthony R. Daniele ◽  
...  
Keyword(s):  
Red Alga ◽  
Mrna Splicing ◽  
Splicing Factors ◽  
Cyanidioschyzon Merolae ◽  
Ribonucleoprotein Particle ◽  
Small Nuclear Ribonucleoprotein ◽  
U1 Snrna ◽  
Associated Proteins ◽  
Compositional Variability ◽  
Nuclear Ribonucleoprotein

The human spliceosome is a large ribonucleoprotein complex that catalyzes pre-mRNA splicing. It consists of five snRNAs and more than 200 proteins. Because of this complexity, much work has focused on the Saccharomyces cerevisiae spliceosome, viewed as a highly simplified system with fewer than half as many splicing factors as humans. Nevertheless, it has been difficult to ascribe a mechanistic function to individual splicing factors or even to discern which are critical for catalyzing the splicing reaction. We have identified and characterized the splicing machinery from the red alga Cyanidioschyzon merolae, which has been reported to harbor only 26 intron-containing genes. The U2, U4, U5, and U6 snRNAs contain expected conserved sequences and have the ability to adopt secondary structures and form intermolecular base-pairing interactions, as in other organisms. C. merolae has a highly reduced set of 43 identifiable core splicing proteins, compared with ∼90 in budding yeast and ∼140 in humans. Strikingly, we have been unable to find a U1 snRNA candidate or any predicted U1-associated proteins, suggesting that splicing in C. merolae may occur without the U1 small nuclear ribonucleoprotein particle. In addition, based on mapping the identified proteins onto the known splicing cycle, we propose that there is far less compositional variability during splicing in C. merolae than in other organisms. The observed reduction in splicing factors is consistent with the elimination of spliceosomal components that play a peripheral or modulatory role in splicing, presumably retaining those with a more central role in organization and catalysis.

scholarly journals A specific 31-nucleotide domain of U1 RNA directly interacts with the 70K small nuclear ribonucleoprotein component.

1989 ◽  
Vol 9 (11) ◽  
pp. 4872-4881 ◽  
Author(s):  
C C Query ◽  
R C Bentley ◽  
J D Keene
Keyword(s):  
Nucleotide Sequence ◽  
Splice Site ◽  
Rna Binding ◽  
Binding Domain ◽  
Specific Domain ◽  
Stem Loop ◽  
Small Nuclear Ribonucleoprotein ◽  
Associated Proteins ◽  
Nuclear Ribonucleoprotein

We have defined the nucleotide sequence of a protein-binding domain within U1 RNA that specifically recognizes and binds both to a U1 small nuclear ribonucleoprotein component (the 70K protein) and to the previously defined RNA-binding domain of the 70K protein. We have investigated direct interactions between purified U1 RNA and 70K protein by reconstitution in vitro. Thirty-one nucleotides of U1 RNA, corresponding to stem-loop I, were required for this interaction. Nucleotides at the 5' end of U1 RNA that are involved in base pairing with the 5' splice site of pre-mRNA were not required for binding. In contrast to other reports, these findings demonstrate that a specific domain of U1 RNA can bind directly to the 70K protein independently of any other snRNP-associated proteins.

Roles of the U5 snRNP in spliceosome dynamics and catalysis

2004 ◽  
Vol 32 (6) ◽  
pp. 928-931 ◽  
Author(s):  
I.A. Turner ◽  
C.M. Norman ◽  
M.J. Churcher ◽  
A.J. Newman
Keyword(s):  
Mrna Splicing ◽  
Small Nuclear Rna ◽  
Protein Coding ◽  
Rna Molecules ◽  
Small Nuclear Ribonucleoprotein ◽  
Associated Proteins ◽  
Gene Transcripts ◽  
Protein Components ◽  
Intron Removal ◽  
Nuclear Ribonucleoprotein

Most protein-coding genes in eukaryotes are interrupted by non-coding intervening sequences (introns), which must be precisely removed from primary gene transcripts (pre-mRNAs) before translation of the message into protein. Intron removal by pre-mRNA splicing occurs in the nucleus and is catalysed by complex ribonucleoprotein machines called spliceosomes. These molecular machines consist of several small nuclear RNA molecules and their associated proteins [together termed snRNP (small nuclear ribonucleoprotein) particles], plus multiple accessory factors. Of particular interest are the U2, U5 and U6 snRNPs, which play crucial roles in the catalytic steps of splicing. In the present review, we summarize our current understanding of the role played by the protein components of the U5 snRNP in pre-mRNA splicing, which include some of the largest and most highly conserved nuclear proteins.

scholarly journals The U1 RNA-binding site of the U1 small nuclear ribonucleoprotein (snRNP)-associated A protein suggests a similarity with U2 snRNPs.

1989 ◽  
Vol 9 (7) ◽  
pp. 2975-2982 ◽  
Author(s):  
C Lutz-Freyermuth ◽  
J D Keene ◽  
C Lutz-Reyermuth
Keyword(s):  
Binding Site ◽  
Rna Binding ◽  
Sequence Similarity ◽  
Binding Assays ◽  
Stem Loop ◽  
Small Nuclear Ribonucleoprotein ◽  
Vitro Binding ◽  
Associated Proteins ◽  
Nuclear Ribonucleoprotein

The site of interaction between human U1 RNA and one of its uniquely associated proteins, A, was examined with in vitro binding assays. The A protein bound directly to stem-loop II of U1 RNA in a region which exhibits sequence similarity to U2 RNA. The similarity with U2 RNA was in a region that has been shown to interact with a U2 RNA-associated protein. The A protein-binding site on U1 RNA overlapped a previously described epitope for an RNA-specific human autoantibody (S. L. Deutscher and J. D. Keene, Proc. Natl. Acad. Sci. USA 85:3299-3303, 1988), supporting the hypothesis that the anti-RNA antibody originated as an anti-idiotypic response to A protein-specific autoantibodies.

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