scholarly journals Recognition of RNA Branch Point Sequences by the KH Domain of Splicing Factor 1 (Mammalian Branch Point Binding Protein) in a Splicing Factor Complex

2001 ◽  
Vol 21 (15) ◽  
pp. 5232-5241 ◽  
Author(s):  
Hadas Peled-Zehavi ◽  
J. Andrew Berglund ◽  
Michael Rosbash ◽  
Alan D. Frankel
Keyword(s):  
Branch Point ◽  
Fusion Proteins ◽  
Rna Binding ◽  
Binding Protein ◽  
Splicing Factor ◽  
Splice Sites ◽  
Reporter System ◽  
Kh Domain ◽  
Tat Fusion Proteins ◽  
Splicing Factor 1

ABSTRACT Mammalian splicing factor 1 (SF1; also mammalian branch point binding protein [mBBP]; hereafter SF1/mBBP) specifically recognizes the seven-nucleotide branch point sequence (BPS) located at 3′ splice sites and participates in the assembly of early spliceosomal complexes. SF1/mBBP utilizes a “maxi-K homology” (maxi-KH) domain for recognition of the single-stranded BPS and requires a cooperative interaction with splicing factor U2AF65 bound to an adjacent polypyrimidine tract (PPT) for high-affinity binding. To investigate how the KH domain of SF1/mBBP recognizes the BPS in conjunction with U2AF and possibly other proteins, we constructed a transcriptional reporter system utilizing human immunodeficiency virus type 1 Tat fusion proteins and examined the RNA-binding specificity of the complex using KH domain and RNA-binding site mutants. We first established that SF1/mBBP and U2AF cooperatively assemble in our reporter system at RNA sites composed of the BPS, PPT, and AG dinucleotide found at 3′ splice sites, with endogenous proteins assembled along with the Tat fusions. We next found that the activities of the Tat fusion proteins on different BPS variants correlated well with the known splicing efficiencies of the variants, supporting a model in which the SF1/mBBP-BPS interaction helps determine splicing efficiency prior to the U2 snRNP-BPS interaction. Finally, the likely RNA-binding surface of the maxi-KH domain was identified by mutagenesis and appears similar to that used by “simple” KH domains, involving residues from two putative α helices, a highly conserved loop, and parts of a β sheet. Using a homology model constructed from the cocrystal structure of a Nova KH domain-RNA complex (Lewis et al., Cell 100:323–332, 2000), we propose a plausible arrangement for SF1/mBBP-U2AF complexes assembled at 3′ splice sites.

scholarly journals Systematic characterization of branch point binding protein, splicing factor 1, gene family in plant development and stress responses

2019 ◽  
Author(s):  
Kai-Lu Zhang ◽  
Zhen Feng ◽  
Jing-Fang Yang ◽  
Tian Yuan ◽  
Di Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Stress Responses ◽  
Messenger Rna ◽  
Rna Binding ◽  
Binding Protein ◽  
Splicing Factor ◽  
Binding Motif ◽  
Splicing Factor 1

Abstract Background: Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic genes to generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. Results: Here, we conducted a systematic characterization of SF1 gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Conclusion: Our comprehensive analysis presents general feature of gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

scholarly journals Systematic characterization of branch point binding protein, splicing factor 1, gene family in plant development and stress responses

2019 ◽  
Author(s):  
Kai-Lu Zhang ◽  
Zhen Feng ◽  
Jing-Fang Yang ◽  
Tian Yuan ◽  
Di Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Stress Responses ◽  
Messenger Rna ◽  
Rna Binding ◽  
Binding Protein ◽  
Splicing Factor ◽  
Binding Motif ◽  
Splicing Factor 1

Abstract Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic genes to generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. To this end, we conducted a systematic characterization of SF1 gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Our analysis presents general feature of gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

scholarly journals miR-322/-503 cluster is expressed in the earliest cardiac progenitor cells and drives cardiomyocyte specification

2016 ◽  
Vol 113 (34) ◽  
pp. 9551-9556 ◽  
Author(s):  
Xiaopeng Shen ◽  
Benjamin Soibam ◽  
Ashley Benham ◽  
Xueping Xu ◽  
Mani Chopra ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Cell Fate ◽  
Rna Binding ◽  
Binding Protein ◽  
Calcium Transient ◽  
Cardiac Progenitor Cells ◽  
Mirna Cluster ◽  
Reporter System ◽  
Screening Assay ◽  
Fate Determination

Understanding the mechanisms of early cardiac fate determination may lead to better approaches in promoting heart regeneration. We used a mesoderm posterior 1 (Mesp1)-Cre/Rosa26-EYFP reporter system to identify microRNAs (miRNAs) enriched in early cardiac progenitor cells. Most of these miRNA genes bear MESP1-binding sites and active histone signatures. In a calcium transient-based screening assay, we identified miRNAs that may promote the cardiomyocyte program. An X-chromosome miRNA cluster, miR-322/-503, is the most enriched in the Mesp1 lineage and is the most potent in the screening assay. It is specifically expressed in the looping heart. Ectopic miR-322/-503 mimicking the endogenous temporal patterns specifically drives a cardiomyocyte program while inhibiting neural lineages, likely by targeting the RNA-binding protein CUG-binding protein Elav-like family member 1 (Celf1). Thus, early miRNAs in lineage-committed cells may play powerful roles in cell-fate determination by cross-suppressing other lineages. miRNAs identified in this study, especially miR-322/-503, are potent regulators of early cardiac fate.

scholarly journals The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0126978 ◽  
Author(s):  
Louise F. Thatcher ◽  
Lars G. Kamphuis ◽  
James K. Hane ◽  
Luis Oñate-Sánchez ◽  
Karam B. Singh
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Kh Domain ◽  
Resistance To Stress ◽  
Jasmonate Signalling

scholarly journals A Role for SRp54 during Intron Bridging of Small Introns with Pyrimidine Tracts Upstream of the Branch Point

1998 ◽  
Vol 18 (9) ◽  
pp. 5425-5434 ◽  
Author(s):  
Catharine F. Kennedy ◽  
Angela Krämer ◽  
Susan M. Berget
Keyword(s):  
Binding Site ◽  
Branch Point ◽  
Splice Site ◽  
Early Recognition ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Sr Protein ◽  
U2 Snrnp ◽  
Auxiliary Factor ◽  
Splicing Factor 1

ABSTRACT One of the earliest steps in pre-mRNA recognition involves binding of the splicing factor U2 snRNP auxiliary factor (U2AF or MUD2 inSaccharomyces cerevisiae) to the 3′ splice site region. U2AF interacts with a number of other proteins, including members of the serine/arginine (SR) family of splicing factors as well as splicing factor 1 (SF1 or branch point bridging protein in S. cerevisiae), thereby participating in bridging either exons or introns. In vertebrates, the binding site for U2AF is the pyrimidine tract located between the branch point and 3′ splice site. Many small introns, especially those in nonvertebrates, lack a classical 3′ pyrimidine tract. Here we show that a 59-nucleotide Drosophila melanogaster intron contains C-rich pyrimidine tracts between the 5′ splice site and branch point that are needed for maximal binding of both U1 snRNPs and U2 snRNPs to the 5′ and 3′ splice site, respectively, suggesting that the tracts are the binding site for an intron bridging factor. The tracts are shown to bind both U2AF and the SR protein SRp54 but not SF1. Addition of a strong 3′ pyrimidine tract downstream of the branch point increases binding of SF1, but in this context, the upstream pyrimidine tracts are inhibitory. We suggest that U2AF- and/or SRp54-mediated intron bridging may be an alternative early recognition mode to SF1-directed bridging for small introns, suggesting gene-specific early spliceosome assembly.

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