scholarly journals Conservation of functional domains involved in RNA binding and protein–protein interactions in human and Saccharomyces cerevisiae pre-mRNA splicing factor SF1

RNA ◽  
1998 ◽  
Vol 4 (5) ◽  
pp. 551-565 ◽  
Author(s):  
JEAN-CHRISTOPHE RAIN ◽  
ZAHRA RAFI ◽  
ZAKARIA RHANI ◽  
PIERRE LEGRAIN ◽  
ANGELA KRÄMER
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Interactions ◽  
Rna Binding ◽  
Mrna Splicing ◽  
Splicing Factor ◽  
Functional Domains ◽  
Protein Protein Interactions

scholarly journals UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex

2016 ◽  
Vol 72 (4) ◽  
pp. 497-511 ◽  
Author(s):  
Galina A. Stepanyuk ◽  
Pedro Serrano ◽  
Eigen Peralta ◽  
Carol L. Farr ◽  
Herbert L. Axelrod ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Splicing Factor ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Protein Protein Interactions ◽  
Rrm Domain ◽  
Nmr Structures ◽  
Binding Interface ◽  
Cell Extracts

RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35–U2AF65 and RBM39–SF3b155, the RBM39-UHM–U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM–ULM binding interface, providing a rationale for the known specificity of UHM–ULM interactions. This study therefore establishes a structural basis for specific UHM–ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.

scholarly journals Sip1, a Novel RS Domain-Containing Protein Essential for Pre-mRNA Splicing

1998 ◽  
Vol 18 (2) ◽  
pp. 676-684 ◽  
Author(s):  
Wan-Jiang Zhang ◽  
Jane Y. Wu
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Sequence Similarity ◽  
Functional Characterization ◽  
Nuclear Extract ◽  
Mrna Splicing ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Interacting Protein

ABSTRACT Previous studies have shown that protein-protein interactions among splicing factors may play an important role in pre-mRNA splicing. We report here identification and functional characterization of a new splicing factor, Sip1 (SC35-interacting protein 1). Sip1 was initially identified by virtue of its interaction with SC35, a splicing factor of the SR family. Sip1 interacts with not only several SR proteins but also with U1-70K and U2AF65, proteins associated with 5′ and 3′ splice sites, respectively. The predicted Sip1 sequence contains an arginine-serine-rich (RS) domain but does not have any known RNA-binding motifs, indicating that it is not a member of the SR family. Sip1 also contains a region with weak sequence similarity to the Drosophila splicing regulator suppressor of white apricot (SWAP). An essential role for Sip1 in pre-mRNA splicing was suggested by the observation that anti-Sip1 antibodies depleted splicing activity from HeLa nuclear extract. Purified recombinant Sip1 protein, but not other RS domain-containing proteins such as SC35, ASF/SF2, and U2AF65, restored the splicing activity of the Sip1-immunodepleted extract. Addition of U2AF65 protein further enhanced the splicing reconstitution by the Sip1 protein. Deficiency in the formation of both A and B splicing complexes in the Sip1-depleted nuclear extract indicates an important role of Sip1 in spliceosome assembly. Together, these results demonstrate that Sip1 is a novel RS domain-containing protein required for pre-mRNA splicing and that the functional role of Sip1 in splicing is distinct from those of known RS domain-containing splicing factors.

scholarly journals RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation

2018 ◽  
Author(s):  
Fang Bai ◽  
Jacob Corll ◽  
Donya N. Shodja ◽  
Ruth Davenport ◽  
Guanqiao Feng ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Protein Interactions ◽  
Rna Binding ◽  
Splicing Factor ◽  
Binding Motif ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Intron Recognition ◽  
U2 Auxiliary Factor ◽  
Auxiliary Factor

AbstractThe last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize RNA Binding Motif Protein48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, ZRSR2/RGH3. Protein-protein interactions between RBM48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggest major and minor spliceosome factors may form complexes during intron recognition. Human RBM48 interacts with ARMC7. Maize RBM48 and ARMC7 have a conserved protein-protein interaction. These data predict that RBM48 is likely to function in U12 splicing throughout eukaryotes and that U12 splicing promotes endosperm cell differentiation in maize.

GRR1 of Saccharomyces cerevisiae is required for glucose repression and encodes a protein with leucine-rich repeats

1991 ◽  
Vol 11 (10) ◽  
pp. 5101-5112
Author(s):  
J S Flick ◽  
M Johnston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Interactions ◽  
Tandem Repeats ◽  
Glucose Repression ◽  
Molecular Data ◽  
Primary Response ◽  
Yeast Cells ◽  
Cell Fractionation ◽  
Protein Protein Interactions ◽  
Yeast Saccharomyces Cerevisiae

Growth of the yeast Saccharomyces cerevisiae on glucose leads to repression of transcription of many genes required for alternative carbohydrate metabolism. The GRR1 gene appears to be of central importance to the glucose repression mechanism, because mutations in GRR1 result in a pleiotropic loss of glucose repression (R. Bailey and A. Woodword, Mol. Gen. Genet. 193:507-512, 1984). We have isolated the GRR1 gene and determined that null mutants are viable and display a number of growth defects in addition to the loss of glucose repression. Surprisingly, grr1 mutations convert SUC2, normally a glucose-repressed gene, into a glucose-induced gene. GRR1 encodes a protein of 1,151 amino acids that is expressed constitutively at low levels in yeast cells. GRR1 protein contains 12 tandem repeats of a sequence similar to leucine-rich motifs found in other proteins that may mediate protein-protein interactions. Indeed, cell fractionation studies are consistent with this view, suggesting that GRR1 protein is tightly associated with a particulate protein fraction in yeast extracts. The combined genetic and molecular data are consistent with the idea that GRR1 protein is a primary response element in the glucose repression pathway and is required for the generation or interpretation of the signal that induces glucose repression.

scholarly journals Saccharomyces cerevisiae as a Tool to Investigate Plant Potassium and Sodium Transporters

2019 ◽  
Vol 20 (9) ◽  
pp. 2133 ◽  
Author(s):  
Antonella Locascio ◽  
Nuria Andrés-Colás ◽  
José Miguel Mulet ◽  
Lynne Yenush
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Interactions ◽  
Model System ◽  
Protein Protein Interactions ◽  
Alkali Cations ◽  
Yeast Saccharomyces Cerevisiae ◽  
Future Directions ◽  
Sodium Transporters ◽  
Adverse Environmental Conditions ◽  
Sodium And Potassium

Sodium and potassium are two alkali cations abundant in the biosphere. Potassium is essential for plants and its concentration must be maintained at approximately 150 mM in the plant cell cytoplasm including under circumstances where its concentration is much lower in soil. On the other hand, sodium must be extruded from the plant or accumulated either in the vacuole or in specific plant structures. Maintaining a high intracellular K+/Na+ ratio under adverse environmental conditions or in the presence of salt is essential to maintain cellular homeostasis and to avoid toxicity. The baker’s yeast, Saccharomyces cerevisiae, has been used to identify and characterize participants in potassium and sodium homeostasis in plants for many years. Its utility resides in the fact that the electric gradient across the membrane and the vacuoles is similar to plants. Most plant proteins can be expressed in yeast and are functional in this unicellular model system, which allows for productive structure-function studies for ion transporting proteins. Moreover, yeast can also be used as a high-throughput platform for the identification of genes that confer stress tolerance and for the study of protein–protein interactions. In this review, we summarize advances regarding potassium and sodium transport that have been discovered using the yeast model system, the state-of-the-art of the available techniques and the future directions and opportunities in this field.

scholarly journals Computational Prediction of Protein-Protein Interactions of Human Tyrosinase

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Su-Fang Wang ◽  
Sangho Oh ◽  
Yue-Xiu Si ◽  
Zhi-Jiang Wang ◽  
Hong-Yan Han ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
3D Structure ◽  
Computational Prediction ◽  
Binding Motif ◽  
Protein Protein Interactions ◽  
Lim Domains ◽  
Binding Partners ◽  
Computational Predictions ◽  
Human Tyrosinase

The various studies on tyrosinase have recently gained the attention of researchers due to their potential application values and the biological functions. In this study, we predicted the 3D structure of human tyrosinase and simulated the protein-protein interactions between tyrosinase and three binding partners, four and half LIM domains 2 (FHL2), cytochrome b-245 alpha polypeptide (CYBA), and RNA-binding motif protein 9 (RBM9). Our interaction simulations showed significant binding energy scores of −595.3 kcal/mol for FHL2, −859.1 kcal/mol for CYBA, and −821.3 kcal/mol for RBM9. We also investigated the residues of each protein facing toward the predicted site of interaction with tyrosinase. Our computational predictions will be useful for elucidating the protein-protein interactions of tyrosinase and studying its binding mechanisms.

scholarly journals Structural Classification of Bacterial Response Regulators: Diversity of Output Domains and Domain Combinations

2006 ◽  
Vol 188 (12) ◽  
pp. 4169-4182 ◽  
Author(s):  
Michael Y. Galperin
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Transcriptional Regulators ◽  
Bacterial Cells ◽  
Protein Protein Interactions ◽  
Response Regulators ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Archaeal Species

ABSTRACT CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (∼14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html .

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