scholarly journals The Fission Yeast RNA-Binding Protein Meu5 Is Involved in Outer Forespore Membrane Breakdown during Spore Formation

2020 ◽  
Vol 6 (4) ◽  
pp. 284
Author(s):  
Bowen Zhang ◽  
Erika Teraguchi ◽  
Kazuki Imada ◽  
Yuhei O. Tahara ◽  
Shuko Nakamura ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Target Genes ◽  
Rna Binding ◽  
De Novo ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Biological Significance ◽  
Spore Wall ◽  
Spore Formation ◽  
Membrane Breakdown

In Schizosaccharomyces pombe, the spore wall confers strong resistance against external stress. During meiosis II, the double-layered intracellular forespore membrane (FSM) forms de novo and encapsulates the nucleus. Eventually, the inner FSM layer becomes the plasma membrane of the spore, while the outer layer breaks down. However, the molecular mechanism and biological significance of this membrane breakdown remain unknown. Here, by genetic investigation of an S. pombe mutant (E22) with normal prespore formation but abnormal spores, we showed that Meu5, an RNA-binding protein known to bind to and stabilize more than 80 transcripts, is involved in this process. We confirmed that the E22 mutant does not produce Meu5 protein, while overexpression of meu5+ in E22 restores the sporulation defect. Furthermore, electron microscopy revealed that the outer membrane of the FSM persisted in meu5∆ spores. Investigation of the target genes of meu5+ showed that a mutant of cyc1+ encoding cytochrome c also showed a severe defect in outer FSM breakdown. Lastly, we determined that outer FSM breakdown occurs coincident with or after formation of the outermost Isp3 layer of the spore wall. Collectively, our data provide novel insights into the molecular mechanism of spore formation.

scholarly journals Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

2011 ◽  
Vol 286 (43) ◽  
pp. 37063-37066 ◽  
Author(s):  
Philip J. Uren ◽  
Suzanne C. Burns ◽  
Jianhua Ruan ◽  
Kusum K. Singh ◽  
Andrew D. Smith ◽  
...  
Keyword(s):  
Complex Network ◽  
Binding Sites ◽  
Target Genes ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Genomic Analyses ◽  
Hu Antigen R

scholarly journals Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance

2019 ◽  
Author(s):  
Ling-Yu Wang ◽  
Sheng-Jun Xiao ◽  
Hiroyuki Kunimoto ◽  
Kazuaki Tokunaga ◽  
Hirotada Kojima ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transcriptional Activity ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Biological Significance ◽  
Nuclear Bodies ◽  
Transient Component ◽  
Cellular Transcription ◽  
Splicing Machinery

AbstractRBM10 is an RNA-binding protein that regulates alternative splicing (AS). This protein localizes to the extra-nucleolar nucleoplasm and S1-1 nuclear bodies (NBs). We investigated the biological significance of RBM10 localization to S1-1 NBs, which is poorly understood. Our analyses revealed that RBM10 possesses two S1-1 NB-targeting sequences (NBTSs), one in the KEKE motif region and another in the C2H2 Zn finger (ZnF). These NBTSs acted synergistically and were sufficient for localization of RBM10 to S1-1 NBs. Furthermore, the C2H2 ZnF not only acted as an NBTS, but was also essential for regulation of AS by RBM10. RBM10 did not participate in S1-1 NB formation. We confirmed the previous finding that localization of RBM10 to S1-1 NBs increases as cellular transcriptional activity decreases and vice versa. These results indicate that RBM10 is a transient component of S1-1 NBs and is sequestered in these structures via its NBTSs when cellular transcription decreases. We propose that the NB-targeting activity of the C2H2 ZnF is induced when it is not bound to pre-mRNA or the splicing machinery complex under conditions of reduced transcription.

scholarly journals α-Actinin TvACTN3 ofTrichomonas vaginalisIs an RNA-Binding Protein That Could Participate in Its Posttranscriptional Iron Regulatory Mechanism

2014 ◽  
Vol 2014 ◽  
pp. 1-20 ◽  
Author(s):  
Jaeson Santos Calla-Choque ◽  
Elisa Elvira Figueroa-Angulo ◽  
Leticia Ávila-González ◽  
Rossana Arroyo
Keyword(s):  
Trichomonas Vaginalis ◽  
Rna Binding ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Iron Concentration ◽  
Rna Binding Protein ◽  
Cross Linking ◽  
Cytoplasmic Protein

Trichomonas vaginalisis a sexually transmitted flagellated protist parasite responsible for trichomoniasis. This parasite is dependent on high levels of iron, favoring its growth and multiplication. Iron also differentially regulates some trichomonad virulence properties by unknown mechanisms. However, there is evidence to support the existence of gene regulatory mechanisms at the transcriptional and posttranscriptional levels that are mediated by iron concentration inT. vaginalis. Thus, the goal of this study was to identify an RNA-binding protein inT. vaginalisthat interacts with the tvcp4 RNA stem-loop structure, which may participate in a posttranscriptional iron regulatory mechanism mediated by RNA-protein interactions. We performed RNA electrophoretic mobility shift assay (REMSA) and supershift, UV cross-linking, Northwestern blot, and western blot (WB) assays using cytoplasmic protein extracts fromT. vaginaliswith the tvcp4 RNA hairpin structure as a probe. We identified a 135-kDa protein isolated by the UV cross-linking assays asα-actinin 3 (TvACTN3) by MALDI-TOF-MS that was confirmed by LS-MS/MS andde novosequencing. TvACTN3 is a cytoplasmic protein that specifically binds to hairpin RNA structures from trichomonads and humans when the parasites are grown under iron-depleted conditions. Thus, TvACTN3 could participate in the regulation of gene expression by iron inT. vaginalisthrough a parallel posttranscriptional mechanism similar to that of the IRE/IRP system.

scholarly journals Posttranscriptional Repression of GacS/GacA-Controlled Genes by the RNA-Binding Protein RsmE Acting Together with RsmA in the Biocontrol Strain Pseudomonas fluorescens CHA0

2005 ◽  
Vol 187 (1) ◽  
pp. 276-285 ◽  
Author(s):  
Cornelia Reimmann ◽  
Claudio Valverde ◽  
Elisabeth Kay ◽  
Dieter Haas
Keyword(s):  
Pseudomonas Fluorescens ◽  
Target Genes ◽  
Rna Binding ◽  
Specific Binding ◽  
Binding Protein ◽  
Regulatory Element ◽  
Rna Binding Protein ◽  
Mobility Shift ◽  
Double Mutation ◽  
Regulatory Rnas

ABSTRACT In the plant-beneficial soil bacterium Pseudomonas fluorescens CHA0, the production of biocontrol factors (antifungal secondary metabolites and exoenzymes) is controlled at a posttranscriptional level by the GacS/GacA signal transduction pathway involving RNA-binding protein RsmA as a key regulatory element. This protein is assumed to bind to the ribosome-binding site of target mRNAs and to block their translation. RsmA-mediated repression is relieved at the end of exponential growth by two GacS/GacA-controlled regulatory RNAs RsmY and RsmZ, which bind and sequester the RsmA protein. A gene (rsmE) encoding a 64-amino-acid RsmA homolog was identified and characterized in strain CHA0. Overexpression of rsmE strongly reduced the expression of target genes (hcnA, for a hydrogen cyanide synthase subunit; aprA, for the main exoprotease; and phlA, for a component of 2,4-diacetylphloroglucinol biosynthesis). Single null mutations in either rsmA or rsmE resulted in a slight increase in the expression of hcnA, aprA, and phlA. By contrast, an rsmA rsmE double mutation led to strongly increased and advanced expression of these target genes and completely suppressed a gacS mutation. Both the RsmE and RsmA levels increased with increasing cell population densities in strain CHA0; however, the amount of RsmA showed less variability during growth. Expression of rsmE was controlled positively by GacA and negatively by RsmA and RsmE. Mobility shift assays demonstrated specific binding of RsmE to RsmY and RsmZ RNAs. The transcription and stability of both regulatory RNAs were strongly reduced in the rsmA rsmE double mutant. In conclusion, RsmA and RsmE together account for maximal repression in the GacS/GacA cascade of strain CHA0.

scholarly journals Kaposi's Sarcoma-Associated Herpesvirus K8 Is an RNA Binding Protein That Regulates Viral DNA Replication in Coordination with a Noncoding RNA

2018 ◽  
Vol 92 (7) ◽  
Author(s):  
Dongcheng Liu ◽  
Yan Wang ◽  
Yan Yuan
Keyword(s):  
Dna Replication ◽  
Noncoding Rna ◽  
Rna Binding ◽  
De Novo ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Noncoding Rnas ◽  
Viral Dna ◽  
Viral Dna Replication

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV) lytic replication and constant primary infection of fresh cells are crucial for viral tumorigenicity. The virus-encoded bZIP family protein K8 plays an important role in viral DNA replication in both viral reactivation andde novoinfection. The mechanism underlying the functional role of K8 in the viral life cycle is elusive. Here, we report that K8 is an RNA binding protein that also associates with many other proteins, including other RNA binding proteins. Many protein-protein interactions involving K8 are mediated by RNA. Using a UVcross-linking andimmunoprecipitation (CLIP) procedure combined with high-throughput sequencing, RNAs that are associated with K8 in BCBL-1 cells were identified, including both viral (PAN, T1.4, T0.7, etc.) and cellular (MALAT-1, MRP, 7SK, etc.) RNAs. An RNA binding motif in K8 was defined, and mutation of the motif abolished the ability of K8 to bind to many noncoding RNAs, as well as viral DNA replication duringde novoinfection, suggesting that the K8 functions in viral replication are carried out through RNA association. The functions of K8 and associated T1.4 RNA were investigated in detail, and the results showed that T1.4 mediates the binding of K8 to ori-Lyt DNA. The T1.4-K8 complex physically bound to KSHV ori-Lyt DNA and recruited other proteins and cofactors to assemble a replication complex. Depletion of T1.4 abolished DNA replication in primary infection. These findings provide mechanistic insights into the role of K8 in coordination with T1.4 RNA in regulating KSHV DNA replication duringde novoinfection.IMPORTANCEGenomewide analyses of the mammalian transcriptome revealed that a large proportion of sequence previously annotated as noncoding regions is actually transcribed and gives rise to stable RNAs. The emergence of a large number of noncoding RNAs suggests that functional RNA-protein complexes, e.g., ribosomes or spliceosomes, are not ancient relics of the last ribo-organism but would be well adapted to a regulatory role in biology. K8 has been puzzling because of its unique characteristics, such as multiple regulatory roles in gene expression and DNA replication without DNA binding capability. This study reveals the mechanism underlying its regulatory role by demonstrating that K8 is an RNA binding protein that binds to DNA and initiates DNA replication in coordination with a noncoding RNA. It is suggested that many K8 functions, if not all, are carried out through its associated RNAs.

scholarly journals Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

2017 ◽  
Author(s):  
Jahan-Yar Parsa ◽  
Selim Boudoukha ◽  
Jordan Burke ◽  
Christina Homer ◽  
Hiten D. Madhani
Keyword(s):  
Genome Stability ◽  
Rna Binding ◽  
De Novo ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Heterochromatin Formation ◽  
Repressor Complex ◽  
Polymerase Pausing ◽  
Heterochromatin Assembly ◽  
Dependent Mechanism

Packaging of pericentromeric DNA into heterochromatin is crucial for genome stability, development and health, yet its endogenous triggers remain poorly understood1. A defining feature of pericentromeric heterochromatin is histone H3 lysine 9 methylation (H3K9me)2–4. In S. pombe, transcripts derived from the pericentromeric dg and dh repeat during S phase5–7 promote heterochromatin formation through two pathways: an RNAi-dependent mechanism involving recruitment of the Clr4 H3K9 methyltransferase complex (CLR-C) via the RITS complex8–13, and RNAi-independent mechanism involving an RNAPII-associated RNA-binding protein Seb1, the repressor complex SHREC, and RNA processing activities14–19. We show here that Seb1 promotes long-lived RNAPII pausing. Pause sites associated with sequence-specific Seb1 RNA binding events are significantly enriched in pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Remarkably, globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking functional RITS, demonstrating that RNAPII pausing can be sufficient to trigger de novo heterochromatin independently of RNAi. These results uncover Seb1-mediated polymerase stalling as a new signal for nucleating heterochromatin assembly in repetitive DNA.

scholarly journals YTH-RNA-binding protein prevents deleterious expression of meiotic proteins by tethering their mRNAs to nuclear foci

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Yuichi Shichino ◽  
Yoko Otsubo ◽  
Yoshitaka Kimori ◽  
Masayuki Yamamoto ◽  
Akira Yamashita
Keyword(s):  
Germ Cells ◽  
Target Genes ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Rna Degradation ◽  
Facultative Heterochromatin ◽  
Nuclear Retention ◽  
Nuclear Exosome ◽  
Nuclear Foci

Accurate and extensive regulation of meiotic gene expression is crucial to distinguish germ cells from somatic cells. In the fission yeast Schizosaccharomyces pombe, a YTH family RNA-binding protein, Mmi1, directs the nuclear exosome-mediated elimination of meiotic transcripts during vegetative proliferation. Mmi1 also induces the formation of facultative heterochromatin at a subset of its target genes. Here, we show that Mmi1 prevents the mistimed expression of meiotic proteins by tethering their mRNAs to the nuclear foci. Mmi1 interacts with itself with the assistance of a homolog of Enhancer of Rudimentary, Erh1. Mmi1 self-interaction is required for foci formation, target transcript elimination, their nuclear retention, and protein expression inhibition. We propose that nuclear foci formed by Mmi1 are not only the site of RNA degradation, but also of sequestration of meiotic transcripts from the translation machinery.

scholarly journals Establishment and validation of an RNA binding protein-associated prognostic model for ovarian cancer

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Chaofan He ◽  
Fuxin Huang ◽  
Kejia Zhang ◽  
Jun Wei ◽  
Ke Hu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Target Genes ◽  
Rna Binding ◽  
Cox Regression ◽  
Binding Protein ◽  
Expression Profiles ◽  
Rna Binding Protein ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Cox Regression Analysis

Abstract Background Ovarian cancer (OC) is one of the most common gynecological malignant tumors worldwide, with high mortality and a poor prognosis. As the early symptoms of malignant ovarian tumors are not obvious, the cause of the disease is still unclear, and the patients’ postoperative quality of life of decreases. Therefore, early diagnosis is a problem requiring an urgent solution. Methods We obtained the gene expression profiles of ovarian cancer and normal samples from TCGA and GTEx databases for differential expression analysis. From existing literature reports, we acquired the RNA-binding protein (RBP) list for the human species. Utilizing the online tool Starbase, we analyzed the interaction relationship between RBPs and their target genes and selected the modules of RBP target genes through Cytoscape. Finally, univariate and multivariate Cox regression analyses were used to determine the prognostic RBP signature. Results We obtained 527 differentially expressed RBPs, which were involved in many important cellular events, such as RNA splicing, the cell cycle, and so on. We predicted several target genes of RBPs, constructed the interaction network of RBPs and their target genes, and obtained many modules from the Cytoscape analysis. Functional enrichment of RBP target genes also includes these important biological processes. Through Cox regression analysis, OC prognostic RBPs were identified and a 10-RBP model constructed. Further analysis showed that the model has high accuracy and sensitivity in predicting the 3/5-year survival rate. Conclusions Our study identified differentially expressed RBPs and their target genes in OC, and the results promote our understanding of the molecular mechanism of ovarian cancer. The current study could develop novel biomarkers for the diagnosis, treatment, and prognosis of OC and provide new ideas and prospects for future clinical research.

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