scholarly journals RNA-Binding Protein Khd1 and Ccr4 Deadenylase Play Overlapping Roles in the Cell Wall Integrity Pathway in Saccharomyces cerevisiae

2011 ◽  
Vol 10 (10) ◽  
pp. 1340-1347 ◽  
Author(s):  
Wataru Ito ◽  
Xia Li ◽  
Kaoru Irie ◽  
Tomoaki Mizuno ◽  
Kenji Irie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Rna Binding ◽  
Binding Protein ◽  
Mrna Level ◽  
Rna Binding Protein ◽  
Cell Lysis ◽  
Cell Wall Integrity ◽  
Nucleotide Exchange ◽  
Mrna Targets

ABSTRACT The Saccharomyces cerevisiae RNA-binding protein Khd1/Hek2 associates with hundreds of potential mRNA targets preferentially, including the mRNAs encoding proteins localized to the cell wall and plasma membrane. We have previously revealed that Khd1 positively regulates expression of MTL1 mRNA encoding a membrane sensor in the cell wall integrity (CWI) pathway. However, a khd1 Δ mutation has no detectable phenotype on cell wall synthesis. Here we show that the khd1 Δ mutation causes a severe cell lysis when combined with the deletion of the CCR4 gene encoding a cytoplasmic deadenylase. We identified the ROM2 mRNA, encoding a guanine nucleotide exchange factor (GEF) for Rho1, as a target for Khd1 and Ccr4. The ROM2 mRNA level was decreased in the khd1 Δ ccr4 Δ mutant, and ROM2 overexpression suppressed the cell lysis of the khd1 Δ ccr4 Δ mutant. We also found that Ccr4 negatively regulates expression of the LRG1 mRNA encoding a GTPase-activating protein (GAP) for Rho1. The LRG1 mRNA level was increased in the ccr4 Δ and khd1 Δ ccr4 Δ mutants, and deletion of LRG1 suppressed the cell lysis of the khd1 Δ ccr4 Δ mutant. Our results presented here suggest that Khd1 and Ccr4 modulate a signal from Rho1 in the CWI pathway by regulating the expression of RhoGEF and RhoGAP.

scholarly journals Regulation of LRG1 expression by RNA‐binding protein Puf5 in the budding yeast cell wall integrity pathway

2018 ◽  
Vol 23 (12) ◽  
pp. 988-997 ◽  
Author(s):  
Nguyen Thi Minh Viet ◽  
Duong Long Duy ◽  
Kazuhiro Saito ◽  
Kaoru Irie ◽  
Yasuyuki Suda ◽  
...  
Keyword(s):  
Cell Wall ◽  
Yeast Cell ◽  
Rna Binding ◽  
Budding Yeast ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cell Wall Integrity ◽  
Yeast Cell Wall ◽  
Cell Wall Integrity Pathway

scholarly journals Different Regulations of ROM2 and LRG1 Expression by Ccr4, Pop2, and Dhh1 in the Saccharomyces cerevisiae Cell Wall Integrity Pathway

mSphere ◽  
2016 ◽  
Vol 1 (5) ◽  
Author(s):  
Xia Li ◽  
Tetsuro Ohmori ◽  
Kaoru Irie ◽  
Yuichi Kimura ◽  
Yasuyuki Suda ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Wall ◽  
Rna Binding ◽  
Budding Yeast ◽  
Mrna Level ◽  
Small Gtpase ◽  
Cell Wall Integrity ◽  
Mrna Levels ◽  
Gene Encoding ◽  
Spatiotemporal Control

ABSTRACT We find here that Ccr4, Pop2, and Dhh1 modulate the levels of mRNAs for specific Rho1 regulators, Rom2 and Lrg1. In budding yeast, Rho1 activity is tightly regulated both temporally and spatially. It is anticipated that Ccr4, Pop2, and Dhh1 may contribute to the precise spatiotemporal control of Rho1 activity by regulating expression of its regulators temporally and spatially. Our finding on the roles of the components of the Ccr4-Not complex in yeast would give important information for understanding the roles of the evolutionary conserved Ccr4-Not complex. Ccr4, a component of the Ccr4-Not cytoplasmic deadenylase complex, is known to be required for the cell wall integrity (CWI) pathway in the budding yeast Saccharomyces cerevisiae. However, it is not fully understood how Ccr4 and other components of the Ccr4-Not complex regulate the CWI pathway. Previously, we showed that Ccr4 functions in the CWI pathway together with Khd1 RNA binding protein. Ccr4 and Khd1 modulate a signal from Rho1 small GTPase in the CWI pathway by regulating the expression of ROM2 mRNA and LRG1 mRNA, encoding a guanine nucleotide exchange factor (GEF) and a GTPase-activating protein (GAP) for Rho1, respectively. Here we examined the possible involvement of the POP2 gene encoding a subunit of the Ccr4-Not complex and the DHH1 gene encoding a DEAD box RNA helicase that associates with the Ccr4-Not complex in the regulation of ROM2 and LRG1 expression. Neither ROM2 mRNA level nor Rom2 function was impaired by pop2Δ or dhh1Δ mutation. The LRG1 mRNA level was increased in pop2Δ and dhh1Δ mutants, as well as the ccr4Δ mutant, and the growth defects caused by pop2Δ and dhh1Δ mutations were suppressed by lrg1Δ mutation. Our results suggest that LRG1 expression is regulated by Ccr4 together with Pop2 and Dhh1 and that ROM2 expression is regulated by Khd1 and Ccr4, but not by Pop2 and Dhh1. Thus, Rho1 activity in the CWI pathway is precisely controlled by modulation of the mRNA levels for Rho1-GEF Rom2 and Rho1-GAP Lrg1. IMPORTANCE We find here that Ccr4, Pop2, and Dhh1 modulate the levels of mRNAs for specific Rho1 regulators, Rom2 and Lrg1. In budding yeast, Rho1 activity is tightly regulated both temporally and spatially. It is anticipated that Ccr4, Pop2, and Dhh1 may contribute to the precise spatiotemporal control of Rho1 activity by regulating expression of its regulators temporally and spatially. Our finding on the roles of the components of the Ccr4-Not complex in yeast would give important information for understanding the roles of the evolutionary conserved Ccr4-Not complex.

scholarly journals MAP kinase Slt2p attenuates cell wall mRNA decay by downregulating the RNA-binding protein Rbp1p in response to stress

2020 ◽  
Author(s):  
Lin-Chun Chang ◽  
Yu-Chieh Wu ◽  
Yu-Yun Chang ◽  
Fang-Jen Lee
Keyword(s):  
Cell Wall ◽  
Map Kinase ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Wall Stress ◽  
Cell Wall Integrity ◽  
Signaling Cascade ◽  
Cell Wall Stress ◽  
The Stability

AbstractThe yeast cell wall integrity (CWI) MAPK pathway is a signaling cascade function in maintaining cell wall integrity under stressful environmental conditions. Recently, the activity and signaling of Slt2p (Mpk1p) MAP kinase has been shown to control assembly of the processing body (P-body) upon cell wall stresses, implicating its posttranscriptional role in decay of cell wall mRNAs. However, how Slt2p MAP kinase directly regulates the stability of cell wall transcripts during cell wall stress remains unclear. Here, we reported that the RNA-binding protein Rbp1p (Ngr1p) is a downstream effector and target of Slt2p MAP kinase during activation of the cell wall stress signaling cascade. In addition to the well-defined target mitochondrial porin mRNA, we found that Rbp1p also negatively regulates the stability of a subset of Slt2p-regulated cell wall transcripts. Deletion of RBP1 increases the level of cell wall transcripts and partially suppresses the hypersensitivity of the slt2Δ deletion strain to cell wall damage. Slt2p is necessary for cell wall stress-induced stabilization of cell wall transcripts. Deletion of RBP1 compromises the destabilization of cell wall transcripts in slt2Δ mutants under cell wall stress. Notably, C-terminal deleted Slt2p impairs its function in promoting turnover of the Rbp1p protein and fails to stabilize cell wall transcripts, although it can complement the growth defect of the slt2Δ strain upon cell wall stress. Altogether, our results demonstrate that MAP kinase Slt2p attenuates CWI mRNA decay in response to cell wall damage by downregulating the activity of the RNA-binding protein Rbp1p.

scholarly journals The RNA-binding protein Sam68 modulates the alternative splicing of Bcl-x

2007 ◽  
Vol 176 (7) ◽  
pp. 929-939 ◽  
Author(s):  
Maria Paola Paronetto ◽  
Tilman Achsel ◽  
Autumn Massiello ◽  
Charles E. Chalfant ◽  
Claudio Sette
Keyword(s):  
Alternative Splicing ◽  
Tyrosine Phosphorylation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Live Cells ◽  
Hnrnp A1 ◽  
Splice Site Selection ◽  
Subnuclear Localization ◽  
Mrna Targets

The RNA-binding protein Sam68 is involved in apoptosis, but its cellular mRNA targets and its mechanism of action remain unknown. We demonstrate that Sam68 binds the mRNA for Bcl-x and affects its alternative splicing. Depletion of Sam68 by RNA interference caused accumulation of antiapoptotic Bcl-x(L), whereas its up-regulation increased the levels of proapoptotic Bcl-x(s). Tyrosine phosphorylation of Sam68 by Fyn inverted this effect and favored the Bcl-x(L) splice site selection. A point mutation in the RNA-binding domain of Sam68 influenced its splicing activity and subnuclear localization. Moreover, coexpression of ASF/SF2 with Sam68, or fusion with an RS domain, counteracted Sam68 splicing activity toward Bcl-x. Finally, Sam68 interacted with heterogenous nuclear RNP (hnRNP) A1, and depletion of hnRNP A1 or mutations that impair this interaction attenuated Bcl-x(s) splicing. Our results indicate that Sam68 plays a role in the regulation of Bcl-x alternative splicing and that tyrosine phosphorylation of Sam68 by Src-like kinases can switch its role from proapoptotic to antiapoptotic in live cells.

scholarly journals Specific interaction of an RNA-binding protein with the 3′-UTR of its target mRNA is critical to oomycete sexual reproduction

2021 ◽  
Vol 17 (10) ◽  
pp. e1010001
Author(s):  
Hui Feng ◽  
Chuanxu Wan ◽  
Zhichao Zhang ◽  
Han Chen ◽  
Zhipeng Li ◽  
...  
Keyword(s):  
Sexual Reproduction ◽  
Rna Binding ◽  
Gene Knockout ◽  
Binding Protein ◽  
Mrna Level ◽  
Specific Interaction ◽  
Rna Binding Protein ◽  
Pythium Ultimum ◽  
Knockout Mutants ◽  
Oospore Formation

Sexual reproduction is an essential stage of the oomycete life cycle. However, the functions of critical regulators in this biological process remain unclear due to a lack of genome editing technologies and functional genomic studies in oomycetes. The notorious oomycete pathogen Pythium ultimum is responsible for a variety of diseases in a broad range of plant species. In this study, we revealed the mechanism through which PuM90, a stage-specific Puf family RNA-binding protein, regulates oospore formation in P. ultimum. We developed the first CRISPR/Cas9 system-mediated gene knockout and in situ complementation methods for Pythium. PuM90-knockout mutants were significantly defective in oospore formation, with empty oogonia or oospores larger in size with thinner oospore walls compared with the wild type. A tripartite recognition motif (TRM) in the Puf domain of PuM90 could specifically bind to a UGUACAUA motif in the mRNA 3′ untranslated region (UTR) of PuFLP, which encodes a flavodoxin-like protein, and thereby repress PuFLP mRNA level to facilitate oospore formation. Phenotypes similar to PuM90-knockout mutants were observed with overexpression of PuFLP, mutation of key amino acids in the TRM of PuM90, or mutation of the 3′-UTR binding site in PuFLP. The results demonstrated that a specific interaction of the RNA-binding protein PuM90 with the 3′-UTR of PuFLP mRNA at the post-transcriptional regulation level is critical for the sexual reproduction of P. ultimum.

PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein in Saccharomyces cerevisiae

1993 ◽  
Vol 13 (10) ◽  
pp. 6102-6113
Author(s):  
J T Anderson ◽  
M R Paddy ◽  
M S Swanson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Uv Light ◽  
Binding Protein ◽  
Consensus Sequence ◽  
Rna Binding Protein ◽  
Polyadenylated Rna ◽  
Polyadenylated Rnas

Proteins that directly associate with nuclear polyadenylated RNAs, or heterogeneous nuclear RNA-binding proteins (hnRNPs), and those that associate with cytoplasmic mRNAs, or mRNA-binding proteins (mRNPs), play important roles in regulating gene expression at the posttranscriptional level. Previous work with a variety of eukaryotic cells has demonstrated that hnRNPs are localized predominantly within the nucleus whereas mRNPs are cytoplasmic. While studying proteins associated with polyadenylated RNAs in Saccharomyces cerevisiae, we discovered an abundant polyuridylate-binding protein, PUB1, which appears to be both an hnRNP and an mRNP. PUB1 and PAB1, the polyadenylate tail-binding protein, are the two major proteins cross-linked by UV light to polyadenylated RNAs in vivo. The deduced primary structure of PUB1 indicates that it is a member of the ribonucleoprotein consensus sequence family of RNA-binding proteins and is structurally related to the human hnRNP M proteins. Even though the PUB1 protein is a major cellular polyadenylated RNA-binding protein, it is nonessential for cell growth. Indirect cellular immunofluorescence combined with digital image processing allowed a detailed comparison of the intracellular distributions of PUB1 and PAB1. While PAB1 is predominantly, and relatively uniformly, distributed within the cytoplasm, PUB1 is localized in a nonuniform pattern throughout both the nucleus and the cytoplasm. The cytoplasmic distribution of PUB1 is considerably more discontinuous than that of PAB1. Furthermore, sucrose gradient sedimentation analysis demonstrates that PAB1 cofractionates with polyribosomes whereas PUB1 does not. These results suggest that PUB1 is both an hnRNP and an mRNP and that it may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm.

scholarly journals RNA-Binding Protein HuR Is Required for Stabilization of SLC11A1 mRNA and SLC11A1 Protein Expression

2005 ◽  
Vol 25 (18) ◽  
pp. 8139-8149 ◽  
Author(s):  
Yong Zhong Xu ◽  
Sergio Di Marco ◽  
Imed Gallouzi ◽  
Marek Rola-Pleszczynski ◽  
Danuta Radzioch
Keyword(s):  
Posttranscriptional Regulation ◽  
Macrophage Activation ◽  
Rna Binding ◽  
Binding Protein ◽  
Mrna Level ◽  
Rna Binding Protein ◽  
Cytoplasmic Localization ◽  
Differentiated Cells ◽  
Undifferentiated Cells ◽  
Solute Carrier

ABSTRACT The solute carrier family 11 member 1 (SLC11A1, formerly NRAMP1) gene is associated with infectious and autoimmune diseases and plays an important role in macrophage activation. Human SLC11A1 mRNA contains an AU-rich element (ARE) within the 3′ untranslated region; however, its role in the regulation of SLC11A1 gene expression has not been elucidated. Here we analyze the expression of SLC11A1 in human monocytes and HL-60 cells and then use HL-60 cells as a model to determine whether RNA-binding protein HuR is associated with the ARE and involved in SLC11A1 mRNA turnover. Our results demonstrate a binding of HuR to the SLC11A1 ARE in phorbol myristate acetate (PMA)-differentiated cells dramatically increased compared to that in undifferentiated cells. Interestingly, PMA-induced accumulation of cytoplasmic HuR occurs in parallel with an increase in the binding of HuR to SLC11A1 ARE and with an increase in the SLC11A1 mRNA level. This suggests that HuR's cytoplasmic localization plays an important role in the regulation of SLC11A1 expression. We also observe that down-regulation of HuR expression by RNA interference (RNAi) results in a decrease in SLC11A1 expression which can be restored by the addition of recombinant HuR protein to the RNAi-treated cells. Finally, we show that HuR overexpression in HL-60 cells significantly increases the SLC11A1 mRNA stability. Taken together, our data demonstrate that HuR is a key mediator of posttranscriptional regulation and expression of the SLC11A1 gene.

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