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Fujii S, Duy DL, Valderrama AL, Takeuchi R, Matsuura E, Ito A, Irie K, Suda Y, Mizuno T, Irie K. Pan2-Pan3 complex, together with Ccr4-Not complex, has a role in the cell growth on non-fermentable carbon sources. Biochem Biophys Res Commun 2021; 570:125-130. [PMID: 34280615 DOI: 10.1016/j.bbrc.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
There are two major deadenylase complexes, Ccr4-Not and Pan2-Pan3, which shorten the 3' poly(A) tail of mRNA and are conserved from yeast to human. We have previously shown that the Ccr4-mediated deadenylation plays the important role in gene expression regulation in the yeast stationary phase cell. In order to further understand the role of deadenylases in different growth condition, in this study we investigated the effect of deletion of both deadenylases on the cell in non-fermentable carbon containing media. We found that both ccr4Δ and ccr4Δ pan2Δ mutants showed similar growth defect in YPD media: when switched to media containing non-fermentable source (Glycerol-Lactate) only the ccr4Δ grew while the ccr4Δ pan2Δ did not. Ccr4, Pan2, and Pan3 were phosphorylated in GlyLac medium, suggesting that the activities of Ccr4, Pan2, and Pan3 may be regulated by phosphorylation in response to change of carbon sources. To get insights how Ccr4 and Pan2 function in the cell growth in media containing non-fermentable source only, we isolated multicopy suppressors for the growth defect on YPGlyLac media of the ccr4Δ pan2Δ mutant and identified two genes, STM1 and REX2, which encode a ribosome-associated protein and a 3'-5' RNA exonuclease, respectively. Our results suggest that the Pan2-Pan3 complex, together with the Ccr4-Not complex, has important roles in the growth on non-fermentable carbon sources.
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Affiliation(s)
- Shiori Fujii
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Duong Long Duy
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Arvin Lapiz Valderrama
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Risa Takeuchi
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eri Matsuura
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ayaka Ito
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan.
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Higuchi Y, Fujii S, Valderrama AL, Irie K, Suda Y, Mizuno T, Irie K. The eIF4E-binding protein Eap1 has similar but independent roles in cell growth and gene expression with the cytoplasmic deadenylase Ccr4. Biosci Biotechnol Biochem 2021; 85:1452-1459. [PMID: 33784392 DOI: 10.1093/bbb/zbab056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 11/12/2022]
Abstract
eIF4E-binding proteins (4E-BPs) are translational repressors that compete with eIF4G for binding to eIF4E. Here we investigated the roles of yeast 4E-BPs, Eap1, and Caf20 in cell wall integrity pathway and gene expression. We found that eap1∆ mutation, but not caf20∆ mutation, showed synthetic growth defect with mutation in ROM2 gene encoding Rho1 GEF. The eap1∆ mutation also showed synthetic lethality with mutation in CCR4 gene encoding cytoplasmic deadenylase. Ccr4 functions in the degradation of LRG1 mRNA encoding Rho1 GAP. Eap1-Y109A L114A, which could not bind to eIF4E, did not suppress the synthetic lethality of eap1∆ ccr4∆ mutant, suggesting that 4E-binding of Eap1 is important for its function. We also found that eap1∆ mutant showed the derepression of stress response gene HSP12. 4E-binding of Eap1 was also required for the repression of HSP12 expression. Our results indicate that Eap1 has similar but independent roles in cell growth and gene expression with Ccr4.
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Affiliation(s)
- Yudai Higuchi
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shiori Fujii
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Arvin Lapiz Valderrama
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
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Tuong Vi DT, Fujii S, Valderrama AL, Ito A, Matsuura E, Nishihata A, Irie K, Suda Y, Mizuno T, Irie K. Pbp1, the yeast ortholog of human Ataxin-2, functions in the cell growth on non-fermentable carbon sources. PLoS One 2021; 16:e0251456. [PMID: 33984024 PMCID: PMC8118320 DOI: 10.1371/journal.pone.0251456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/26/2021] [Indexed: 12/05/2022] Open
Abstract
Pbp1, the yeast ortholog of human Ataxin-2, was originally isolated as a poly(A) binding protein (Pab1)-binding protein. Pbp1 regulates the Pan2-Pan3 deadenylase complex, thereby modulating the mRNA stability and translation efficiency. However, the physiological significance of Pbp1 remains unclear since a yeast strain harboring PBP1 deletion grows similarly to wild-type strain on normal glucose-containing medium. In this study, we found that Pbp1 has a role in cell growth on the medium containing non-fermentable carbon sources. While the pbp1Δ mutant showed a similar growth compared to the wild-type cell on a normal glucose-containing medium, the pbp1Δ mutant showed a slower growth on the medium containing glycerol and lactate. Microarray analyses revealed that expressions of the genes involved in gluconeogenesis, such as PCK1 and FBP1, and of the genes involved in mitochondrial function, such as COX10 and COX11, were decreased in the pbp1Δ mutant. Pbp1 regulated the expressions of PCK1 and FBP1 via their promoters, while the expressions of COX10 and COX11 were regulated by Pbp1, not through their promoters. The decreased expressions of COX10 and COX11 in the pbp1Δ mutant were recovered by the loss of Dcp1 decapping enzyme or Xrn1 5’-3’exonuclease. Our results suggest that Pbp1 regulates the expressions of the genes involved in gluconeogenesis and mitochondrial function through multiple mechanisms.
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Affiliation(s)
- Dang Thi Tuong Vi
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shiori Fujii
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Arvin Lapiz Valderrama
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Ayaka Ito
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eri Matsuura
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ayaka Nishihata
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
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Valderrama AL, Fujii S, Duy DL, Irie K, Mizuno T, Suda Y, Irie K. Pbp1 mediates the aberrant expression of genes involved in growth defect of
ccr4
∆ and
pop2
∆ mutants in yeast
Saccharomyces cerevisiae. Genes Cells 2021; 26:381-398. [DOI: 10.1111/gtc.12846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/11/2021] [Accepted: 03/21/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Arvin Lapiz Valderrama
- Ph.D. Program in Human Biology School of Integrative and Global Majors University of Tsukuba Tsukuba Japan
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
| | - Shiori Fujii
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
| | - Duong Long Duy
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
- Live Cell Super‐resolution Imaging Research Team RIKEN Center for Advanced Photonics Wako Japan
| | - Kenji Irie
- Ph.D. Program in Human Biology School of Integrative and Global Majors University of Tsukuba Tsukuba Japan
- Department of Molecular Cell Biology Graduate School of Comprehensive Human Sciences Faculty of Medicine University of Tsukuba Tsukuba Japan
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Will JC, Valderrama AL, Yoon PW. Preventable Hospitalizations for Congestive Heart Failure: Establishing a Baseline to Monitor Trends and Disparities. Prev Chronic Dis 2012. [DOI: 10.5888/pcd9.110260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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