1
|
Hatakawa Y, Nakamura R, Akizawa T, Konishi M, Matsuda A, Oe T, Saito M, Ito F. SKGQA, a Peptide Derived from the ANA/BTG3 Protein, Cleaves Amyloid-β with Proteolytic Activity. Biomolecules 2024; 14:586. [PMID: 38785993 PMCID: PMC11118129 DOI: 10.3390/biom14050586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Despite the extensive research conducted on Alzheimer's disease (AD) over the years, no effective drug for AD treatment has been found. Therefore, the development of new drugs for the treatment of AD is of the utmost importance. We recently reported the proteolytic activities of JAL-TA9 (YKGSGFRMI) and ANA-TA9 (SKGQAYRMA), synthetic peptides of nine amino acids each, derived from the Box A region of Tob1 and ANA/BTG3 proteins, respectively. Furthermore, two components of ANA-TA9, ANA-YA4 (YRMI) at the C-terminus end and ANA-SA5 (SKGQA) at the N-terminus end of ANA-TA9, exhibited proteolytic activity against amyloid-β (Aβ) fragment peptides. In this study, we identified the active center of ANA-SA5 using AEBSF, a serine protease inhibitor, and a peptide in which the Ser residue of ANA-SA5 was replaced with Leu. In addition, we demonstrate the proteolytic activity of ANA-SA5 against the soluble form Aβ42 (a-Aβ42) and solid insoluble form s-Aβ42. Furthermore, ANA-SA5 was not cytotoxic to A549 cells. These results indicate that ANA-SA5 is a promising Catalytide and a potential candidate for the development of new peptide drugs targeting Aβ42 for AD treatment.
Collapse
Affiliation(s)
- Yusuke Hatakawa
- Department of Bio-Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan; (Y.H.); (T.O.)
| | - Rina Nakamura
- O-Force Co., Ltd., 3454 Irino Kuroshio-cho, Hata-gun 789-1931, Kochi, Japan or (R.N.); or (T.A.)
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-cho, Nankoku 783-8505, Kochi, Japan;
| | - Toshifumi Akizawa
- O-Force Co., Ltd., 3454 Irino Kuroshio-cho, Hata-gun 789-1931, Kochi, Japan or (R.N.); or (T.A.)
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-cho, Nankoku 783-8505, Kochi, Japan;
| | - Motomi Konishi
- Department of Integrative Pharmacy, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata 573-0101, Osaka, Japan;
| | - Akira Matsuda
- Laboratory of Medicinal and Biochemical Analysis, Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshinkai, Kure 737-0112, Hiroshima, Japan;
| | - Tomoyuki Oe
- Department of Bio-Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan; (Y.H.); (T.O.)
| | - Motoaki Saito
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-cho, Nankoku 783-8505, Kochi, Japan;
| | - Fumiaki Ito
- O-Force Co., Ltd., 3454 Irino Kuroshio-cho, Hata-gun 789-1931, Kochi, Japan or (R.N.); or (T.A.)
- The Institute of Prophylactic Pharmacology, 1-58, Rinku-oraikita, Izumisano 598-8531, Osaka, Japan
| |
Collapse
|
2
|
Peng G, Liu T, Qi X, Wang Y, Ren J, Peng J, Du X, Hu S, Wu S, Zhao Y, Li D, Zheng H. A genome-wide CRISPR screening uncovers that TOB1 acts as a key host factor for FMDV infection via both IFN and EGFR mediated pathways. PLoS Pathog 2024; 20:e1012104. [PMID: 38512977 PMCID: PMC10986976 DOI: 10.1371/journal.ppat.1012104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 04/02/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
The interaction between foot-and-mouth disease virus (FMDV) and the host is extremely important for virus infection, but there are few researches on it, which is not conducive to vaccine development and FMD control. In this study, we designed a porcine genome-scale CRISPR/Cas9 knockout library containing 93,859 single guide RNAs targeting 16,886 protein-coding genes, 25 long ncRNAs, and 463 microRNAs. Using this library, several previously unreported genes required for FMDV infection are highly enriched post-FMDV selection in IBRS-2 cells. Follow-up studies confirmed the dependency of FMDV on these genes, and we identified a functional role for one of the FMDV-related host genes: TOB1 (Transducer of ERBB2.1). TOB1-knockout significantly inhibits FMDV infection by positively regulating the expression of RIG-I and MDA5. We further found that TOB1-knockout led to more accumulation of mRNA transcripts of transcription factor CEBPA, and thus its protein, which further enhanced transcription of RIG-I and MDA5 genes. In addition, TOB1-knockout was shown to inhibit FMDV adsorption and internalization mediated by EGFR/ERBB2 pathway. Finally, the FMDV lethal challenge on TOB1-knockout mice confirmed that the deletion of TOB1 inhibited FMDV infection in vivo. These results identify TOB1 as a key host factor involved in FMDV infection in pigs.
Collapse
Affiliation(s)
- Gaochuang Peng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tianran Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaolan Qi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuzhe Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Jingjing Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jiangling Peng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Siyu Hu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Sen Wu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Yaofeng Zhao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Dan Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|
3
|
Nakashima M, Suga N, Ikeda Y, Yoshikawa S, Matsuda S. Circular RNAs, Noncoding RNAs, and N6-methyladenosine Involved in the Development of MAFLD. Noncoding RNA 2024; 10:11. [PMID: 38392966 PMCID: PMC10893449 DOI: 10.3390/ncrna10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) and N6-methyladenosine (m6A), have been shown to play a critical role in the development of various diseases including obesity and metabolic disorder-associated fatty liver disease (MAFLD). Obesity is a chronic disease caused by excessive fat accumulation in the body, which has recently become more prevalent and is the foremost risk factor for MAFLD. Causes of obesity may involve the interaction of genetic, behavioral, and social factors. m6A RNA methylation might add a novel inspiration for understanding the development of obesity and MAFLD with post-transcriptional regulation of gene expression. In particular, circRNAs, microRNAs (miRNAs), and m6A might be implicated in the progression of MAFLD. Interestingly, m6A modification can modulate the translation, degradation, and other functions of ncRNAs. miRNAs/circRNAs can also modulate m6A modifications by affecting writers, erasers, and readers. In turn, ncRNAs could modulate the expression of m6A regulators in different ways. However, there is limited evidence on how these ncRNAs and m6A interact to affect the promotion of liver diseases. It seems that m6A can occur in DNA, RNA, and proteins that may be associated with several biological properties. This study provides a mechanistic understanding of the association of m6A modification and ncRNAs with liver diseases, especially for MAFLD. Comprehension of the association between m6A modification and ncRNAs may contribute to the development of treatment tactics for MAFLD.
Collapse
Affiliation(s)
| | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| |
Collapse
|
4
|
Krempl C, Lazzaretti D, Sprangers R. A structural biology view on the enzymes involved in eukaryotic mRNA turnover. Biol Chem 2023; 404:1101-1121. [PMID: 37709756 DOI: 10.1515/hsz-2023-0182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
The cellular environment contains numerous ribonucleases that are dedicated to process mRNA transcripts that have been targeted for degradation. Here, we review the three dimensional structures of the ribonuclease complexes (Pan2-Pan3, Ccr4-Not, Xrn1, exosome) and the mRNA decapping enzymes (Dcp2, DcpS) that are involved in mRNA turnover. Structures of major parts of these proteins have been experimentally determined. These enzymes and factors do not act in isolation, but are embedded in interaction networks which regulate enzyme activity and ensure that the appropriate substrates are recruited. The structural details of the higher order complexes that form can, in part, be accurately deduced from known structural data of sub-complexes. Interestingly, many of the ribonuclease and decapping enzymes have been observed in structurally different conformations. Together with experimental data, this highlights that structural changes are often important for enzyme function. We conclude that the known structural data of mRNA decay factors provide important functional insights, but that static structural data needs to be complemented with information regarding protein motions to complete the picture of how transcripts are turned over. In addition, we highlight multiple aspects that influence mRNA turnover rates, but that have not been structurally characterized so far.
Collapse
Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Lazzaretti
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| |
Collapse
|
5
|
Zhao Q, Pavanello L, Bartlam M, Winkler GS. Structure and function of molecular machines involved in deadenylation-dependent 5'-3' mRNA degradation. Front Genet 2023; 14:1233842. [PMID: 37876592 PMCID: PMC10590902 DOI: 10.3389/fgene.2023.1233842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
In eukaryotic cells, the synthesis, processing, and degradation of mRNA are important processes required for the accurate execution of gene expression programmes. Fully processed cytoplasmic mRNA is characterised by the presence of a 5'cap structure and 3'poly(A) tail. These elements promote translation and prevent non-specific degradation. Degradation via the deadenylation-dependent 5'-3' degradation pathway can be induced by trans-acting factors binding the mRNA, such as RNA-binding proteins recognising sequence elements and the miRNA-induced repression complex. These factors recruit the core mRNA degradation machinery that carries out the following steps: i) shortening of the poly(A) tail by the Ccr4-Not and Pan2-Pan3 poly (A)-specific nucleases (deadenylases); ii) removal of the 5'cap structure by the Dcp1-Dcp2 decapping complex that is recruited by the Lsm1-7-Pat1 complex; and iii) degradation of the mRNA body by the 5'-3' exoribonuclease Xrn1. In this review, the biochemical function of the nucleases and accessory proteins involved in deadenylation-dependent mRNA degradation will be reviewed with a particular focus on structural aspects of the proteins and enzymes involved.
Collapse
Affiliation(s)
- Qi Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Lorenzo Pavanello
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | | |
Collapse
|
6
|
Pavanello L, Hall M, Winkler GS. Regulation of eukaryotic mRNA deadenylation and degradation by the Ccr4-Not complex. Front Cell Dev Biol 2023; 11:1153624. [PMID: 37152278 PMCID: PMC10157403 DOI: 10.3389/fcell.2023.1153624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Accurate and precise regulation of gene expression programmes in eukaryotes involves the coordinated control of transcription, mRNA stability and translation. In recent years, significant progress has been made about the role of sequence elements in the 3' untranslated region for the regulation of mRNA degradation, and a model has emerged in which recruitment of the Ccr4-Not complex is the critical step in the regulation of mRNA decay. Recruitment of the Ccr4-Not complex to a target mRNA results in deadenylation mediated by the Caf1 and Ccr4 catalytic subunits of the complex. Following deadenylation, the 5' cap structure is removed, and the mRNA subjected to 5'-3' degradation. Here, the role of the human Ccr4-Not complex in cytoplasmic deadenylation of mRNA is reviewed, with a particular focus on mechanisms of its recruitment to mRNA by sequence motifs in the 3' untranslated region, codon usage, as well as general mechanisms involving the poly(A) tail.
Collapse
Affiliation(s)
- Lorenzo Pavanello
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Michael Hall
- School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | | |
Collapse
|
7
|
Nakamura R, Konishi M, Higashi Y, Saito M, Akizawa T. Five-mer peptides prevent short-term spatial memory deficits in Aβ25-35-induced Alzheimer's model mouse by suppressing Aβ25-35 aggregation and resolving its aggregate form. Alzheimers Res Ther 2023; 15:83. [PMID: 37076912 PMCID: PMC10114458 DOI: 10.1186/s13195-023-01229-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/10/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND The development of drugs for Alzheimer's disease (AD), which is related to the misfolding and aggregation of amyloid-β (Aβ), is high in demand due to the growing number of AD patients. In this study, we screened 22 kinds of 5-mer synthetic peptides derived from the Box A region of Tob1 protein to find a peptide effective against Aβ aggregation. METHODS A Thioflavin T (ThT) assay was performed to evaluate aggregation and screen aggregation inhibitors. Male ICR mice (6 weeks old) were administered saline, 9 nmol Aβ25-35, or a mixture of 9 nmol Aβ25-35 and 9 nmol GSGFK in the right lateral ventricle. Short-term spatial memory was assessed through Y-maze. Microglia cells (BV-)2 cells were plated on 24-well plates (4 × 104 cells/well) and incubated for 48 h, and then, the cells were treated with 0.01, 0.05, 0.1, 0.2, or 0.5 mM GSGFK. After incubation for 24 h, bead uptake was evaluated using a laser confocal microscope and Cytation 5. RESULTS We found two kinds of peptides, GSGNR and GSGFK, that were not only suppressed by aggregation of Aβ25-35 but also resolved the aggregated Aβ25-35. Results obtained from the Y-maze test on an Aβ25-35-induced AD model mouse indicated that GSGFK prevents the deficits in short-term memory induced by Aβ25-35. The effect of GSGFK on phagocytosis in BV-2 cells proved that GSGFK activates the phagocytic ability of microglia. CONCLUSIONS In conclusion, 5-mer peptides prevent short-term memory deficit in Aβ25-35 induced AD model mouse by reducing the aggregated Aβ25-35. They may also upregulate the phagocytic ability of microglia, which makes 5-mer peptides suitable candidates as therapeutic drugs against AD.
Collapse
Affiliation(s)
- Rina Nakamura
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-Cho, Nankoku, Kochi, 783-8505, Japan
- O-Force Co., Ltd, 3454 Irino Kuroshio-Cho, Hata-Gun, Kochi, 789-1931, Japan
| | - Motomi Konishi
- Department of Integrative Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-Cho, Hirakata, Osaka, 573-0101, Japan
| | - Youichirou Higashi
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-Cho, Nankoku, Kochi, 783-8505, Japan
| | - Motoaki Saito
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-Cho, Nankoku, Kochi, 783-8505, Japan
| | - Toshifumi Akizawa
- Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu, Oko-Cho, Nankoku, Kochi, 783-8505, Japan.
- O-Force Co., Ltd, 3454 Irino Kuroshio-Cho, Hata-Gun, Kochi, 789-1931, Japan.
| |
Collapse
|
8
|
Ikeda Y, Morikawa S, Nakashima M, Yoshikawa S, Taniguchi K, Sawamura H, Suga N, Tsuji A, Matsuda S. CircRNAs and RNA-Binding Proteins Involved in the Pathogenesis of Cancers or Central Nervous System Disorders. Noncoding RNA 2023; 9:ncrna9020023. [PMID: 37104005 PMCID: PMC10142617 DOI: 10.3390/ncrna9020023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Circular RNAs (circRNAs), a newly recognized group of noncoding RNA transcripts, have established widespread attention due to their regulatory role in cell signaling. They are covalently closed noncoding RNAs that form a loop, and are typically generated during the splicing of precursor RNAs. CircRNAs are key post-transcriptional and post-translational regulators of gene expression programs that might influence cellular response and/or function. In particular, circRNAs have been considered to function as sponges of specific miRNA, regulating cellular processes at the post-transcription stage. Accumulating evidence has shown that the aberrant expression of circRNAs could play a key role in the pathogenesis of several diseases. Notably, circRNAs, microRNAs, and several RNA-binding proteins, including the antiproliferative (APRO) family proteins, could be indispensable gene modulators, which might be strongly linked to the occurrence of diseases. In addition, circRNAs have attracted general interest for their stability, abundance in the brain, and their capability to cross the blood–brain barrier. Here, we present the current findings and theragnostic potentials of circRNAs in several diseases. With this, we aim to provide new insights to support the development of novel diagnostic and/or therapeutic strategies for these diseases.
Collapse
|
9
|
Raisch T, Valkov E. Regulation of the multisubunit CCR4-NOT deadenylase in the initiation of mRNA degradation. Curr Opin Struct Biol 2022; 77:102460. [PMID: 36116370 PMCID: PMC9771892 DOI: 10.1016/j.sbi.2022.102460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/19/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]
Abstract
The conserved CCR4-NOT complex initiates the decay of mRNAs by catalyzing the shortening of their poly(A) tails in a process known as deadenylation. Recent studies have provided mechanistic insights into the action and regulation of this molecular machine. The two catalytic enzymatic subunits of the complex hydrolyze polyadenosine RNA. Notably, the non-catalytic subunits substantially enhance the complex's affinity and sequence selectivity for polyadenosine by directly contacting the RNA. An additional regulatory mechanism is the active recruitment of the CCR4-NOT to transcripts targeted for decay by RNA-binding proteins that recognize motifs or sequences residing predominantly in untranslated regions. This targeting and strict control of the mRNA deadenylation process emerges as a crucial nexus during post-transcriptional regulation of gene expression.
Collapse
Affiliation(s)
- Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
| |
Collapse
|
10
|
Nakamura R, Akizawa T, Konishi M. Structure-Activity Relationship of 5-mer Catalytides, GSGYR and RYGSG. Biomolecules 2022; 12:biom12121766. [PMID: 36551193 PMCID: PMC9775622 DOI: 10.3390/biom12121766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
We recently discovered JAL-TA9 (YKGSGFRMI), a short hydrolytic peptide that we termed a Catalytide. The catalytic center of JAL-TA9 was modeled using MM2 and MMFF94 parameters and identified as GSGFR. Additionally, a structure-activity relationship study showed that GSGYR cleaved Aβ11-29. Here, we developed a novel Catalytide in silico. Molecular dynamics simulations of GSGYR and RYGSG using MM2 and MMFF94 parameters suggested that both peptides may form catalytic triads and oxyanion holes. The hydrolytic potency of RYGSG was five times higher than that of GSGYR. Moreover, both peptides showed three common cleavage positions for Aβ11-29; namely, L17-V18, V18-F19, and E22-D23. The aggregation ratio analyzed by the thioflavin-T assay correlated well with proteolytic activity, suggesting that the aggregation of Aβ11-29 was suppressed by the cleavage reaction. Docking simulations with the carbonyl carbon of L17 or the carbonyl carbon of E22 in Aβ11-29 were conducted using the secondary structures of GSGYR and RYGSG. The distance between the hydroxyl group of serine and the carbonyl carbon of the two cleavage sites proved that RYGSG was closer to Aβ11-29 than to GSGYR. This study demonstrated that Catalytides are useful for understanding structure-activity relationships.
Collapse
Affiliation(s)
- Rina Nakamura
- Laboratory of Pharmacology, School of Medicine, Koch University, Nankoku 783-0047, Japan
- O-Force Co., Ltd., 3454 Irino Kuroshio-cho, Hata-gun, Kochi 789-1931, Japan
| | - Toshifumi Akizawa
- Laboratory of Pharmacology, School of Medicine, Koch University, Nankoku 783-0047, Japan
- O-Force Co., Ltd., 3454 Irino Kuroshio-cho, Hata-gun, Kochi 789-1931, Japan
| | - Motomi Konishi
- Department of Integrative Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata 573-0101, Japan
- Correspondence: ; Tel.: +81-72-866-3128
| |
Collapse
|
11
|
Kots E, Mlynarczyk C, Melnick A, Khelashvili G. Conformational transitions in BTG1 antiproliferative protein and their modulation by disease mutants. Biophys J 2022; 121:3753-3764. [PMID: 35459639 PMCID: PMC9617077 DOI: 10.1016/j.bpj.2022.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/15/2022] [Indexed: 12/01/2022] Open
Abstract
B cell translocation gene 1 (BTG1) protein belongs to the BTG/transducer of ERBB2 (TOB) family of antiproliferative proteins whose members regulate various key cellular processes such as cell cycle progression, apoptosis, and differentiation. Somatic missense mutations in BTG1 are found in ∼70% of a particularly malignant and disseminated subtype of diffuse large B cell lymphoma (DLBCL). Antiproliferative activity of BTG1 has been linked to its ability to associate with transcriptional cofactors and various enzymes. However, molecular mechanisms underlying these functional interactions and how the disease-linked mutations in BTG1 affect these mechanisms are currently unknown. To start filling these knowledge gaps, here, using atomistic molecular dynamics (MD) simulations, we explored structural, dynamic, and kinetic characteristics of BTG1 protein, and studied how various DLBCL mutations affect these characteristics. We focused on the protein region formed by α2 and α4 helices, as this interface has been reported not only to serve as a binding hotspot for several cellular partners but also to harbor sites for the majority of known DLBCL mutations. Markov state modeling analysis of extensive MD simulations revealed that the α2-α4 interface in the wild-type (WT) BTG1 undergoes conformational transitions between closed and open metastable states. Importantly, we show that some of the mutations in this region that are observed in DLBCL, such as Q36H, F40C, Q45P, E50K (in α2), and A83T and A84E (in α4), either overstabilize one of these two metastable states or give rise to new conformations in which these helices are distorted (i.e., kinked or unfolded). Based on these results, we conclude that the rapid interconversion between the closed and open conformations of the α2-α4 interface is an essential component of the BTG1 functional dynamics that can prime the protein for functional associations with its binding partners. Disruption of the native dynamic equilibrium by DLBCL mutants leads to the ensemble of conformations in BTG1 that are unlikely structurally and/or kinetically to enable productive functional interactions with the binding proteins.
Collapse
Affiliation(s)
- Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Coraline Mlynarczyk
- Division of Hematology/Oncology, Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York.
| |
Collapse
|
12
|
Poetz F, Lebedeva S, Schott J, Lindner D, Ohler U, Stoecklin G. Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation. Genome Biol 2022; 23:193. [PMID: 36096941 PMCID: PMC9465963 DOI: 10.1186/s13059-022-02760-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/23/2022] [Indexed: 01/14/2023] Open
Abstract
Background Cytoplasmic polyadenylation element-binding protein 4 (CPEB4) is known to associate with cytoplasmic polyadenylation elements (CPEs) located in the 3′ untranslated region (UTR) of specific mRNAs and assemble an activator complex promoting the translation of target mRNAs through cytoplasmic polyadenylation. Results Here, we find that CPEB4 is part of an alternative repressor complex that mediates mRNA degradation by associating with the evolutionarily conserved CCR4-NOT deadenylase complex. We identify human CPEB4 as an RNA-binding protein (RBP) with enhanced association to poly(A) RNA upon inhibition of class I histone deacetylases (HDACs), a condition known to cause widespread degradation of poly(A)-containing mRNA. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis using endogenously tagged CPEB4 in HeLa cells reveals that CPEB4 preferentially binds to the 3′UTR of immediate early gene mRNAs, at G-containing variants of the canonical U- and A-rich CPE located in close proximity to poly(A) sites. By transcriptome-wide mRNA decay measurements, we find that the strength of CPEB4 binding correlates with short mRNA half-lives and that loss of CPEB4 expression leads to the stabilization of immediate early gene mRNAs. Akin to CPEB4, we demonstrate that CPEB1 and CPEB2 also confer mRNA instability by recruitment of the CCR4-NOT complex. Conclusions While CPEB4 was previously known for its ability to stimulate cytoplasmic polyadenylation, our findings establish an additional function for CPEB4 as the RNA adaptor of a repressor complex that enhances the degradation of short-lived immediate early gene mRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02760-5.
Collapse
Affiliation(s)
- Fabian Poetz
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Svetlana Lebedeva
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
| | - Johanna Schott
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Doris Lindner
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Uwe Ohler
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany.,Department of Biology, Humboldt Universität Berlin, 10099, Berlin, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany. .,Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany.
| |
Collapse
|
13
|
Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
Collapse
Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
14
|
Ameerul A, Almasmoum H, Pavanello L, Dominguez C, Sebastiaan Winkler G. Structural model of the human BTG2–PABPC1 complex by combining mutagenesis, NMR chemical shift perturbation data and molecular docking. J Mol Biol 2022; 434:167662. [DOI: 10.1016/j.jmb.2022.167662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
|
15
|
Zhang Q, Pavanello L, Potapov A, Bartlam M, Winkler GS. Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements. Protein Sci 2022; 31:758-764. [PMID: 34923703 PMCID: PMC8862426 DOI: 10.1002/pro.4262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 11/11/2022]
Abstract
Regulated degradation of mature, cytoplasmic mRNA is a key step in eukaryotic gene regulation. This process is typically initiated by the recruitment of deadenylase enzymes by cis-acting elements in the 3' untranslated region resulting in the shortening and removal of the 3' poly(A) tail of the target mRNA. The Ccr4-Not complex, a major eukaryotic deadenylase, contains two exoribonuclease subunits with selectivity toward poly(A): Caf1 and Ccr4. The Caf1 deadenylase subunit binds the MIF4G domain of the large subunit CNOT1 (Not1) that is the scaffold of the complex. The Ccr4 nuclease is connected to the complex via its leucine-rich repeat (LRR) domain, which binds Caf1, whereas the catalytic activity of Ccr4 is provided by its EEP domain. While the relative positions of the MIF4G domain of CNOT1, the Caf1 subunit, and the LRR domain of Ccr4 are clearly defined in current models, the position of the EEP nuclease domain of Ccr4 is ambiguous. Here, we use X-ray crystallography, the AlphaFold resource of predicted protein structures, and pulse electron paramagnetic resonance spectroscopy to determine and validate the position of the EEP nuclease domain of Ccr4 resulting in an improved model of the human Ccr4-Not nuclease module.
Collapse
Affiliation(s)
- Qionglin Zhang
- Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Lorenzo Pavanello
- School of PharmacyUniversity of NottinghamNottinghamUK,Present address:
LifeArcStevenage Bioscience Catalyst Open Innovation CampusStevenageUK
| | - Alexey Potapov
- School of Physics and Astronomy, Sir Peter Mansfield Imaging CentreUniversity of NottinghamNottinghamUK
| | - Mark Bartlam
- Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | | |
Collapse
|
16
|
Stoney PN, Yanagiya A, Nishijima S, Yamamoto T. CNOT7 outcompetes its paralog CNOT8 for integration into the CCR4-NOT complex. J Mol Biol 2022; 434:167523. [DOI: 10.1016/j.jmb.2022.167523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
|
17
|
Ikeda Y, Taniguchi K, Nagase N, Tsuji A, Kitagishi Y, Matsuda S. Reactive oxygen species may influence on the crossroads of stemness, senescence, and carcinogenesis in a cell via the roles of APRO family proteins. EXPLORATION OF MEDICINE 2021. [DOI: 10.37349/emed.2021.00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Excessive reactive oxygen species (ROS) may cause oxidative stress which is involved in aging and in the pathogenesis of various human diseases. Whereas unregulated levels of the ROS may be harmful, regulated basal level of ROS are even necessary to support cellular functions as a second messenger for homeostasis under physiological conditions. Therefore, redox medicine could develop as a new therapeutic concept for human health-benefits. Here, we introduce the involvement of ROS on the crossroads of stemness, senescence, and carcinogenesis in a stem cell and cancer cell biology. Amazingly, the anti-proliferative (APRO) family anti-proliferative proteins characterized by immediate early growth responsive genes may also be involved in the crossroads machinery. The biological functions of APRO proteins (APROs) seem to be quite intricate, however, which might be a key modulator of microRNAs (miRNAs). Given the crucial roles of ROS and APROs for pathophysiological functions, upcoming novel therapeutics should include vigilant modulation of the redox state. Next generation of medicine including regenerative medicine and/or cancer therapy will likely comprise strategies for altering the redox environment with the APROs via the modulation of miRNAs as well as with the regulation of ROS of cells in a sustainable manner.
Collapse
Affiliation(s)
- Yuka Ikeda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Kurumi Taniguchi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Nozomi Nagase
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Ai Tsuji
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| |
Collapse
|
18
|
Liu R, Zhou Y, Li Q, Chen B, Zhou Z, Wang L, Wang L, Sang Q, Jin L. A novel homozygous missense variant in BTG4 causes zygotic cleavage failure and female infertility. J Assist Reprod Genet 2021; 38:3261-3266. [PMID: 34647228 DOI: 10.1007/s10815-021-02340-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022] Open
Abstract
PURPOSE "Zygotic cleavage failure" is an embryonic phenotype that causes female infertility and failure of in vitro fertilization and/or intracytoplasmic sperm injection. We aimed to identify pathogenic variants in a female infertility patient from a consanguineous family with the "zygotic cleavage failure" phenotype. METHODS Whole-exome sequencing was performed in the affected patient; Sanger sequencing was used to confirm the identified variant. The functional effect of the identified variant was further investigated in HeLa cells. RESULTS We identified a novel homozygous missense mutation in BTG4 (c.285G > C, p.W95C) in the affected individual. Co-immunoprecipitation in HeLa cells showed the complete loss of the interaction between the p.W95C BTG4 variant protein and CNOT7. CONCLUSION This study confirms our previous research and expands the mutational spectrum of BTG4. Our findings complement the diagnostic genetic basis for "zygotic cleavage failure" patients and suggest that BTG4 may be a good target for future therapeutic strategies.
Collapse
Affiliation(s)
- Ruyi Liu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, and the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Yifan Zhou
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qiaoli Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, and the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Zhou Zhou
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, and the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Lan Wang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lei Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, and the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Qing Sang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, and the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Lei Jin
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
19
|
Chen Y, Khazina E, Izaurralde E, Weichenrieder O. Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex. Nucleic Acids Res 2021; 49:6489-6510. [PMID: 34038562 PMCID: PMC8216464 DOI: 10.1093/nar/gkab414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/07/2023] Open
Abstract
The CCR4 and CAF1 deadenylases physically interact to form the CCR4-CAF1 complex and function as the catalytic core of the larger CCR4-NOT complex. Together, they are responsible for the eventual removal of the 3′-poly(A) tail from essentially all cellular mRNAs and consequently play a central role in the posttranscriptional regulation of gene expression. The individual properties of CCR4 and CAF1, however, and their respective contributions in different organisms and cellular environments are incompletely understood. Here, we determined the crystal structure of a human CCR4-CAF1 complex and characterized its enzymatic and substrate recognition properties. The structure reveals specific molecular details affecting RNA binding and hydrolysis, and confirms the CCR4 nuclease domain to be tethered flexibly with a considerable distance between both enzyme active sites. CCR4 and CAF1 sense nucleotide identity on both sides of the 3′-terminal phosphate, efficiently differentiating between single and consecutive non-A residues. In comparison to CCR4, CAF1 emerges as a surprisingly tunable enzyme, highly sensitive to pH, magnesium and zinc ions, and possibly allowing distinct reaction geometries. Our results support a picture of CAF1 as a primordial deadenylase, which gets assisted by CCR4 for better efficiency and by the assembled NOT proteins for selective mRNA targeting and regulation.
Collapse
Affiliation(s)
- Ying Chen
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| |
Collapse
|
20
|
Amine H, Ripin N, Sharma S, Stoecklin G, Allain FH, Séraphin B, Mauxion F. A conserved motif in human BTG1 and BTG2 proteins mediates interaction with the poly(A) binding protein PABPC1 to stimulate mRNA deadenylation. RNA Biol 2021; 18:2450-2465. [PMID: 34060423 PMCID: PMC8632095 DOI: 10.1080/15476286.2021.1925476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antiproliferative BTG/Tob proteins interact directly with the CAF1 deadenylase subunit of the CCR4-NOT complex. This binding requires the presence of two conserved motifs, boxA and boxB, characteristic of the BTG/Tob APRO domain. Consistently, these proteins were shown to stimulate mRNA deadenylation and decay in several instances. Two members of the family, BTG1 and BTG2, were reported further to associate with the protein arginine methyltransferase PRMT1 through a motif, boxC, conserved only in this subset of proteins. We recently demonstrated that BTG1 and BTG2 also contact the first RRM domain of the cytoplasmic poly(A) binding protein PABPC1. To decipher the mode of interaction of BTG1 and BTG2 with partners, we performed nuclear magnetic resonance experiments as well as mutational and biochemical analyses. Our data demonstrate that, in the context of an APRO domain, the boxC motif is necessary and sufficient to allow interaction with PABPC1 but, unexpectedly, that it is not required for BTG2 association with PRMT1. We show further that the presence of a boxC motif in an APRO domain endows it with the ability to stimulate deadenylation in cellulo and in vitro. Overall, our results identify the molecular interface allowing BTG1 and BTG2 to activate deadenylation, a process recently shown to be necessary for maintaining T-cell quiescence.
Collapse
Affiliation(s)
- Hamza Amine
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland
| | - Sahil Sharma
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Cancer Research Center (DKFZ)-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Cancer Research Center (DKFZ)-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Frédéric H Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zürich, Switzerland
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Fabienne Mauxion
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| |
Collapse
|
21
|
Ye X, Axhemi A, Jankowsky E. Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2021; 27:465-476. [PMID: 33408095 PMCID: PMC7962489 DOI: 10.1261/rna.078006.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The 3' to 5' exonuclease Pop2p (Caf1p) is part of the CCR4-NOT deadenylation complex that removes poly(A) tails from mRNAs in cells. Pop2p is structurally conserved in eukaryotes, but Saccharomyces cerevisiae Pop2p harbors noncanonical amino acids in its catalytic center. The enzymatic properties of S. cerevisiae Pop2p are not well defined. Here we characterize the RNA exonuclease activity of recombinant S. cerevisiae Pop2p. We find that S. cerevisiae Pop2p degrades RNAs via two alternative reactions pathways, one generating nucleotides with 5'-phosphates and RNA intermediates with 3'-hydroxyls, and the other generating nucleotides with 3'-phosphates and RNA intermediates with 3'-phosphates. The enzyme is not able to initiate the reaction on RNAs with a 3'-phosphate, which leads to accumulation of RNAs with 3'-phosphates that can exceed 10 nt and are resistant to further degradation by S. cerevisiae Pop2p. We further demonstrate that S. cerevisiae Pop2p degrades RNAs in three reaction phases: an initial distributive phase, a second processive phase and a third phase during which processivity gradually declines. We also show that mutations of subsets of amino acids in the catalytic center, including those previously thought to inactivate the enzyme, moderately reduce, but not eliminate activity. Only mutation of all five amino acids in the catalytic center diminishes activity of Pop2p to background levels. Collectively, our results reveal robust exonuclease activity of S. cerevisiae Pop2p with unusual enzymatic properties, characterized by alternative degradation pathways, multiple reaction phases and functional redundancy of amino acids in the catalytic core.
Collapse
Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Armend Axhemi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| |
Collapse
|
22
|
Song XH, Liao XY, Zheng XY, Liu JQ, Zhang ZW, Zhang LN, Yan YB. Human Ccr4 and Caf1 Deadenylases Regulate Proliferation and Tumorigenicity of Human Gastric Cancer Cells via Modulating Cell Cycle Progression. Cancers (Basel) 2021; 13:cancers13040834. [PMID: 33671234 PMCID: PMC7922635 DOI: 10.3390/cancers13040834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cancer cells generally reprogram their gene expression profiles to satisfy continuous growth, proliferation, and metastasis. Most eukaryotic mRNAs are degraded in a deadenylation-dependent pathway, in which deadenylases are the key enzymes. We found that human Ccr4 (hCcr4a/b) and Caf1 (hCaf1a/b), the dominant cytosolic deadenylases, were dysregulated in several types of cancers including stomach adenocarcinoma. Stably knocking down hCaf1a/b or hCcr4a/b blocks cell cycle progression by enhancing the levels of cell cycle inhibitors and by inhibiting the formation of processing bodies, which are cytosolic foci involved in mRNA metabolism. More importantly, depletion of hCaf1a/b or hCcr4a/b dramatically inhibits cell proliferation and tumorigenicity. Our results suggest that perturbating global RNA metabolism may provide a potential novel strategy for cancer treatment. Abstract Cancer cells generally have reprogrammed gene expression profiles to meet the requirements of survival, continuous division, and metastasis. An interesting question is whether the cancer cells will be affected by interfering their global RNA metabolism. In this research, we found that human Ccr4a/b (hCcr4a/b) and Caf1a/b (hCaf1a/b) deadenylases, the catalytic components of the Ccr4-Not complex, were dysregulated in several types of cancers including stomach adenocarcinoma. The impacts of the four deadenylases on cancer cell growth were studied by the establishment of four stable MKN28 cell lines with the knockdown of hCcr4a/b or hCaf1a/b or transient knockdown in several cell lines. Depletion of hCcr4a/b or hCaf1a/b significantly inhibited cell proliferation and tumorigenicity. Mechanistic studies indicated that the cells were arrested at the G2/M phase by knocking down hCaf1a, while arrested at the G0/G1 phase by depleting hCaf1b or hCcr4a/b. The four enzymes did not affect the levels of CDKs and cyclins but modulated the levels of CDK–cyclin inhibitors. We identified that hCcr4a/b, but not hCaf1a/b, targeted the p21 mRNA in the MKN28 cells. Furthermore, depletion of any one of the four deadenylases dramatically impaired processing-body formation in the MKN28 and HEK-293T cells. Our results highlight that perturbating global RNA metabolism may severely affect cancer cell proliferation, which provides a potential novel strategy for cancer treatment.
Collapse
Affiliation(s)
- Xiao-Hui Song
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xiao-Yan Liao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xu-Ying Zheng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Jia-Qian Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Zhe-Wei Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Li-Na Zhang
- College of Life Science and Chemistry, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
| |
Collapse
|
23
|
Almasmoum HA, Airhihen B, Seedhouse C, Winkler GS. Frequent loss of BTG1 activity and impaired interactions with the Caf1 subunit of the Ccr4-Not deadenylase in non-Hodgkin lymphoma. Leuk Lymphoma 2020; 62:281-290. [PMID: 33021411 DOI: 10.1080/10428194.2020.1827243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations in the highly similar genes B-cell translocation gene 1 (BTG1) and BTG2 are identified in approximately 10-15% of non-Hodgkin lymphoma cases, which may suggest a direct involvement of BTG1 and BTG2 in malignant transformation. However, it is unclear whether or how disease-associated mutations impair the function of these genes. Therefore, we selected 16 BTG1 variants based on in silico analysis. We then evaluated (i) the ability of these variants to interact with the known protein-binding partners CNOT7 and CNOT8, which encode the Caf1 catalytic subunit of the Ccr4-Not deadenylase complex; (ii) the activity of the variant proteins in cell cycle progression; (iii) translational repression; and (iv) mRNA degradation. Based on these analyses, we conclude that mutations in BTG1 may contribute to malignant transformation and tumor cell proliferation by interfering with its anti-proliferative activity and ability to interact with CNOT7 and CNOT8.
Collapse
Affiliation(s)
- Hibah Ali Almasmoum
- School of Pharmacy, The University of Nottingham, University Park, Nottingham, UK.,Department of Haematology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK.,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Blessing Airhihen
- School of Pharmacy, The University of Nottingham, University Park, Nottingham, UK
| | - Claire Seedhouse
- Department of Haematology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, University Park, Nottingham, UK
| | | |
Collapse
|
24
|
Zheng W, Zhou Z, Sha Q, Niu X, Sun X, Shi J, Zhao L, Zhang S, Dai J, Cai S, Meng F, Hu L, Gong F, Li X, Fu J, Shi R, Lu G, Chen B, Fan H, Wang L, Lin G, Sang Q. Homozygous Mutations in BTG4 Cause Zygotic Cleavage Failure and Female Infertility. Am J Hum Genet 2020; 107:24-33. [PMID: 32502391 DOI: 10.1016/j.ajhg.2020.05.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Zygotic cleavage failure (ZCF) is a unique early embryonic phenotype resulting in female infertility and recurrent failure of in vitro fertilization (IVF) and/or intracytoplasmic sperm injection (ICSI). With this phenotype, morphologically normal oocytes can be retrieved and successfully fertilized, but they fail to undergo cleavage. Until now, whether this phenotype has a Mendelian inheritance pattern and which underlying genetic factors play a role in its development remained to be elucidated. B cell translocation gene 4 (BTG4) is a key adaptor of the CCR4-NOT deadenylase complex, which is involved in maternal mRNA decay in mice, but no human diseases caused by mutations in BTG4 have previously been reported. Here, we identified four homozygous mutations in BTG4 (GenBank: NM_017589.4) that are responsible for the phenotype of ZCF, and we found they followed a recessive inheritance pattern. Three of them-c.73C>T (p.Gln25Ter), c.1A>G (p.?), and c.475_478del (p.Ile159LeufsTer15)-resulted in complete loss of full-length BTG4 protein. For c.166G>A (p.Ala56Thr), although the protein level and distribution of mutant BTG4 was not altered in zygotes from affected individuals or in HeLa cells, the interaction between BTG4 and CNOT7 was abolished. In vivo studies further demonstrated that the process of maternal mRNA decay was disrupted in the zygotes of the affected individuals, which provides a mechanistic explanation for the phenotype of ZCF. Thus, we provide evidence that ZCF is a Mendelian phenotype resulting from mutations in BTG4. These findings contribute to our understanding of the role of BTG4 in human early embryonic development and provide a genetic marker for female infertility.
Collapse
Affiliation(s)
- Wei Zheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Zhou Zhou
- Institute of Pediatrics, Children's Hospital of Fudan University and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology and Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Qianqian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Xiangli Niu
- Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Juanzi Shi
- Reproductive Medicine Center, Shaanxi Maternal and Child Care Service Center, Shaanxi, 710069, China
| | - Lei Zhao
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Shuoping Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Jing Dai
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Sufen Cai
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Fei Meng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Liang Hu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, China; Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, 410078, China
| | - Fei Gong
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, China; Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, 410078, China
| | - Xiaoran Li
- Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Jing Fu
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Rong Shi
- Reproductive Medicine Center, Shaanxi Maternal and Child Care Service Center, Shaanxi, 710069, China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, China; Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, 410078, China
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Shanghai, 200032, China
| | - Hengyu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lei Wang
- Institute of Pediatrics, Children's Hospital of Fudan University and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology and Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Shanghai Center for Women and Children's Health, Shanghai, 200062, China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, China; Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, 410078, China.
| | - Qing Sang
- Institute of Pediatrics, Children's Hospital of Fudan University and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology and Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
25
|
Mostafa D, Takahashi A, Yanagiya A, Yamaguchi T, Abe T, Kureha T, Kuba K, Kanegae Y, Furuta Y, Yamamoto T, Suzuki T. Essential functions of the CNOT7/8 catalytic subunits of the CCR4-NOT complex in mRNA regulation and cell viability. RNA Biol 2020; 17:403-416. [PMID: 31924127 PMCID: PMC6999631 DOI: 10.1080/15476286.2019.1709747] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Shortening of mRNA poly(A) tails (deadenylation) to trigger their decay is mediated mainly by the CCR4-NOT deadenylase complex. While four catalytic subunits (CNOT6, 6L 7, and 8) have been identified in the mammalian CCR4-NOT complex, their individual biological roles are not fully understood. In this study, we addressed the contribution of CNOT7/8 to viability of primary mouse embryonic fibroblasts (MEFs). We found that MEFs lacking CNOT7/8 expression [Cnot7/8-double knockout (dKO) MEFs] undergo cell death, whereas MEFs lacking CNOT6/6L expression (Cnot6/6l-dKO MEFs) remain viable. Co-immunoprecipitation analyses showed that CNOT6/6L are also absent from the CCR4-NOT complex in Cnot7/8-dKO MEFs. In contrast, either CNOT7 or CNOT8 still interacts with other subunits in the CCR4-NOT complex in Cnot6/6l-dKO MEFs. Exogenous expression of a CNOT7 mutant lacking catalytic activity in Cnot7/8-dKO MEFs cannot recover cell viability, even though CNOT6/6L exists to some extent in the CCR4-NOT complex, confirming that CNOT7/8 is essential for viability. Bulk poly(A) tail analysis revealed that mRNAs with longer poly(A) tails are more numerous in Cnot7/8-dKO MEFs than in Cnot6/6l-dKO MEFs. Consistent with elongated poly(A) tails, more mRNAs are upregulated and stabilized in Cnot7/8-dKO MEFs than in Cnot6/6l-dKO MEFs. Importantly, Cnot6/6l-dKO mice are viable and grow normally to adulthood. Taken together, the CNOT7/8 catalytic subunits are essential for deadenylation, which is necessary to maintain cell viability, whereas CNOT6/6L are not.
Collapse
Affiliation(s)
- Dina Mostafa
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Akiko Yanagiya
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Taku Kureha
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yumi Kanegae
- Research Center for Medical Science, Jikei University School of Medicine, Tokyo, Japan
| | - Yasuhide Furuta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory for Immunogenetics, Riken Center of Integrative Medical Sciences, Yokohama, Japan
| | - Toru Suzuki
- Laboratory for Immunogenetics, Riken Center of Integrative Medical Sciences, Yokohama, Japan
| |
Collapse
|
26
|
Bai Y, Qiao L, Xie N, Li Y, Nie Y, Pan Y, Shi Y, Wang J, Liu N. TOB1 suppresses proliferation in K-Ras wild-type pancreatic cancer. Cancer Med 2019; 9:1503-1514. [PMID: 31891232 PMCID: PMC7013073 DOI: 10.1002/cam4.2756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/25/2022] Open
Abstract
TOB1 participates in various kinds of cancers. However, its role in pancreatic cancer has rarely been reported. In this study, we explored the expression and mechanisms of TOB1 in regulating the malignant phenotype of pancreatic cancer cells. TOB1 expression was determined by data mining and immunohistochemistry (IHC), and its localization was observed by immunofluorescence. CCK‐8 cell proliferation, colony formation, flow cytometric, transwell migration, and Western blot (WB) assays were used to examine how it impacts the malignant phenotype of pancreatic cancer. Furthermore, Foxa2 binding to TOB1 was tested by dual‐luciferase reporter assays, and RNA‐Seq was performed to identify signaling pathways. We found TOB1 was downregulated in pancreatic cancer tissues and was mainly located in the cytoplasm. TOB1 overexpression reduced the proliferation of K‐Ras wild‐type pancreatic cancer cells but made no difference to cell migration and invasion. Foxa2 overexpression significantly enhanced TOB1 promoter activity. Moreover, overexpressing TOB1 substantially enriched the calcium pathway in K‐Ras wild‐type pancreatic cancer cells. In conclusion, TOB1 may suppress the proliferation of K‐Ras wild‐type pancreatic cancer cells by regulating calcium pathway genes.
Collapse
Affiliation(s)
- Yuru Bai
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Geriatric Respiratory and Endocrinology (The Third Unit of Cadre's Ward), the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lu Qiao
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ning Xie
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Li
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, the Fourth Military Medical University, Xi'an, Shaanxi, China.,Xijing Hospital of Digestive Diseases, Xijing Hospital, the Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yan Pan
- State Key Laboratory of Cancer Biology, the Fourth Military Medical University, Xi'an, Shaanxi, China.,Xijing Hospital of Digestive Diseases, Xijing Hospital, the Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yupeng Shi
- State Key Laboratory of Cancer Biology, the Fourth Military Medical University, Xi'an, Shaanxi, China.,Xijing Hospital of Digestive Diseases, Xijing Hospital, the Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jinhai Wang
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Na Liu
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| |
Collapse
|
27
|
Aoki ST, Porter DF, Prasad A, Wickens M, Bingman CA, Kimble J. An RNA-Binding Multimer Specifies Nematode Sperm Fate. Cell Rep 2019; 23:3769-3775. [PMID: 29949762 PMCID: PMC6066285 DOI: 10.1016/j.celrep.2018.05.095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 05/30/2018] [Indexed: 11/27/2022] Open
Abstract
FOG-3 is a master regulator of sperm fate in Caenorhabditis elegans and homologous to Tob/BTG proteins, which in mammals are monomeric adaptors that recruit enzymes to RNA binding proteins. Here, we determine the FOG-3 crystal structure and in vitro demonstrate that FOG-3 forms dimers that can multi-merize. The FOG-3 multimeric structure has a basic surface potential, suggestive of binding nucleic acid. Consistent with that prediction, FOG-3 binds directly to nearly 1,000 RNAs in nematode spermatogenic germ cells. Most binding is to the 3′ UTR, and most targets (94%) are oogenic mRNAs, even though assayed in spermatogenic cells. When tethered to a reporter mRNA, FOG-3 represses its expression. Together these findings elucidate the molecular mechanism of sperm fate specification and reveal the evolution of a protein from monomeric to multimeric form with acquisition of a distinct mode of mRNA repression. The mechanism of the sperm or oocyte fate decision has been elusive. Aoki et al. report that nematode FOG-3, a Tob/BTG protein driving sperm fate, has evolved from monomeric to multimeric form with acquisition of a divergent Tob/BTG mechanism for mRNA repression.
Collapse
Affiliation(s)
- Scott T Aoki
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
28
|
Hanet A, Räsch F, Weber R, Ruscica V, Fauser M, Raisch T, Kuzuoğlu-Öztürk D, Chang CT, Bhandari D, Igreja C, Wohlbold L. HELZ directly interacts with CCR4-NOT and causes decay of bound mRNAs. Life Sci Alliance 2019; 2:2/5/e201900405. [PMID: 31570513 PMCID: PMC6769256 DOI: 10.26508/lsa.201900405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022] Open
Abstract
The putative UPF1-like SF1 helicase HELZ directly interacts with the CCR4–NOT deadenylase complex to induce translational repression and 5′-to-3′ decay of bound mRNAs. Eukaryotic superfamily (SF) 1 helicases have been implicated in various aspects of RNA metabolism, including transcription, processing, translation, and degradation. Nevertheless, until now, most human SF1 helicases remain poorly understood. Here, we have functionally and biochemically characterized the role of a putative SF1 helicase termed “helicase with zinc-finger,” or HELZ. We discovered that HELZ associates with various mRNA decay factors, including components of the carbon catabolite repressor 4-negative on TATA box (CCR4–NOT) deadenylase complex in human and Drosophila melanogaster cells. The interaction between HELZ and the CCR4–NOT complex is direct and mediated by extended low-complexity regions in the C-terminal part of the protein. We further reveal that HELZ requires the deadenylase complex to mediate translational repression and decapping-dependent mRNA decay. Finally, transcriptome-wide analysis of Helz-null cells suggests that HELZ has a role in the regulation of the expression of genes associated with the development of the nervous system.
Collapse
Affiliation(s)
- Aoife Hanet
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Felix Räsch
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Vincenzo Ruscica
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maria Fauser
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Tobias Raisch
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Duygu Kuzuoğlu-Öztürk
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Helen Diller Family Cancer Research, University of California San Francisco, San Francisco, CA, USA
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dipankar Bhandari
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lara Wohlbold
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
29
|
Hatakawa Y, Nakamura R, Konishi M, Sakane T, Saito M, Akizawa T. Catalytides derived from the Box A region in the ANA/BTG3 protein cleave amyloid-β fragment peptide. Heliyon 2019; 5:e02454. [PMID: 31687556 PMCID: PMC6819762 DOI: 10.1016/j.heliyon.2019.e02454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/25/2019] [Accepted: 09/06/2019] [Indexed: 01/25/2023] Open
Abstract
We have recently reported about shorter proteolytic peptides termed Catalytide as general name. JAL-TA9 (YKGSGFRMI), a fragment peptide derived from Box A region of Tob1 protein, is the first Catalytide and cleaves Aβ42 and its fragment peptides. Herein, we demonstrate the enzymatic properties of ANA-TA9 corresponding region to JAL-TA9 in ANA/BTG3 protein. ANA-TA9 showed the auto-proteolytic activity and cleaved 3 kinds of synthetic fragment peptides derived from Aβ42, especially on the central region of Aβ42 with a serine protease like activity. Interestingly, 2 kinds of components, ANA-SA5 (SKGQA) and ANA-YA4 (YRMI), also showed similar proteolytic activity. These results indicate that ANA-TA9 is composed of two different Catalytides.
Collapse
Affiliation(s)
- Yusuke Hatakawa
- Pharmaceutical Technology, Kobe Pharmaceutical University, 4-19-1, Motoyamakita, Higashinada, Kobe, 658-8558, Japan
| | - Rina Nakamura
- O-Force Co., Ltd, 3454 Irino Kuroshio-cho, Hata-gun, Kochi 789-1931, Japan.,Laboratory of Pharmacology, School of Medicine, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, 783-0047, Japan
| | - Motomi Konishi
- Laboratory of Clinical Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Toshiyasu Sakane
- Pharmaceutical Technology, Kobe Pharmaceutical University, 4-19-1, Motoyamakita, Higashinada, Kobe, 658-8558, Japan
| | - Motoaki Saito
- Laboratory of Pharmacology, School of Medicine, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, 783-0047, Japan
| | - Toshifumi Akizawa
- O-Force Co., Ltd, 3454 Irino Kuroshio-cho, Hata-gun, Kochi 789-1931, Japan.,Laboratory of Pharmacology, School of Medicine, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, 783-0047, Japan
| |
Collapse
|
30
|
Salem ESB, Vonberg AD, Borra VJ, Gill RK, Nakamura T. RNAs and RNA-Binding Proteins in Immuno-Metabolic Homeostasis and Diseases. Front Cardiovasc Med 2019; 6:106. [PMID: 31482095 PMCID: PMC6710452 DOI: 10.3389/fcvm.2019.00106] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
The increasing prevalence of worldwide obesity has emerged as a major risk factor for type 2 diabetes (T2D), hepatosteatosis, and cardiovascular disease. Accumulating evidence indicates that obesity has strong inflammatory underpinnings tightly linked to the development of metabolic diseases. However, the molecular mechanisms by which obesity induces aberrant inflammation associated with metabolic diseases are not yet clearly defined. Recently, RNAs have emerged as important regulators of stress responses and metabolism. RNAs are subject to changes in modification status, higher-order structure, and cellular localization; all of which could affect the affinity for RNA-binding proteins (RBPs) and thereby modify the RNA-RBP networks. Proper regulation and management of RNA characteristics are fundamental to cellular and organismal homeostasis, as well as paramount to health. Identification of multiple single nucleotide polymorphisms (SNPs) within loci of fat mass- and obesity-associated protein (FTO) gene, an RNA demethylase, through genome-wide association studies (GWAS) of T2D, and functional assessments of FTO in mice, support the concept that disruption in RNA modifications leads to the development of human diseases including obesity and metabolic disorder. In obesity, dynamic alterations in modification and localization of RNAs appear to modulate the RNA-RBP networks and activate proinflammatory RBPs, such as double-stranded RNA (dsRNA)-dependent protein kinase (PKR), Toll-like receptor (TLR) 3 and TLR7, and RNA silencing machinery. These changes induce aberrant inflammation and the development of metabolic diseases. This review will describe the current understanding of the underlying causes of these common and altered characteristics of RNA-RBP networks which will pave the way for developing novel approaches to tackle the pandemic issue of obesity.
Collapse
Affiliation(s)
- Esam S B Salem
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew D Vonberg
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Vishnupriya J Borra
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Rupinder K Gill
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Takahisa Nakamura
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| |
Collapse
|
31
|
Duan TL, He GJ, Hu LD, Yan YB. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Cells 2019; 8:cells8080836. [PMID: 31387300 PMCID: PMC6721724 DOI: 10.3390/cells8080836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.
Collapse
Affiliation(s)
- Tian-Li Duan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang-Jun He
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
32
|
Shimo HM, Terassi C, Lima Silva CC, Zanella JDL, Mercaldi GF, Rocco SA, Benedetti CE. Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance. MOLECULAR PLANT PATHOLOGY 2019; 20:1105-1118. [PMID: 31115151 PMCID: PMC6640180 DOI: 10.1111/mpp.12815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Poly(A) tail shortening is a critical step in messenger RNA (mRNA) decay and control of gene expression. The carbon catabolite repressor 4 (CCR4)-associated factor 1 (CAF1) component of the CCR4-NOT deadenylase complex plays an essential role in mRNA deadenylation in most eukaryotes. However, while CAF1 has been extensively investigated in yeast and animals, its role in plants remains largely unknown. Here, we show that the Citrus sinensis CAF1 (CsCAF1) is a magnesium-dependent deadenylase implicated in resistance against the citrus canker bacteria Xanthomonas citri. CsCAF1 interacted with proteins of the CCR4-NOT complex, including CsVIP2, a NOT2 homologue, translin-associated factor X (CsTRAX) and the poly(A)-binding proteins CsPABPN and CsPABPC. CsCAF1 also interacted with PthA4, the main X. citri effector required for citrus canker elicitation. We also present evidence suggesting that PthA4 inhibits CsCAF1 deadenylase activity in vitro and stabilizes the mRNA encoded by the citrus canker susceptibility gene CsLOB1, which is transcriptionally activated by PthA4 during canker formation. Moreover, we show that an inhibitor of CsCAF1 deadenylase activity significantly enhanced canker development, despite causing a reduction in PthA4-dependent CsLOB1 transcription. These results thus link CsCAF1 with canker development and PthA4-dependent transcription in citrus plants.
Collapse
Affiliation(s)
- Hugo Massayoshi Shimo
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Carolina Terassi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Caio Cesar Lima Silva
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Jackeline de Lima Zanella
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Silvana Aparecida Rocco
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| |
Collapse
|
33
|
Calvanese L, Squeglia F, Romano M, D'Auria G, Falcigno L, Berisio R. Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence. J Biomol Struct Dyn 2019; 38:2455-2467. [PMID: 31299874 DOI: 10.1080/07391102.2019.1643786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribonuclease AS (RNase AS) is a crucial enzyme for virulence of Mycobacterium tuberculosis. We previously observed that RNase AS structurally resembles RNase T from Escherichia coli, an important enzyme for tRNA maturation and turnover. Here, we combine X-ray crystallography and molecular dynamics (MD) to investigate the specificity and dynamic properties of substrate binding. Both X-ray and MD data provide structural determinants that corroborate the strict substrate specificity of RNase AS to cleave only adenosine residues, due to the structural features of adenine base. Beside suggesting tRNA as most likely substrate of RNase AS, MD and modeling studies identify key enzyme-ligand interactions, both involving the catalytic site and the double helix region of tRNA, which is locked by interactions with a set of arginine residues. The MD data also evidence a ligand-induced conformational change of the enzyme which is transferred from one chain to the adjacent one. These data will explain the dimeric nature of both RNase AS and RNase T, with two catalytic grooves composed of both chains. Also, they account for the dichotomy of tRNA, which contains both the substrate poly(A) chain and an inhibiting double strand RNA. Indeed, they provide a possible mechanism of allosteric regulation, which unlocks one catalytic groove when the second groove is inhibited by the double strand region of tRNA. Finally, a full comprehension of the molecular details of tRNA maturation processes is essential to develop novel strategies to modulate RNA processing, for therapeutic purposes. AbbreviationsMDmolecular dynamicsPDBProtein Data BankRMSDroot mean square deviationRMSFroot mean square fluctuationRNAribonucleotidic acidRNase ASRibonuclease ASCommunicated by Ramasamy H. Sarma.
Collapse
Affiliation(s)
- Luisa Calvanese
- CIRPeB, University of Naples Federico II, Naples, Italy.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Flavia Squeglia
- Institute of Bio-Structures and Bio-Imaging - CNR-IBB, Naples, Italy
| | - Maria Romano
- Department of Life Sciences, Imperial College London, London, UK
| | - Gabriella D'Auria
- CIRPeB, University of Naples Federico II, Naples, Italy.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Lucia Falcigno
- CIRPeB, University of Naples Federico II, Naples, Italy.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Rita Berisio
- Institute of Bio-Structures and Bio-Imaging - CNR-IBB, Naples, Italy
| |
Collapse
|
34
|
Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation. Nat Commun 2019; 10:3173. [PMID: 31320642 PMCID: PMC6639331 DOI: 10.1038/s41467-019-11094-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
CCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails of messenger RNA or deadenylation. Here, we reconstitute a complete, recombinant human CCR4-NOT complex. Our reconstitution strategy permits strict compositional control to test mechanistic hypotheses with purified component variants. CCR4-NOT is more active and selective for poly(A) than the isolated exonucleases, CCR4a and CAF1, which have distinct deadenylation profiles in vitro. The exonucleases require at least two out of three conserved non-enzymatic modules (CAF40, NOT10:NOT11 or NOT) for full activity in CCR4-NOT. CAF40 and the NOT10:NOT11 module both bind RNA directly and stimulate deadenylation in a partially redundant manner. Linear motifs from different RNA-binding factors that recruit CCR4-NOT to specific mRNAs via protein-protein interactions with CAF40 can inhibit bulk deadenylation. We reveal an additional layer of regulatory complexity to the human deadenylation machinery, which may prime it either for general or target-specific degradation. The CCR4-NOT complex shortens poly(A) tails of messenger RNAs. By biochemical reconstitution of the entire human CCR4-NOT complex, the authors show the stimulatory roles of non-enzymatic subunits and the importance of the interaction between CAF40 and RNA binding proteins in targeted deadenylation.
Collapse
|
35
|
Abstract
The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.
Collapse
Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland.
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland
| |
Collapse
|
36
|
Nakamura R, Konishi M, Taniguchi M, Hatakawa Y, Akizawa T. The discovery of shorter synthetic proteolytic peptides derived from Tob1 protein. Peptides 2019; 116:71-77. [PMID: 30930080 DOI: 10.1016/j.peptides.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 01/17/2023]
Abstract
We screened nearly 1000 synthetic peptides and found that JAL-AK22 (KYEGHWYPEKPYKGSGFRCIHI), which is derived from the BoxA domain in the Tob1 protein, activates both unfolded and folded proMMP-7. Interestingly, the smaller derivative of JAL-AK22, termed JAL-TA9 (YKGSGFRMI) possessed auto-proteolytic activity and cleaved three synthetic peptides fragment (MMP18-33, MMP18-40, and Aβ11-29) under physiological conditions. The kcat of JAL-TA9 was 4.58 × 10-4 min-1 against MMP18-33 and 6.5 × 10-4 min-1 against MMP18-40. These kinetic parameters are lower than those of general proteinases like trypsin, for which the kcat is 247.2 × 105 min-1 against benzoyl-l-arginine ethyl ester. In addition, a 5-mer peptide derived from JAL-TA9, GSGFR also cleaved Aβ11-29. These proteolytic activities were inhibited by AEBSF (4-(2-Aminoethyl) benzenesulfonyl fluoride hydrochloride), a serine protease inhibitor. Our results demonstrate that some small synthetic peptides have protease activity. Thus, we propose calling small peptides possessing with protease activity Catalytides (catalytic peptides). We expect that our findings will stimulate the development of novel Catalytides and related applications such as the development of strategic peptide drugs.
Collapse
Affiliation(s)
- Rina Nakamura
- O-Force Co. Ltd., 3454 Irino, Kuroshio-cho, Hata-gun, Kochi, 789-1931, Japan; Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu Oko-cho, Nankoku, Kochi, 783-8505, Japan; Laboratory of Clinical Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Motomi Konishi
- Laboratory of Clinical Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan.
| | - Masanari Taniguchi
- Laboratory of Clinical Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Yusuke Hatakawa
- Laboratory of Clinical Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Toshifumi Akizawa
- O-Force Co. Ltd., 3454 Irino, Kuroshio-cho, Hata-gun, Kochi, 789-1931, Japan; Department of Pharmacology, Kochi Medical School, Kochi University, Kohasu Oko-cho, Nankoku, Kochi, 783-8505, Japan; Laboratory of Clinical Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| |
Collapse
|
37
|
Chapat C, Chettab K, Simonet P, Wang P, De La Grange P, Le Romancer M, Corbo L. Alternative splicing of CNOT7 diversifies CCR4-NOT functions. Nucleic Acids Res 2017; 45:8508-8523. [PMID: 28591869 PMCID: PMC5737658 DOI: 10.1093/nar/gkx506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/26/2017] [Indexed: 12/11/2022] Open
Abstract
The CCR4-associated factor CAF1, also called CNOT7, is a catalytic subunit of the CCR4–NOT complex, which has been implicated in all aspects of the mRNA life cycle, from mRNA synthesis in the nucleus to degradation in the cytoplasm. In human cells, alternative splicing of the CNOT7 gene yields a second CNOT7 transcript leading to the formation of a shorter protein, CNOT7 variant 2 (CNOT7v2). Biochemical characterization indicates that CNOT7v2 interacts with CCR4–NOT subunits, although it does not bind to BTG proteins. We report that CNOT7v2 displays a distinct expression profile in human tissues, as well as a nuclear sub-cellular localization compared to CNOT7v1. Despite a conserved DEDD nuclease domain, CNOT7v2 is unable to degrade a poly(A) tail in vitro and preferentially associates with the protein arginine methyltransferase PRMT1 to regulate its activity. Using both in vitro and in cellulo systems, we have also demonstrated that CNOT7v2 regulates the inclusion of CD44 variable exons. Altogether, our findings suggest a preferential involvement of CNOT7v2 in nuclear processes, such as arginine methylation and alternative splicing, rather than mRNA turnover. These observations illustrate how the integration of a splicing variant inside CCR4–NOT can diversify its cell- and tissue-specific functions.
Collapse
Affiliation(s)
- Clément Chapat
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Kamel Chettab
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Pierre Simonet
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Peng Wang
- McGill University, Department of Biochemistry, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
| | | | - Muriel Le Romancer
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Laura Corbo
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| |
Collapse
|
38
|
Sharma S, Poetz F, Bruer M, Ly-Hartig TBN, Schott J, Séraphin B, Stoecklin G. Acetylation-Dependent Control of Global Poly(A) RNA Degradation by CBP/p300 and HDAC1/2. Mol Cell 2017; 63:927-38. [PMID: 27635759 DOI: 10.1016/j.molcel.2016.08.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 05/09/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
Abstract
Acetylation of histones and transcription-related factors is known to exert epigenetic and transcriptional control of gene expression. Here we report that histone acetyltransferases (HATs) and histone deacetylases (HDACs) also regulate gene expression at the posttranscriptional level by controlling poly(A) RNA stability. Inhibition of HDAC1 and HDAC2 induces massive and widespread degradation of normally stable poly(A) RNA in mammalian and Drosophila cells. Acetylation-induced RNA decay depends on the HATs p300 and CBP, which acetylate the exoribonuclease CAF1a, a catalytic subunit of the CCR4-CAF1-NOT deadenlyase complex and thereby contribute to accelerating poly(A) RNA degradation. Taking adipocyte differentiation as a model, we observe global stabilization of poly(A) RNA during differentiation, concomitant with loss of CBP/p300 expression. Our study uncovers reversible acetylation as a fundamental switch by which HATs and HDACs control the overall turnover of poly(A) RNA.
Collapse
Affiliation(s)
- Sahil Sharma
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Fabian Poetz
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius Bruer
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Thi Bach Nga Ly-Hartig
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Johanna Schott
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France; Centre National de Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France; INSERM U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Georg Stoecklin
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| |
Collapse
|
39
|
Ukleja M, Valpuesta JM, Dziembowski A, Cuellar J. Beyond the known functions of the CCR4-NOT complex in gene expression regulatory mechanisms: New structural insights to unravel CCR4-NOT mRNA processing machinery. Bioessays 2016; 38:1048-58. [PMID: 27502453 DOI: 10.1002/bies.201600092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large protein assemblies are usually the effectors of major cellular processes. The intricate cell homeostasis network is divided into numerous interconnected pathways, each controlled by a set of protein machines. One of these master regulators is the CCR4-NOT complex, which ultimately controls protein expression levels. This multisubunit complex assembles around a scaffold platform, which enables a wide variety of well-studied functions from mRNA synthesis to transcript decay, as well as other tasks still being identified. Solving the structure of the entire CCR4-NOT complex will help to define the distribution of its functions. The recently published three-dimensional reconstruction of the complex, in combination with the known crystal structures of some of the components, has begun to address this. Methodological improvements in structural biology, especially in cryoelectron microscopy, encourage further structural and protein-protein interaction studies, which will advance our comprehension of the gene expression machinery.
Collapse
Affiliation(s)
- Marta Ukleja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland. .,Faculty of Biology, Department of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland. .,Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain. .,Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK.
| | - José María Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Department of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Jorge Cuellar
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| |
Collapse
|
40
|
Zhang Q, Yan D, Guo E, Ding B, Yang W, Liu R, Yamamoto T, Bartlam M. Structural basis for inhibition of the deadenylase activity of human CNOT6L. FEBS Lett 2016; 590:1270-9. [PMID: 27013054 DOI: 10.1002/1873-3468.12160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 11/08/2022]
Abstract
Human CNOT6L/CCR4, a member of the endonuclease-exonuclease-phosphatase (EEP) family enzymes, is one of the two deadenylase enzymes in the conserved CCR4-NOT complex. Here, we report inhibitor-bound crystal structures of the human CNOT6L nuclease domain in complex with the nucleotide CMP and the aminoglycoside neomycin. Deadenylase activity assays show that nucleotides are effective inhibitors of both CNOT6L and CNOT7, with AMP more effective than other nucleotides, and that neomycin is a weak deadenylase inhibitor. Structural analysis shows that all inhibitors occupy the substrate and magnesium-binding sites of CNOT6L, suggesting that inhibitors compete with both substrate and divalent magnesium ions for overlapping binding sites.
Collapse
Affiliation(s)
- Qionglin Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Dongke Yan
- College of Life Sciences, Nankai University, Tianjin, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Erhong Guo
- College of Life Sciences, Nankai University, Tianjin, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Bojian Ding
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wen Yang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ruihua Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami, Okinawa, Japan
| | - Mark Bartlam
- College of Life Sciences, Nankai University, Tianjin, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| |
Collapse
|
41
|
BTG4 is a meiotic cell cycle-coupled maternal-zygotic-transition licensing factor in oocytes. Nat Struct Mol Biol 2016; 23:387-94. [PMID: 27065194 DOI: 10.1038/nsmb.3204] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/11/2016] [Indexed: 12/29/2022]
Abstract
The mRNAs stored in oocytes undergo general decay during the maternal-zygotic transition (MZT), and their stability is tightly interconnected with meiotic cell-cycle progression. However, the factors that trigger decay of maternal mRNA and couple this event to oocyte meiotic maturation remain elusive. Here, we identified B-cell translocation gene-4 (BTG4) as an MZT licensing factor in mice. BTG4 bridged CNOT7, a catalytic subunit of the CCR4-NOT deadenylase, to eIF4E, a key translation initiation factor, and facilitated decay of maternal mRNA. Btg4-null females produced morphologically normal oocytes but were infertile, owing to early developmental arrest. The intrinsic MAP kinase cascade in oocytes triggered translation of Btg4 mRNA stored in fully grown oocytes by targeting the 3' untranslated region, thereby coupling CCR4-NOT deadenylase-mediated decay of maternal mRNA with oocyte maturation and fertilization. This is a key step in oocyte cytoplasmic maturation that determines the developmental potential of mammalian embryos.
Collapse
|
42
|
Stupfler B, Birck C, Séraphin B, Mauxion F. BTG2 bridges PABPC1 RNA-binding domains and CAF1 deadenylase to control cell proliferation. Nat Commun 2016; 7:10811. [PMID: 26912148 PMCID: PMC4773420 DOI: 10.1038/ncomms10811] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/24/2016] [Indexed: 12/12/2022] Open
Abstract
While BTG2 plays an important role in cellular differentiation and cancer, its precise molecular function remains unclear. BTG2 interacts with CAF1 deadenylase through its APRO domain, a defining feature of BTG/Tob factors. Our previous experiments revealed that expression of BTG2 promoted mRNA poly(A) tail shortening through an undefined mechanism. Here we report that the APRO domain of BTG2 interacts directly with the first RRM domain of the poly(A)-binding protein PABPC1. Moreover, PABPC1 RRM and BTG2 APRO domains are sufficient to stimulate CAF1 deadenylase activity in vitro in the absence of other CCR4–NOT complex subunits. Our results unravel thus the mechanism by which BTG2 stimulates mRNA deadenylation, demonstrating its direct role in poly(A) tail length control. Importantly, we also show that the interaction of BTG2 with the first RRM domain of PABPC1 is required for BTG2 to control cell proliferation. BTG2 promotes mRNA poly(A) tail shortening and regulates cellular differentiation. Here, Stupfler et al. show that the BTG2 APRO domain interacts with PABPC1 RRM1, allowing the former to recruit and stimulate the poly(A) tail shortening activity of CAF1 deadenylase and to control cell proliferation.
Collapse
Affiliation(s)
- Benjamin Stupfler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Fabienne Mauxion
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| |
Collapse
|
43
|
Faraji F, Hu Y, Yang HH, Lee MP, Winkler GS, Hafner M, Hunter KW. Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7. PLoS Genet 2016; 12:e1005820. [PMID: 26807845 PMCID: PMC4726497 DOI: 10.1371/journal.pgen.1005820] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/31/2015] [Indexed: 12/15/2022] Open
Abstract
Accumulating evidence supports the role of an aberrant transcriptome as a driver of metastatic potential. Deadenylation is a general regulatory node for post-transcriptional control by microRNAs and other determinants of RNA stability. Previously, we demonstrated that the CCR4-NOT scaffold component Cnot2 is an inherited metastasis susceptibility gene. In this study, using orthotopic metastasis assays and genetically engineered mouse models, we show that one of the enzymatic subunits of the CCR4-NOT complex, Cnot7, is also a metastasis modifying gene. We demonstrate that higher expression of Cnot7 drives tumor cell autonomous metastatic potential, which requires its deadenylase activity. Furthermore, metastasis promotion by CNOT7 is dependent on interaction with CNOT1 and TOB1. CNOT7 ribonucleoprotein-immunoprecipitation (RIP) and integrated transcriptome wide analyses reveal that CNOT7-regulated transcripts are enriched for a tripartite 3'UTR motif bound by RNA-binding proteins known to complex with CNOT7, TOB1, and CNOT1. Collectively, our data support a model of CNOT7, TOB1, CNOT1, and RNA-binding proteins collectively exerting post-transcriptional control on a metastasis suppressive transcriptional program to drive tumor cell metastasis.
Collapse
Affiliation(s)
- Farhoud Faraji
- Metastasis Susceptibility Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- School of Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard H. Yang
- Metastasis Susceptibility Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maxwell P. Lee
- Metastasis Susceptibility Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kent W. Hunter
- Metastasis Susceptibility Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
44
|
Takahashi A, Adachi S, Morita M, Tokumasu M, Natsume T, Suzuki T, Yamamoto T. Post-transcriptional Stabilization of Ucp1 mRNA Protects Mice from Diet-Induced Obesity. Cell Rep 2015; 13:2756-67. [PMID: 26711342 DOI: 10.1016/j.celrep.2015.11.056] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 10/10/2015] [Accepted: 11/17/2015] [Indexed: 11/24/2022] Open
Abstract
Uncoupling protein 1 (Ucp1) contributes to thermogenesis, and its expression is regulated at the transcriptional level. Here, we show that Ucp1 expression is also regulated post-transcriptionally. In inguinal white adipose tissue (iWAT) of mice fed a high-fat diet (HFD), Ucp1 level decreases concomitantly with increases in Cnot7 and its interacting partner Tob. HFD-fed mice lacking Cnot7 and Tob express elevated levels of Ucp1 mRNA in iWAT and are resistant to diet-induced obesity. Ucp1 mRNA has an elongated poly(A) tail and persists in iWAT of Cnot7(-/-) and/or Tob(-/-) mice on a HFD. Ucp1 3'-UTR-containing mRNA is more stable in cells expressing mutant Tob that is unable to bind Cnot7 than in WT Tob-expressing cells. Tob interacts with BRF1, which binds to an AU-rich element in the Ucp1 3'-UTR. BRF1 knockdown partially restores the stability of Ucp1 3'-UTR-containing mRNA. Thus, the Cnot7-Tob-BRF1 axis inhibits Ucp1 expression and contributes to obesity.
Collapse
Affiliation(s)
- Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa 904-0412, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Masahiro Morita
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Miho Tokumasu
- Cell Signal Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa 904-0412, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Toru Suzuki
- Cell Signal Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa 904-0412, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa 904-0412, Japan.
| |
Collapse
|
45
|
Lee HS, Kundu J, Kim RN, Shin YK. Transducer of ERBB2.1 (TOB1) as a Tumor Suppressor: A Mechanistic Perspective. Int J Mol Sci 2015; 16:29815-28. [PMID: 26694352 PMCID: PMC4691146 DOI: 10.3390/ijms161226203] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/22/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023] Open
Abstract
Transducer of ERBB2.1 (TOB1) is a tumor-suppressor protein, which functions as a negative regulator of the receptor tyrosine-kinase ERBB2. As most of the other tumor suppressor proteins, TOB1 is inactivated in many human cancers. Homozygous deletion of TOB1 in mice is reported to be responsible for cancer development in the lung, liver, and lymph node, whereas the ectopic overexpression of TOB1 shows anti-proliferation, and a decrease in the migration and invasion abilities on cancer cells. Biochemical studies revealed that the anti-proliferative activity of TOB1 involves mRNA deadenylation and is associated with the reduction of both cyclin D1 and cyclin-dependent kinase (CDK) expressions and the induction of CDK inhibitors. Moreover, TOB1 interacts with an oncogenic signaling mediator, β-catenin, and inhibits β-catenin-regulated gene transcription. TOB1 antagonizes the v-akt murine thymoma viral oncogene (AKT) signaling and induces cancer cell apoptosis by activating BCL2-associated X (BAX) protein and inhibiting the BCL-2 and BCL-XL expressions. The tumor-specific overexpression of TOB1 results in the activation of other tumor suppressor proteins, such as mothers against decapentaplegic homolog 4 (SMAD4) and phosphatase and tensin homolog-10 (PTEN), and blocks tumor progression. TOB1-overexpressing cancer cells have limited potential of growing as xenograft tumors in nude mice upon subcutaneous implantation. This review addresses the molecular basis of TOB1 tumor suppressor function with special emphasis on its regulation of intracellular signaling pathways.
Collapse
Affiliation(s)
- Hun Seok Lee
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Juthika Kundu
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Ryong Nam Kim
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
- Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul 08826, Korea.
| | - Young Kee Shin
- Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
- Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul 08826, Korea.
- The Center for Anti-cancer Companion Diagnostics, School of Biological Science, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 08826, Korea.
| |
Collapse
|
46
|
Bai Y, Tashiro S, Nagatoishi S, Suzuki T, Yan D, Liu R, Tsumoto K, Bartlam M, Yamamoto T. Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach. Protein Cell 2015; 6:924-8. [PMID: 26518565 PMCID: PMC4656213 DOI: 10.1007/s13238-015-0225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Affiliation(s)
- Yuwei Bai
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shinya Tashiro
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Satoru Nagatoishi
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Toru Suzuki
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Onna-son, Kunigami, Okinawa, 904-0412, Japan
| | - Dongke Yan
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Kouhei Tsumoto
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Onna-son, Kunigami, Okinawa, 904-0412, Japan
| |
Collapse
|
47
|
Cantharidin represses invasion of pancreatic cancer cells through accelerated degradation of MMP2 mRNA. Sci Rep 2015; 5:11836. [PMID: 26135631 PMCID: PMC4488834 DOI: 10.1038/srep11836] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/22/2015] [Indexed: 12/22/2022] Open
Abstract
Cantharidin is an active constituent of mylabris, a traditional Chinese medicine, and is a potent and selective inhibitor of protein phosphatase 2A (PP2A) that plays an important role in cell cycle control, apoptosis, and cell-fate determination. In the present study, we found that cantharidin repressed the invasive ability of pancreatic cancer cells and downregulated matrix metalloproteinase 2 (MMP2) expression through multiple pathways, including ERK, JNK, PKC, NF-κB, and β-catenin. Interestingly, transcriptional activity of the MMP2 promoter increased after treatment with PP2A inhibitors, suggesting the involvement of a posttranscriptional mechanism. By using an mRNA stability assay, we found accelerated degradation of MMP2 mRNA after treatment of cantharidin. Microarray analyses revealed that multiple genes involved in the 3' → 5' decay pathway were upregulated, especially genes participating in cytoplasmic deadenylation. The elevation of these genes were further demonstrated to be executed through ERK, JNK, PKC, NF-κB, and β-catenin pathways. Knockdown of PARN, RHAU, and CNOT7, three critical members involved in cytoplasmic deadenylation, attenuated the downregulation of MMP2. Hence, we present the mechanism of repressed invasion by cantharidin and other PP2A inhibitors through increased degradation of MMP2 mRNA by elevated cytoplasmic deadenylation.
Collapse
|
48
|
Waghray S, Williams C, Coon JJ, Wickens M. Xenopus CAF1 requires NOT1-mediated interaction with 4E-T to repress translation in vivo. RNA (NEW YORK, N.Y.) 2015; 21:1335-45. [PMID: 26015597 PMCID: PMC4478352 DOI: 10.1261/rna.051565.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/22/2015] [Indexed: 05/25/2023]
Abstract
RNA-regulatory factors bound to 3' UTRs control translation and stability. Repression often is associated with poly(A) removal. The deadenylase CAF1 is a core component of the CCR4-NOT complex. Our prior studies established that CAF1 represses translation independent of deadenylation. We sought the mechanism of its deadenylation-independent repression in Xenopus oocytes. Our data reveal a chain of interacting proteins that links CAF1 to CCR4-NOT and to Xp54 and 4E-T. Association of CAF1 with NOT1, the major subunit of CCR4-NOT, is required for repression by CAF1 tethered to a reporter mRNA. Affinity purification-mass spectrometry and coimmunoprecipitation revealed that at least five members of the CCR4-NOT complex were recruited by CAF1. The recruitment of these proteins required NOT1, as did the ability of tethered CAF1 to repress translation. In turn, NOT1 was needed to recruit Xp54 and 4E-T. We examined the role of 4E-T in repression using mutations that disrupted either eIF4E-dependent or -independent mechanisms. Expression of a 4E-T truncation that still bound eIF4E alleviated repression by tethered CAF1, NOT1, and Xp54. In contrast, a mutant 4E-T that failed to bind eIF4E did not. Repression of global translation was affected only by the eIF4E-dependent mechanism. Reporters bearing IRES elements revealed that repression via tethered CAF1 and Xp54 is cap- and eIF4E-independent, but requires one or more of eIF4A, eIF4B, and eIF4G. We propose that RNA-binding proteins, and perhaps miRNAs, repress translation through an analogous chain of interactions that begin with the 3' UTR-bound repressor and end with the noncanonical activity of 4E-T.
Collapse
Affiliation(s)
- Shruti Waghray
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Clay Williams
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| |
Collapse
|
49
|
The enzyme activities of Caf1 and Ccr4 are both required for deadenylation by the human Ccr4-Not nuclease module. Biochem J 2015; 469:169-76. [PMID: 25944446 PMCID: PMC4613498 DOI: 10.1042/bj20150304] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/06/2015] [Indexed: 01/02/2023]
Abstract
In eukaryotic cells, the shortening and removal of the poly(A) tail (deadenylation) of cytoplasmic mRNA is a key event in regulated mRNA degradation. A major enzyme involved in deadenylation is the Ccr4-Not deadenylase complex, which can be recruited to its target mRNA by RNA-binding proteins or the miRNA repression complex. In addition to six non-catalytic components, the complex contains two enzymatic subunits with ribonuclease activity: Ccr4 and Caf1 (Pop2). In vertebrates, each deadenylase subunit is encoded by two paralogues: Caf1, which can interact with the anti-proliferative protein BTG2, is encoded by CNOT7 and CNOT8, whereas Ccr4 is encoded by the highly similar genes CNOT6 and CNOT6L. Currently, it is unclear whether the catalytic subunits work co-operatively or whether the nuclease components have unique roles in deadenylation. We therefore developed a method to express and purify a minimal human BTG2-Caf1-Ccr4 nuclease sub-complex from bacterial cells. By using chemical inhibition and well-characterized inactivating amino acid substitutions, we demonstrate that the enzyme activities of Caf1 and Ccr4 are both required for deadenylation in vitro. These results indicate that Caf1 and Ccr4 cooperate in mRNA deadenylation and suggest that the enzyme activities of Caf1 and Ccr4 are regulated via allosteric interactions within the nuclease module.
Collapse
|
50
|
Chen Y, Wang C, Wu J, Li L. BTG/Tob family members Tob1 and Tob2 inhibit proliferation of mouse embryonic stem cells via Id3 mRNA degradation. Biochem Biophys Res Commun 2015; 462:208-14. [PMID: 25951976 DOI: 10.1016/j.bbrc.2015.04.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 04/18/2015] [Indexed: 02/06/2023]
Abstract
The mammalian BTG/Tob family is a group of proteins with anti-proliferative ability, and there are six members including BTG1, BTG2/PC3/Tis21, BTG3/ANA, BTG4/PC3B, Tob1/Tob and Tob2. Among them, Tob subfamily members, specifically Tob1/Tob and Tob2, have the most extensive C-terminal regions. As previously reported, overexpression of BTG/Tob proteins is associated with the inhibition of G1 to S-phase cell cycle progression and decreased cell proliferation in a variety of cell types. Tob subfamily proteins have similar anti-proliferative effects on cell cycle progression in cultured tumor cells. An important unresolved question is whether or not they have function in rapidly proliferating cells, such as embryonic stem cells (ESCs). Tob1 and Tob2 were expressed ubiquitously in mouse ESCs (mESCs), suggesting a possible role in early embryonic development and mESCs. To address the above question and explore the possible functions of the Tob subfamily in ESCs, we established ESCs from different genotypic knockout inner cell mass (ICM). We found that Tob1(-/-), Tob2(-/-), and Tob1/2 double knockout (DKO, Tob1(-/-) & Tob2(-/-)) ESCs grew faster than wild type (WT) ESCs without losing pluripotency, and we provide a possible mechanistic explanation for these observations: Tob1 and Tob2 inhibit the cell cycle via degradation of Id3 mRNA, which is a set of directly targeted genes of BMP4 signaling in mESCs that play critical roles in the maintenance of ESC properties. Together, our data suggest that BTG/Tob family protein Tob1 and Tob2 regulation cell proliferation does not compromise the basic properties of mESCs.
Collapse
Affiliation(s)
- Yuanfan Chen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing 100191, China; SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai 200120, China
| | - Chenchen Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing 100191, China; SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai 200120, China
| | - Jenny Wu
- SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai 200120, China
| | - Lingsong Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing 100191, China; SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai 200120, China.
| |
Collapse
|