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Wu L, Zhang M, Zhang R, Yu H, Wang H, Li J, Wang Y, Hu Z, Wang Y, Luo Z, Li L, Wang L, Peng L, Xia T. Down-regulation of OsMYB103L distinctively alters beta-1,4-glucan polymerization and cellulose microfibers assembly for enhanced biomass enzymatic saccharification in rice. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:245. [PMID: 34961560 PMCID: PMC8713402 DOI: 10.1186/s13068-021-02093-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/13/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND As a major component of plant cell walls, cellulose provides the most abundant biomass resource convertible for biofuels. Since cellulose crystallinity and polymerization have been characterized as two major features accounting for lignocellulose recalcitrance against biomass enzymatic saccharification, genetic engineering of cellulose biosynthesis is increasingly considered as a promising solution in bioenergy crops. Although several transcription factors have been identified to regulate cellulose biosynthesis and plant cell wall formation, much remains unknown about its potential roles for genetic improvement of lignocellulose recalcitrance. RESULTS In this study, we identified a novel rice mutant (Osfc9/myb103) encoded a R2R3-MYB transcription factor, and meanwhile generated OsMYB103L-RNAi-silenced transgenic lines. We determined significantly reduced cellulose levels with other major wall polymers (hemicellulose, lignin) slightly altered in mature rice straws of the myb103 mutant and RNAi line, compared to their wild type (NPB). Notably, the rice mutant and RNAi line were of significantly reduced cellulose features (crystalline index/CrI, degree of polymerization/DP) and distinct cellulose nanofibers assembly. These alterations consequently improved lignocellulose recalcitrance for significantly enhanced biomass enzymatic saccharification by 10-28% at p < 0.01 levels (n = 3) after liquid hot water and chemical (1% H2SO4, 1% NaOH) pretreatments with mature rice straws. In addition, integrated RNA sequencing with DNA affinity purification sequencing (DAP-seq) analyses revealed that the OsMYB103L might specifically mediate cellulose biosynthesis and deposition by regulating OsCesAs and other genes associated with microfibril assembly. CONCLUSIONS This study has demonstrated that down-regulation of OsMYB103L could specifically improve cellulose features and cellulose nanofibers assembly to significantly enhance biomass enzymatic saccharification under green-like and mild chemical pretreatments in rice. It has not only indicated a powerful strategy for genetic modification of plant cell walls in bioenergy crops, but also provided insights into transcriptional regulation of cellulose biosynthesis in plants.
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Affiliation(s)
- Leiming Wu
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
- College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingliang Zhang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ran Zhang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Haizhong Yu
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Hailang Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Jingyang Li
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, China
| | - Youmei Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Zhen Hu
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Yanting Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lingqiang Wang
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Liangcai Peng
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Tao Xia
- Biomass & Bioenergy Research Centre, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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2
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Motizuki M, Koinuma D, Yokoyama T, Itoh Y, Omata C, Miyazono K, Saitoh M, Miyazawa K. TGF-β-induced cell motility requires downregulation of ARHGAPs to sustain Rac1 activity. J Biol Chem 2021; 296:100545. [PMID: 33741342 PMCID: PMC8079281 DOI: 10.1016/j.jbc.2021.100545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 01/06/2023] Open
Abstract
Transforming growth factor-β (TGF-β) signaling promotes cancer progression. In particular, the epithelial-mesenchymal transition (EMT) induced by TGF-β is considered crucial to the malignant phenotype of cancer cells. Here, we report that the EMT-associated cellular responses induced by TGF-β are mediated by distinct signaling pathways that diverge at Smad3. By expressing chimeric Smad1/Smad3 proteins in SMAD3 knockout A549 cells, we found that the β4 region in the Smad3 MH1 domain is essential for TGF-β-induced cell motility, but is not essential for other EMT-associated responses including epithelial marker downregulation. TGF-β was previously reported to enhance cell motility by activating Rac1 via phosphoinositide 3-kinase. Intriguingly, TGF-β-dependent signaling mediated by Smad3's β4 region causes the downregulation of multiple mRNAs that encode GTPase activating proteins that target Rac1 (ARHGAPs), thereby attenuating Rac1 inactivation. Therefore, two independent pathways downstream of TGF-β type I receptor contribute cooperatively to sustained Rac1 activation, thereby leading to enhanced cell motility.
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Affiliation(s)
- Mitsuyoshi Motizuki
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Daizo Koinuma
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Yokoyama
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Chiho Omata
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Saitoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan; Center for Medical Education and Science, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan.
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3
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Badri KR, Yue M, Carretero OA, Aramgam SL, Cao J, Sharkady S, Kim GH, Taylor GA, Byron KL, Schuger L. Blood pressure homeostasis is maintained by a P311-TGF-β axis. J Clin Invest 2013; 123:4502-12. [PMID: 24091331 DOI: 10.1172/jci69884] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/18/2013] [Indexed: 12/22/2022] Open
Abstract
P311 is an 8-kDa intracellular protein that is highly conserved across species and is expressed in the nervous system as well as in vascular and visceral smooth muscle cells. P311-null (P311-/-) mice display learning and memory defects, but alterations in their vasculature have not been previously described. Here we report that P311-/- mice are markedly hypotensive with accompanying defects in vascular tone and VSMC contractility. Functional abnormalities in P311-/- mice resulted from decreased total and active levels of TGF-β1, TGF-β2, and TGF-β3 that arise as a specific consequence of decreased translation. Vascular hypofunctionality was fully rescued in vitro and in vivo by exogenous TGF-β1-TGF-β3. Conversely, P311-transgenic (P311(TG)) mice had elevated levels of TGF-β1-TGF-β3 and subsequent hypertension. Consistent with findings attained in mouse models, arteries recovered from hypertensive human patients displayed increased P311 expression. Thus, we identified P311 as the first protein known to modulate TGF-β translation and the first pan-regulator of TGF-β expression under steady-state conditions. Together, our findings point to P311 as a critical blood pressure regulator and establish a potential link between P311 expression and the development of hypertensive disease.
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MESH Headings
- Animals
- Aorta/pathology
- Aorta/physiopathology
- Aortography
- Blood Pressure
- Cells, Cultured
- Female
- Gene Expression
- Gene Expression Regulation
- Homeostasis
- Humans
- Hypotension/genetics
- Hypotension/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Muscle Contraction
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transforming Growth Factor beta/genetics
- Transforming Growth Factor beta/metabolism
- Transforming Growth Factor beta/physiology
- Up-Regulation
- rho GTP-Binding Proteins/metabolism
- rhoA GTP-Binding Protein
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4
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Wang G, Li C, Wang Y, Chen G. Cooperative assembly of Co-Smad4 MH1 with R-Smad1/3 MH1 on DNA: a molecular dynamics simulation study. PLoS One 2013; 8:e53841. [PMID: 23326519 PMCID: PMC3542330 DOI: 10.1371/journal.pone.0053841] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/03/2012] [Indexed: 11/23/2022] Open
Abstract
Background Smads, the homologs of Sma and MAD proteins, play a key role in gene expression regulation in the transforming growth factor-β (TGF-β) signaling pathway. Recent experimental studies have revealed that Smad4/R-Smad heterodimers bound on DNA are energetically more favorable than homodimeric R-Smad/R-Smad complexes bound on DNA, which indicates that Smad4 might act as binding vehicle to cooperatively assemble with activated R-Smads on DNA in the nucleus. However, the details of interaction mechanism for cooperative recruitment of Smad4 protein to R-Smad proteins on DNA, and allosteric communication between the Smad4-DNA and R-Smad-DNA interfaces via DNA mediating are not yet clear so far. Methodology In the present work, we have constructed a series of Smadn+DNA+Smadn (n = 1, 3, 4) models and carried out molecular dynamics simulations, free energy calculations and DNA dynamics analysis for them to study the interaction properties of Smadn (n = 1, 3, 4) with DNA molecule. Results The results revealed that the binding of Smad4 protein to DNA molecule facilitates energetically the formation of the heteromeric Smad4+DNA+Smad1/3 complex by increasing the affinity of Smad1/3 with DNA molecule. Further investigations through the residue/base motion correlation and DNA dynamics analyses predicted that the binding of Smad4 protein to DNA molecule in the heteromeric Smad4+DNA+Smad1/3 model induces an allosteric communication from the Smad4-DNA interface to Smad1/Smad3-DNA interface via DNA base-pair helical motions, surface conformation changes and new hydrogen bond formations. The present work theoretically explains the mechanism of cooperative recruitment of Smad4 protein to Smad1/3 protein via DNA-mediated indirect readout mode in the nucleus.
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Affiliation(s)
- Guihong Wang
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic China
| | - Chaoqun Li
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic China
| | - Yan Wang
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic China
- * E-mail: (YW); (GC)
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic China
- * E-mail: (YW); (GC)
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5
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Matsumoto Y, Otsuka F, Hino J, Miyoshi T, Takano M, Miyazato M, Makino H, Kangawa K. Bone morphogenetic protein-3b (BMP-3b) inhibits osteoblast differentiation via Smad2/3 pathway by counteracting Smad1/5/8 signaling. Mol Cell Endocrinol 2012; 350:78-86. [PMID: 22155034 DOI: 10.1016/j.mce.2011.11.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/17/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
Despite the involvement of BMP-3b (also called GDF-10) in osteogenesis, embryogenesis and adipogenesis, the functional receptors and intracellular signaling of BMP-3b have yet to be elucidated. In the present study, we investigated the cellular mechanism of BMP-3b in osteoblast differentiation using mouse myoblastic C2C12 cells. BMP-3b stimulated activin/TGF-β-responsive promoter activities. The stimulatory actions of BMP-3b on activin/TGF-β-responsive activities were suppressed by co-treatment with BMP-2. BMP-responsive promoter activities stimulated by BMP-2 were significantly inhibited by treatment with BMP-3b. BMP-3b suppressed the expression of osteoblastic markers including Runx2, osteocalcin and type-1 collagen induced by BMP-2, -4, -6 and -7. BMP-2-induced Smad1/5/8 phosphorylation and mRNA levels of the BMP target gene Id-1 were suppressed by co-treatment with BMP-3b, although BMP-3b failed to activate Smad1/5/8 signaling. Of interest, the BMP-3b suppression of BMP-2-induced Id-1 expression was not observed in cells overexpressing Smad4 molecules. On the other hand, BMP-3b directly activated Smad2/3 phosphorylation and activin/TGF-β target gene PAI-1 mRNA expression, while BMP-2 suppressed BMP-3b-induced Smad2/3 signal activation. BMP-2 inhibition of BMP-3b-induced PAI-1 expression was also reversed by overexpression of Smad4. Analysis using inhibitors for BMP-Smad1/5/8 pathways revealed that these BMP-3b effects were mediated via receptors other than ALK-2, -3 and -6. Furthermore, results of inhibitory studies using extracellular domains for BMP receptor constructs showed that the activity of BMP-3b was functionally facilitated by a combination of ALK-4 and ActRIIA. Collectively, BMP-3b plays an inhibitory role in the process of osteoblast differentiation, in which BMP-3b and BMP-2 are mutually antagonistic possibly by competing with the availability of Smad4.
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Affiliation(s)
- Yoshinori Matsumoto
- Department of Medicine and Clinical Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kitaku, Okayama 700-8558, Japan
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6
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Dempe S, Stroh-Dege AY, Schwarz E, Rommelaere J, Dinsart C. SMAD4: a predictive marker of PDAC cell permissiveness for oncolytic infection with parvovirus H-1PV. Int J Cancer 2010; 126:2914-27. [PMID: 19856310 DOI: 10.1002/ijc.24992] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) represents the eighth frequent solid tumor and fourth leading cause of cancer death. Because current treatments against PDAC are still unsatisfactory, new anticancer strategies are required, including oncolytic viruses. Among these, autonomous parvoviruses (PV), like MVMp (minute virus of mice) and H-1PV are being explored as candidates for cancer gene therapy. Human PDAC cell lines were identified to display various susceptibilities to an infection with H-1PV. The correlation between the integrity of the transcription factor SMAD4, mutated in 50% of all PDAC, and H-1PV permissiveness was particularly striking. Indeed, mutation or deletion of SMAD4 dramatically reduced the activity of the P4 promoter and, consequently, the accumulation of the pivotal NS1 protein. By means of DNA affinity immunoblotting, novel binding sites for SMAD4 and c-JUN transcription factors could be identified in the P4 promoter of H-1PV. The overexpression of wild-type SMAD4 in deficient cell lines (AsPC-1, Capan-1) stimulated the activity of the P4 promoter, whereas interference of endogenous SMAD4 function with a dominant-negative mutant decreased the viral promoter activity in wild-type SMAD4-expressing cells (Panc-1, MiaPaCa-2) reducing progeny virus production. In conclusion, the importance of members of the SMAD family for H-1PV early promoter P4 activity should guide us to select SMAD4-positive PDACs, which may be possible targets for an H-1PV-based cancer therapy.
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Affiliation(s)
- Sebastian Dempe
- Abt F010, Infection and Cancer Program, Tumor Virology Division, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg, Germany
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7
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BabuRajendran N, Palasingam P, Narasimhan K, Sun W, Prabhakar S, Jauch R, Kolatkar PR. Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors. Nucleic Acids Res 2010; 38:3477-88. [PMID: 20147459 PMCID: PMC2879523 DOI: 10.1093/nar/gkq046] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Smad1 is a downstream effector of the BMP signaling pathway that binds regulatory DNA to execute gene expression programs leading to, for example, the maintenance of pluripotency in mice. On the contrary, the TGF-β-activated Smad3 triggers strikingly different programs such as mesodermal differentiation in early development. Because Smad1 and Smad3 contain identical amino acids at the DNA contact interface it is unclear how they elicit distinctive bioactivities. Here, we report the crystal structure of the MH1 domain of Smad1 bound to a palindromic Smad binding element. Surprisingly, the DNA contact interface of Smad1 is drastically rearranged when compared to Smad3. The N-terminal helix 1 of Smad1 is dislodged from its intramolecular binding site and adopts a domain swapped arrangement with a symmetry-related molecule. As a consequence, helix 2 kinks away from the double helix disabling several key phosphate backbone interactions. Thermal melting analysis corroborates a decompacted conformation of Smad1 and DNA binding assays indicate a lower overall affinity of Smad1 to DNA but increased cooperativity when binding to palindromic DNA motifs. These findings suggest that Smad1 and Smad3 evolved differential qualities to assemble on composite DNA elements and to engage in co-factor interactions by remodeling their N-termini.
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Affiliation(s)
- Nithya BabuRajendran
- Laboratory of Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore
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8
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Inagaki K, Otsuka F, Miyoshi T, Yamashita M, Takahashi M, Goto J, Suzuki J, Makino H. p38-Mitogen-activated protein kinase stimulated steroidogenesis in granulosa cell-oocyte cocultures: role of bone morphogenetic proteins 2 and 4. Endocrinology 2009; 150:1921-30. [PMID: 19022884 DOI: 10.1210/en.2008-0851] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Roles of the p38-MAPK pathway in steroidogenesis were investigated using coculture of rat granulosa cells with oocytes. Activin and FSH readily phosphorylated p38 in granulosa cells. Activin effect on p38 phosphorylation was abolished by a selective activin receptor-like kinase-4, -5, and -7 inhibitor, SB431542. SB431542 decreased FSH-induced estradiol but had no effect on progesterone production with a marginal cAMP reduction, suggesting that endogenous activin is primarily involved in estradiol synthesis. FSH-induced p38 activation was not affected either by SB431542 or follistatin, suggesting that FSH activates p38 not through the endogenous activin. Bone morphogenetic protein (BMP)-2 and BMP-4 also enhanced FSH-induced p38 phosphorylation, which was augmented by oocyte action. A specific p38 inhibitor, SB203580, decreased FSH-induced estradiol production. However, FSH-induced cAMP accumulation was not changed by SB203580, suggesting that p38 activation is linked to estradiol synthesis independently of cAMP. BMP-2 and BMP-4 inhibited FSH- and forskolin (FSK)-induced progesterone and cAMP synthesis regardless of oocyte action. BMP-2, BMP-4, and activin increased FSH-induced estradiol production, which was enhanced in the presence of oocytes. In contrast to activin that enhanced FSK-induced estradiol, BMP-2 and BMP-4 had no effects on FSK-induced estradiol production, suggesting that BMP-2 and BMP-4 directly activate FSH-receptor signaling. Given that activin increased, but BMP-2 and BMP-4 decreased, FSH-induced cAMP, the effects of BMP-2 and BMP-4 on estradiol enhancement appeared to be diverged from the cAMP-protein kinase A pathway. Thus, BMP-2 and BMP-4 differentially regulate steroidogenesis by stimulating FSH-induced p38 and suppressing cAMP. The former is involved in estradiol production and enhanced by oocyte action, whereas the latter leads to reduction of progesterone synthesis.
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Affiliation(s)
- Kenichi Inagaki
- Department of Medicine and Clinical Science, Okayama University Graduate School of Medicine, Okayama City, Japan
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9
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Makkar P, Metpally RPR, Sangadala S, Reddy BVB. Modeling and analysis of MH1 domain of Smads and their interaction with promoter DNA sequence motif. J Mol Graph Model 2008; 27:803-12. [PMID: 19157940 DOI: 10.1016/j.jmgm.2008.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Revised: 12/09/2008] [Accepted: 12/12/2008] [Indexed: 01/11/2023]
Abstract
The Smads are a group of related intracellular proteins critical for transmitting the signals to the nucleus from the transforming growth factor-beta (TGF-beta) superfamily of proteins at the cell surface. The prototypic members of the Smad family, Mad and Sma, were first described in Drosophila and Caenorhabditis elegans, respectively. Related proteins in Xenopus, Humans, Mice and Rats were subsequently identified, and are now known as Smads. Smad protein family members act downstream in the TGF-beta signaling pathway mediating various biological processes, including cell growth, differentiation, matrix production, apoptosis and development. Smads range from about 400-500 amino acids in length and are grouped into the receptor-regulated Smads (R-Smads), the common Smads (Co-Smads) and the inhibitory Smads (I-Smads). There are eight Smads in mammals, Smad1/5/8 (bone morphogenetic protein regulated) and Smad2/3 (TGF-beta/activin regulated) are termed R-Smads, Smad4 is denoted as Co-Smad and Smad6/7 are inhibitory Smads. A typical Smad consists of a conserved N-terminal Mad Homology 1 (MH1) domain and a C-terminal Mad Homology 2 (MH2) domain connected by a proline rich linker. The MH1 domain plays key role in DNA recognition and also facilitates the binding of Smad4 to the phosphorylated C-terminus of R-Smads to form activated complex. The MH2 domain exhibits transcriptional activation properties. In order to understand the structural basis of interaction of various Smads with their target proteins and the promoter DNA, we modeled MH1 domain of the remaining mammalian Smads based on known crystal structures of Smad3-MH1 domain bound to GTCT Smad box DNA sequence (1OZJ). We generated a B-DNA structure using average base-pair parameters of Twist, Tilt, Roll and base Slide angles. We then modeled interaction pose of the MH1 domain of Smad1/5/8 to their corresponding DNA sequence motif GCCG. These models provide the structural basis towards understanding functional similarities and differences among various Smads.
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Affiliation(s)
- Pooja Makkar
- Graduate Center Biochemistry Department and Laboratory of Bioinformatics &in silico Drug Design, Queens College of City University of New York, 65-30 Kissena Blvd, Flushing, NY 11367, USA
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10
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Gao S, Laughon A. Flexible interaction of Drosophila Smad complexes with bipartite binding sites. ACTA ACUST UNITED AC 2007; 1769:484-96. [PMID: 17610966 DOI: 10.1016/j.bbaexp.2007.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2006] [Revised: 04/24/2007] [Accepted: 05/29/2007] [Indexed: 01/11/2023]
Abstract
A subset of BMP-responsive enhancer elements are characterized by pairing of a GC-rich Smad1 binding site and an SBE-type Smad4 binding site. Such paired, or bipartite, sites are in some cases just 5 bp apart and thus might be contacted by a single Smad1-Smad4 complex. Other potential pairings are separated as much as 60 bp but it is not known whether such longer distances can be spanned by a Smad1-Smad4 complex, indeed binding of native Smad1-Smad4 complexes to any of these bipartite elements has yet to be reported. Here we report that a complex of the homologous Drosophila Smad proteins, Mad and Medea, is capable of concerted binding to GC-rich and SBE sites separated by as much as 20 bp. The wider the separation, the more severely binding affinity was reduced by shortening of the linker region that tethers the DNA binding domain of Medea. In contrast, length of the Mad linker did not affect the allowed distance between paired sites, rather it contributes specifically to Mad contact with the GC-rich site. Finally, we show that Smad1 and Smad4 can participate in binding to bipartite sites.
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Affiliation(s)
- Sheng Gao
- Laboratory of Genetics, University of Wisconsin, 425G Henry Mall, Madison, WI 53706, USA
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11
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Gao S, Laughon A. Decapentaplegic-responsive Silencers Contain Overlapping Mad-binding Sites. J Biol Chem 2006; 281:25781-90. [PMID: 16829514 DOI: 10.1074/jbc.m603371200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Smad proteins regulate transcription in response to transforming growth factor-beta signaling pathways by binding to two distinct types of DNA sites. The sequence GTCT is recognized by all receptor-activated Smads and by Smad4. The subset of Smads that responds to bone morphogenetic protein signaling recognizes a distinct class of GC-rich sites in addition to GTCT. Recent work has shown that Drosophila Mad protein, the homologue of bone morphogenetic protein rSmads, binds to GRCGNC sites through the same MH1 domain beta-hairpin interface used to contact GTCT sites. However, binding to GRCGNC requires base-specific contact by two Mad proteins, and here we provide evidence that this is achieved by contact of the two Mad subunits that overlap across the two central base pairs of the site. This topology is supported by results indicating that His-93, which is located at the tip of the Mad beta-hairpin, is in close proximity to base pairs 2 and 5. Also consistent with the model is disruption of binding by mutation of Glu-39 and Glu-40, which are predicted to lie at the interface of the two overlapping Mad MH1 domains. As predicted from the overlapping model, binding is disrupted by insertion of 1 bp in the middle of the site, whereas insertion of 2 bp creates abutting sites that can be bound by the Mad-Medea heterotrimer without requiring Glu-39 and Glu-40. Overlapping Mad sites predominate in decapentaplegic response elements, consistent with a high degree of specificity in response to signaling.
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Affiliation(s)
- Sheng Gao
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
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Gao S, Steffen J, Laughon A. Dpp-responsive Silencers Are Bound by a Trimeric Mad-Medea Complex. J Biol Chem 2005; 280:36158-64. [PMID: 16109720 DOI: 10.1074/jbc.m506882200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transcriptional regulation by transforming growth factor-beta signaling is mediated by the Smad family of transcription factors. It is generally accepted that Smads must interact with other transcription factors to bind to their targets. However, recently it has been shown that a complex of the Drosophila Smad proteins, Mad and Medea, binds with high affinity to silencer elements that repress brinker and bag of marbles in response to Dpp signaling. Here we report that these silencers are bound by a heterotrimer containing two Mad subunits and one Medea subunit. We found that the MH1 domains of all three subunits contributed directly to sequence-specific DNA contact, thus accounting for the exceptionally high stability of the Smad-silencer complex. The Medea MH1 domain binds to a canonical Smad box (GTCT), whereas the Mad MH1 domains bind to a GC-rich sequence resembling Mad binding sites previously identified in Dpp-responsive enhancer elements. The consensus for this sequence, GRCGNC, differs from that of the canonical Smad box, but we found that Mad binding nonetheless required the same beta-hairpin amino acids that mediate base-specific contact with GTCT. Binding was also affected by alanine substitutions in Mad and Med at a subset of basic residues within and flanking helix 2, indicating a contribution to binding of the GRCGNC and GTCT sites. The slight alteration of the Dpp silencers caused them to activate transcription in response to Dpp signaling, indicating that the potential for Smad complexes to recognize specific targets need not be limited to repression.
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Affiliation(s)
- Sheng Gao
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
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Kurisaki K, Kurisaki A, Valcourt U, Terentiev AA, Pardali K, Ten Dijke P, Heldin CH, Ericsson J, Moustakas A. Nuclear factor YY1 inhibits transforming growth factor beta- and bone morphogenetic protein-induced cell differentiation. Mol Cell Biol 2003; 23:4494-510. [PMID: 12808092 PMCID: PMC164850 DOI: 10.1128/mcb.23.13.4494-4510.2003] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2002] [Revised: 12/19/2002] [Accepted: 04/07/2003] [Indexed: 12/19/2022] Open
Abstract
Smad proteins transduce transforming growth factor beta (TGF-beta) and bone morphogenetic protein (BMP) signals that regulate cell growth and differentiation. We have identified YY1, a transcription factor that positively or negatively regulates transcription of many genes, as a novel Smad-interacting protein. YY1 represses the induction of immediate-early genes to TGF-beta and BMP, such as the plasminogen activator inhibitor 1 gene (PAI-1) and the inhibitor of differentiation/inhibitor of DNA binding 1 gene (Id-1). YY1 inhibits binding of Smads to their cognate DNA elements in vitro and blocks Smad recruitment to the Smad-binding element-rich region of the PAI-1 promoter in vivo. YY1 interacts with the conserved N-terminal Mad homology 1 domain of Smad4 and to a lesser extent with Smad1, Smad2, and Smad3. The YY1 zinc finger domain mediates the association with Smads and is necessary for the repressive effect of YY1 on Smad transcriptional activity. Moreover, downregulation of endogenous YY1 by antisense and small interfering RNA strategies results in enhanced transcriptional responses to TGF-beta or BMP. Ectopic expression of YY1 inhibits, while knockdown of endogenous YY1 enhances, TGF-beta- and BMP-induced cell differentiation. In contrast, overexpression or knockdown of YY1 does not affect growth inhibition induced by TGF-beta or BMP. Accordingly, YY1 does not interfere with the regulation of immediate-early genes involved in the TGF-beta growth-inhibitory response, the cell cycle inhibitors p15 and p21, and the proto-oncogene c-myc. In conclusion, YY1 represses Smad transcriptional activities in a gene-specific manner and thus regulates cell differentiation induced by TGF-beta superfamily pathways.
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Affiliation(s)
- Keiko Kurisaki
- Ludwig Institute for Cancer Research, Biomedical Center, SE-751 24 Uppsala, Sweden
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14
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Mizuide M, Hara T, Furuya T, Takeda M, Kusanagi K, Inada Y, Mori M, Imamura T, Miyazawa K, Miyazono K. Two short segments of Smad3 are important for specific interaction of Smad3 with c-Ski and SnoN. J Biol Chem 2003; 278:531-6. [PMID: 12426322 DOI: 10.1074/jbc.c200596200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
c-Ski and SnoN are transcriptional co-repressors that inhibit transforming growth factor-beta signaling through interaction with Smad proteins. Among receptor-regulated Smads, c-Ski and SnoN bind more strongly to Smad2 and Smad3 than to Smad1. Here, we show that c-Ski and SnoN bind to the "SE" sequence in the C-terminal MH2 domain of Smad3, which is exposed on the N-terminal upper side of the toroidal structure of the MH2 oligomer. The "QPSMT" sequence, located in the vicinity of SE, supports the interaction with c-Ski and SnoN. Sequences similar to SE and QPSMT are found in Smad2, but not in Smad1. The N-terminal MH1 domain and linker region of Smad3 protrude from the N-terminal upper side of the MH2 oligomer toroid. Smurf2 induces ubiquitin-dependent degradation of SnoN, since it appears to be located close to SnoN through binding to the linker region of Smad2. In contrast, transcription factors Mixer and FoxH3 (FAST1) bind to the bottom side of the Smad3 MH2 toroid; therefore, c-Ski does not affect the interaction of Smads with these transcription factors. Our findings thus demonstrate the stoichiometry of how multiple molecules can associate with the Smad oligomers and how the Smad-interacting proteins functionally interact with each other.
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Affiliation(s)
- Masafumi Mizuide
- Department of Biochemistry, The Cancer Institute of the Japanese Foundation for Cancer Research (JFCR), Tokyo 170-8455, Japan
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Miyazawa K, Shinozaki M, Hara T, Furuya T, Miyazono K. Two major Smad pathways in TGF-beta superfamily signalling. Genes Cells 2002; 7:1191-204. [PMID: 12485160 DOI: 10.1046/j.1365-2443.2002.00599.x] [Citation(s) in RCA: 509] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Members of the transforming growth factor-beta (TGF-beta) superfamily bind to two different serine/threonine kinase receptors, i.e. type I and type II receptors. Upon ligand binding, type I receptors specifically activate intracellular Smad proteins. R-Smads are direct substrates of type I receptors; Smads 2 and 3 are specifically activated by activin/nodal and TGF-beta type I receptors, whereas Smads 1, 5 and 8 are activated by BMP type I receptors. Nearly 30 proteins have been identified as members of the TGF-beta superfamily in mammals, and can be classified based on whether they activate activin/TGF-beta-specific R-Smads (AR-Smads) or BMP-specific R-Smads (BR-Smads). R-Smads form complexes with Co-Smads and translocate into the nucleus, where they regulate the transcription of target genes. AR-Smads bind to various proteins, including transcription factors and transcriptional co-activators or co-repressors, whereas BR-Smads interact with other proteins less efficiently than AR-Smads. Id proteins are induced by BR-Smads, and play important roles in exhibiting some biological effects of BMPs. Understanding the mechanisms of TGF-beta superfamily signalling is thus important for the development of new ways to treat various clinical diseases in which TGF-beta superfamily signalling is involved.
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Affiliation(s)
- Keiji Miyazawa
- Department of Molecular Pathology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan
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Welt C, Sidis Y, Keutmann H, Schneyer A. Activins, inhibins, and follistatins: from endocrinology to signaling. A paradigm for the new millennium. Exp Biol Med (Maywood) 2002; 227:724-52. [PMID: 12324653 DOI: 10.1177/153537020222700905] [Citation(s) in RCA: 237] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
It has been 70 years since the name inhibin was used to describe a gonadal factor that negatively regulated pituitary hormone secretion. The majority of this period was required to achieve purification and definitive characterization of inhibin, an event closely followed by identification and characterization of activin and follistatin (FS). In contrast, the last 15-20 years saw a virtual explosion of information regarding the biochemistry, physiology, and biosynthesis of these proteins, as well as identification of activin receptors, and a unique mechanism for FS action-the nearly irreversible binding and neutralization of activin. Many of these discoveries have been previously summarized; therefore, this review will cover the period from the mid 1990s to present, with particular emphasis on emerging themes and recent advances. As the field has matured, recent efforts have focused more on human studies, so the endocrinology of inhibin, activin, and FS in the human is summarized first. Another area receiving significant recent attention is local actions of activin and its regulation by both FS and inhibin. Because activin and FS are produced in many tissues, we chose to focus on a few particular examples with the most extensive experimental support, the pituitary and the developing follicle, although nonreproductive actions of activin and FS are also discussed. At the cellular level, it now seems that activin acts largely as an autocrine and/or paracrine growth factor, similar to other members of the transforming growh factor beta superfamily. As we discuss in the next section, its actions are regulated extracellularly by both inhibin and FS. In the final section, intracellular mediators and modulators of activin signaling are reviewed in detail. Many of these are shared with other transforming growh factor beta superfamily members as well as unrelated molecules, and in a number of cases, their physiological relevance to activin signal propagation remains to be elucidated. Nevertheless, taken together, recent findings suggest that it may be more appropriate to consider a new paradigm for inhibin, activin, and FS in which activin signaling is regulated extracellularly by both inhibin and FS whereas a number of intracellular proteins act to modulate cellular responses to these activin signals. It is therefore the balance between activin and all of its modulators, rather than the actions of any one component, that determines the final biological outcome. As technology and model systems become more sophisticated in the next few years, it should become possible to test this concept directly to more clearly define the role of activin, inhibin, and FS in reproductive physiology.
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Affiliation(s)
- Corrine Welt
- Reproductive Endocrine Unit and Endocrine Unit, Massachusetts General Hospital, Boston 02114, USA
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López-Rovira T, Chalaux E, Massagué J, Rosa JL, Ventura F. Direct binding of Smad1 and Smad4 to two distinct motifs mediates bone morphogenetic protein-specific transcriptional activation of Id1 gene. J Biol Chem 2002; 277:3176-85. [PMID: 11700304 DOI: 10.1074/jbc.m106826200] [Citation(s) in RCA: 242] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bone morphogenetic proteins (BMPs) are potent inhibitors of myoblast differentiation and inducers of bone formation both in vivo and in vitro. Expression of Id1, a negative regulator of basic helix-loop-helix transcription factors, is up-regulated by BMPs and contributes to the antimyogenic effects of this family of cytokines. In this report, we have identified a specific BMP-2 immediate early response enhancer in the human Id1 gene. Transcriptional activation of the enhancer was increased by overexpression of BMP-responsive Smads, and Smad4 and was completely abrogated in Smad4-deficient cells. Deletion analysis demonstrates that the responsive region is composed of two separate DNA binding elements, a set of overlapping GC boxes, which bind BMP-regulated Smads upon BMP stimulation, and three repeats of CAGAC boxes. Gel shift and oligonucleotide pull-down assays demonstrated that these two types of motifs were capable of binding their corresponding Smads. However, deletion or mutation of either DNA binding element was nonadditive, since disruption of either GC or CAGAC boxes resulted in complete or severe loss of BMP-2 responsiveness. These data suggest the simultaneous requirement of two independent DNA binding elements to allow functional cooperativity of BMP-regulated Smads and Smad4 in BMP-activated gene promoters.
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Affiliation(s)
- Teresa López-Rovira
- Departament de Ciències Fisiològiques II, Campus de Bellvitge, Universitat de Barcelona, Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Spain
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Abstract
Smad proteins transduce signals from transforming growth factor-β (TGF-β) superfamily ligands that regulate cell proliferation, differentiation and death through activation of receptor serine/threonine kinases. Phosphorylation of receptor-activated Smads (R-Smads) leads to formation of complexes with the common mediator Smad (Co-Smad), which are imported to the nucleus. Nuclear Smad oligomers bind to DNA and associate with transcription factors to regulate expression of target genes. Alternatively, nuclear R-Smads associate with ubiquitin ligases and promote degradation of transcriptional repressors, thus facilitating target gene regulation by TGF-β. Smads themselves can also become ubiquitinated and are degraded by proteasomes. Finally, the inhibitory Smads (I-Smads) block phosphorylation of R-Smads by the receptors and promote ubiquitination and degradation of receptor complexes, thus inhibiting signalling.
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Affiliation(s)
- A Moustakas
- Ludwig Institute for Cancer Research, Box 595, SE-751 24 Uppsala, Sweden.
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