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PLoS One. 2011; 6(10): e25871.
Published online Oct 18, 2011. doi:  10.1371/journal.pone.0025871
PMCID: PMC3196520
The E3 Ubiquitin Ligase Activity of Trip12 Is Essential for Mouse Embryogenesis
Masashi Kajiro,1 Mai Tsuchiya,1 Yoh-ichi Kawabe,2 Ryohei Furumai,2 Naoya Iwasaki,1 Yuki Hayashi,1 Miyuki Katano,2 Yuka Nakajima,1,2 Natsuka Goto,1 Tatsuya Watanabe,1 Akiko Murayama,1,2 Hisashi Oishi,3 Masatsugu Ema,3 Satoru Takahashi,3 Hiroyuki Kishimoto,1,2 and Junn Yanagisawa1,2*
1Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba Science City, Ibaraki, Japan
2Center for Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba Science City, Ibaraki, Japan
3Department of Anatomy and Embryology, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tennoudai, Tsukuba, Japan
Patrick Callaerts, Editor
VIB & Katholieke Universiteit Leuven, Belgium
* E-mail: junny/at/agbi.tsukuba.ac.jp
Conceived and designed the experiments: M. Kajiro YK JY. Performed the experiments: M. Kajiro MT YK RF NI YH M. Katano HO ME ST HK JY. Analyzed the data: M. Kajiro MT YK HK JY. Contributed reagents/materials/analysis tools: YN NG TW AM. Wrote the paper: M. Kajiro HK JY.
Received February 28, 2011; Accepted September 13, 2011.
Protein ubiquitination is a post-translational protein modification that regulates many biological conditions [1], [2], [3], [4]. Trip12 is a HECT-type E3 ubiquitin ligase that ubiquitinates ARF and APP-BP1 [5], [6]. However, the significance of Trip12 in vivo is largely unknown. Here we show that the ubiquitin ligase activity of Trip12 is indispensable for mouse embryogenesis. A homozygous mutation in Trip12 (Trip12mt/mt) that disrupts the ubiquitin ligase activity resulted in embryonic lethality in the middle stage of development. Trip12mt/mt embryos exhibited growth arrest and increased expression of the negative cell cycle regulator p16 [7], [8], [9], [10]. In contrast, Trip12mt/mt ES cells were viable. They had decreased proliferation, but maintained both the undifferentiated state and the ability to differentiate. Trip12mt/mt ES cells had increased levels of the BAF57 protein (a component of the SWI/SNF chromatin remodeling complex) and altered gene expression patterns. These data suggest that Trip12 is involved in global gene expression and plays an important role in mouse development.
Protein ubiquitination plays an important role in various cellular events [1], [2], [3], [4]. Ubiquitination occurs through sequential steps that are catalyzed by activating (E1), conjugating (E2), and ligase (E3) enzymes. In this reaction, the specificity for distinct substrates is determined by the ubiquitin ligase enzymes. From a mechanistic standpoint, ubiquitin ligases fall into two groups: HECT domain E3s and RING domain E3s [11], [12], [13]. The HECT family contains a diverse N-terminal region and a conserved C-terminal HECT domain, which has a reactive Cys residue. HECT-type ubiquitin ligases form a thioester intermediate with ubiquitin at the conserved Cys residue before transferring ubiquitin to the target proteins [12], [13].
Trip12 encodes a HECT domain containing an E3 ubiquitin ligase, which was originally identified as a thyroid hormone receptor-interacting protein in a yeast two-hybrid screen [14]. Recent reports indicate that Trip12 ubiquitinates ARF and APP-BP1 and regulates BAF57 turnover [5], [6], [15]. In this study, we showed that the ubiquitin ligase activity of Trip12 is essential for mouse development. We generated mice in which the coding region of the HECT domain within Trip12 was mutated (Trip12mt/mt mice). Targeted inactivation of Trip12 resulted in abnormal p16 induction and embryonic lethality in mice. We also found that Trip12mt/mt ES cells were viable but had decreased cell cycle progression. Trip12mt/mt ES cells had accumulated levels of the BAF57 protein and different gene expression patterns. Our data suggest that Trip12 is involved in global gene expression and is essential for mouse development.
Generation of Trip12 mutant mice
To study the function of Trip12 in vivo, we generated Trip12 mutant mice by replacing exon 33 with FLAG and HA epitope tag sequences in frame and a neomycin resistant gene. This mutant Trip12 lacks the catalytic core for the ubiquitin ligase activity and has FLAG and HA epitope sequences at the C-terminus (Fig. 1A). The targeting vector was linearized, electroporated into ES cells and ES cells were grown under G418 selection. Selected ES cell clones were verified by Southern blot analysis and several clones were correctly targeted (Fig. 1B). We also detected the mutant Trip12 proteins in the targeted clones by Western blotting using an anti-HA antibody (Fig. 1C). Heterozygous Trip12+/mt mice were viable and fertile and did not exhibit any overt phenotype. To elucidate the Trip12 expression pattern in mouse embryos, anti-HA staining was performed. As shown in Fig. 1D, Trip12 is ubiquitously expressed in the embryo at E9.5 (Fig. 1D).
Figure 1
Figure 1
Generation of Trip12 mutant mice.
TRIP12 ubiquitin ligase activity is essential for mouse embryogenesis
Trip12+/mt mice were intercrossed in order to produce Trip12mt/mt mice. However, no Trip12mt/mt mice were generated, suggesting that the ubiquitin ligase activity of Trip12 is essential for mouse development. To characterize the timing of this embryonic lethality, embryos derived from the Trip12+/mt intercross were genotyped at different stages of gestation. Trip12+/+, Trip12+/mt, and Trip12mt/mt embryos were born at the expected Mendelian ratio and were viable up to E8.5, while no Trip12mt/mt embryos were observed between E11.5 and E13.5 (Table 1). From these results, we concluded that Trip12 plays an important role in mouse embryogenesis.
Table 1
Table 1
Genotypes of the offspring from Trip12+/mt intercrosses.
Phenotypes of Trip12mt/mt embryos
To characterize the nature of this embryonic lethality, we studied the morphology of embryos from timed Trip12+/mt intercrosses at different stages of gestation. An examination of these embryos at various developmental stages revealed that the development of Trip12mt/mt embryos appeared to be delayed at E8.5 (Fig. 2A). Despite this developmental delay, there were no gross morphological abnormalities in Trip12mt/mt embryos. We also confirmed that the number of somites was decreased in Trip12mt/mt embryos compared to wild-type embryos at E9.5 (Fig. 2B).
Figure 2
Figure 2
Analysis of wild-type (+/+) and Trip12 mutant (mt/mt) embryos.
The Trip12mt/mt embryos were further characterized histologically at different developmental stages. In addition to a developmental delay, Trip12mt/mt embryos had abnormal placenta formation (Fig. 2C). Normal labyrinth formation was not observed and a number of erythrocytes accumulated in the placenta of Trip12mt/mt embryos (Fig. 2C right panel). This phenotype might be caused by impaired development of the allantois [16].
Given Trip12 enzymatic activity which is involved in ARF regulation (4), we examined whether mutant show altered expression of ARF and related proteins which could explain the developmental arrest of Trip12mt/mt embryos. Therefore, we examined the expression levels of several cell cycle-related genes and found that p16 and ARF expression levels were increased in Trip12mt/mt embryos (Fig. 2D). p16 is a cyclin-dependent kinase inhibitor and ARF increases p53 protein stability and promotes p53-dependent cell cycle arrest [7], [8], [9], [10]. However, the expression level of p21, a p53 target gene, was virtually unchanged. In addition, mutant embryo didn't show increased apoptosis compared to wild type embryo at corresponding developmental stage (Fig. S1). These data indicate that the embryonic lethality of Trip12mt/mt mice may be caused by abnormal p16 induction rather than p53 activation.
Generation and characterization of Trip12mt/mt ES cells
To further investigate the function of Trip12, we generated two Trip12mt/mt ES cell clones [17 and #2] (Fig. 3A, 3B, and 3C). We examined the ability of Trip12mt/mt ES cells to self-renew and differentiate. The expression levels of Nanog and Oct-4 were comparable in the two Trip12mt/mt ES cell clones and wild-type cell cultures with or without LIF (Fig. 3D). To assess whether ES cell differentiation was affected, we compared embryoid body (EB) formation on days 0 and 10. Trip12mt/mt ES cells displayed the same EB morphology (data not shown), and the expression patterns of endodermal (AFP)-, mesodermal (Flk-1)-, and ectodermal (NCAM)-specific genes were also similar between wild-type and Trip12mt/mt ES cells (Fig. 3E). These results suggest that Trip12 has a minor role in ES cell differentiation.
Figure 3
Figure 3
Generation and characterization of Trip12 mutant (mt/mt) ES cells.
Trip12mt/mt ES cells exhibit cell cycle defects
Next, we tested whether the Trip12 mutation leads to a defect in cell proliferation. The MTT assay showed that Trip12mt/mt ES cells had decreased cell growth (Fig. 4A). Therefore, we analyzed cell cycle progression by flow cytometry, and found that the G2-M and SubG1 populations were increased in Trip12mt/mt ES cells (Fig. 4B). We further examined the expression levels of p16, ARF, and p21. Unexpectedly, the expression levels of these genes were virtually unchanged in the cells (Fig. 4C). It was previously reported that Trip12 ubiquitinates ARF and inhibits p53-dependent transcription [6]. However, there were no detectable alterations in p53-related protein levels in Trip12mt/mt ES cells (Fig. 4D).
Figure 4
Figure 4
Cell cycle defects in Trip12 mutant (mt/mt) ES cells.
Trip12 negatively regulates BAF57 protein stability and is involved in global gene expression in ES cells
Recent reports also suggest that Trip12 regulates BAF57 protein turnover [15]. Therefore, we examined whether inactivation of the Trip12 ubiquitin ligase activity affects the stability of BAF57. As shown in Fig. 5A, the endogenous BAF57 protein levels were increased in Trip12mt/mt ES cells (Fig. 5A). We also confirmed that endogenous BAF57 interacts with Trip12mt from targeted allele in ES cells (Fig. 5B). In addition, cycloheximide experiments showed that the turnover rate of endogenous BAF57 was decreased in Trip12mt/mt ES cells (t1/2[dbl greater-than sign]6 h) compared to that in wild-type cells (t1/2≈4 h) (Fig. 5C). As shown in Fig. 5D, ectopically expressed wild type and mutant Trip12 were interacting with GST-BAF57 and mutant Trip12 showed stronger interaction than wild type suggesting that loss of catalytic activity of Trip12 resulted in decreased dissociation of BAF57 from Trip12. These data demonstrate that the ubiquitin ligase activity of Trip12 is required for BAF57 turnover in ES cells. BAF57 is a component of the SWI/SNF chromatin remodeling complex and involved in a variety of cellular processes [18], [19], [20], [21], [22], [23], [24], [25], [26]. Therefore, a gene expression study using microarray analysis was performed to elucidate the underlying mechanism that leads to cell proliferation defects in Trip12mt/mt ES cells. Microarray analysis of variance identified a total of 7635 genes that were significantly expressed in wild-type and Trip12mt/mt ES cells (p-values<0.05). To identify statistically significant functional categories by gene ontology, we selected genes that had greater than 2-fold changes in expression and placed these genes into DAVID [27]. As shown in Fig. 5D, both up- and down-regulated genes were enriched in the developmental process (Fig. 5D). These data suggest that Trip12 regulates gene expression by destabilizing BAF57 during mouse development.
Figure 5
Figure 5
Loss of the ubiquitin ligase activity of Trip12 induces BAF57 protein accumulation in ES cells.
In this report, we have determined that the E3 ubiquitin ligase activity of Trip12 is indispensable for mouse development. Previous reports indicated that Trip12 promotes the ubiquitination and degradation of ARF [6]. The down-regulation of Trip12 expression stabilizes ARF and enhances ARF-dependent, p53-mediated cell cycle arrest in normal human fibroblasts [6]. However, in our experiments, the p53 pathway was not activated in either Trip12mt/mt mice or Trip12mt/mt ES cells. Although Trip12mt/mt mice had increased ARF expression levels, the p21 (which is a well known p53 target gene) expression levels were unchanged in these mice. These findings suggest that the growth arrest phenotype of Trip12mt/mt mice was caused by p16 expression rather than ARF induction. Previous reports also showed that Trip12-mediated ARF ubiquitination is inhibited by c-Myc [6]. It is known that c-Myc expression levels are higher in mouse embryos and ES cells compared to differentiated cells [17], [28], [29], [30]. Considering these results, we speculate that Trip12 minimally contributes to ARF ubiquitination during mice embryogenesis because of elevated c-Myc expression. On one hand, our experiments showed that BAF57 protein stability was regulated by Trip12-mediated ubiquitination and that the expression profiles of several genes were changed between wild-type and Trip12mt/mt ES cells. This finding suggests that the ubiquitination activity of Trip12 is tightly regulated by individual target proteins. Further experiments using conditional knockout approaches and the Trip12 protein complex that is purified from different cell types may help elucidate the exact in vivo functions of the Trip12 protein.
Cell culture and embryoid body (EB) formation
E14 ES cells (ATCC) were maintained on mouse embryo fibroblast (MEF) feeder cell layers in Dulbecco-modified Eagle medium containing 14% KnockOut Serum Replacement (Invirtogen), 1% fetal bovine serum, 100 units/ml LIF, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, and 100 µM 2-mercaptoethanol. For EB formation assays, 2×105 cells were seeded into 35 mm low attachment sterile cell plate in 2 ml ES cell medium without LIF. Fresh medium was provided every two days.
Targeting vectors and generation of Trip12 mutant mice
The targeting vectors for Trip12 were constructed by inserting FLAG and HA epitope tag sequences in frame and Neo or IRES-hyg cassette into the exon 33 of the mouse Trip12 genome. Correctly targeted ES cell clone were injected into C57BL/6 blastocysts, producing chimeric mice. Highly chimeric males were mated to females, and then the progeny were intercrossed. All experiments were performed in accordance with the Declaration of Helsinki and were approved by University of Tsukuba Ethics Committee for Animal Experiments (approval ID:040042).
Western Blot
Cells were lysed in TNE buffer [10 mM Tris-HCl (pH 7.8), 1% NP-40, 150 mM NaCl, 1 mM EDTA, 1 µM phenylmethylsulfonyl fluoride, and 1 µg/ml aprotinin]. The proteins were separated by SDS-PAGE, transferred onto PVDF membranes (Millipore), immunoblotted with indicated antibodies. The antibodies employed in this study included mouse monoclonal antibodies specific for β-Actin (Sigma); rat monoclonal antibody for HA (Roche) and ARF (Calbiochem). Rabbit polyclonal antibody for BAF57 (GeneTex) and Trip12 (Bethyl Laboratories).
Real-time RT-PCR
Embryos and cells were homogenized in 1 ml of sepasol (nacalai tesque) and total RNA was extracted according to the instruction manual. cDNA was synthesized from total RNA using RevatraAce reverse transcriptase (Toyobo) and random primers. Real-time PCRs were performed to amplify fragments representing for the indicated mRNA expression. We used primers 5′- CATCTGGAGCAGCATGGAGTC-3′ and 5′-GGGTACGACCGAAAGAGTTCG-3′ for p16, 5′-GTTCTTGGTCACTGTGAGGATTCAG-3′ and 5′-CCATCATCATCACCTGGTCCAG-3′ for ARF, 5′-TTGCACTCTGGTGTCTGAGC-3′ and 5′-TGCGCTTGGAGTGATAGAAA-3′ for p21, 5′-TTGGGTCTCAGGCAAACTCT-3′ and 5′-CTGTTGGCCCTTTTGTTTTG-3′ for p27, 5′-AGTACCTCAGCCTCCAGCAGAT-3′ and 5′-GCTTGCACTTCATCCTTTGGTT-3′ for Nanog, 5′-CACGAGTGGAAAGCAACTCA-3′ and 5′-TTCATGTCCTGGGACTCCTC-3′ for Oct-4, 5′-CATGAACAGGTTCATCTATG-3′ and 5′-GTTGTCAGCTTTGCAGCATG-3′ for AFP, 5′-TGTCTATGTTCGAGATTACAG-3′ and 5′-CATTGAGGTTTGAAATCGAC-3′ for Flk-1, 5′-GGTCATTGTGAATGTACCAC-3′ and 5′-CCTTTGTCCAGCTCATGGTG-3′ for NCAM,
Cycloheximide treatment
Cells were treated with 100 µg/ml cycloheximide to prevent de novo protein synthesis, and lysed at various time points following cycloheximide treatment. The proteins were then separated by SDS-PAGE and detected by immunoblotting.
Whole mount immunostaining
Whole mount immunostaining of embryos were performed as described previously [31].
Microarray procedure and data analysis
The microarray procedure was performed as described in the Affymetrix GeneChip Expression Analysis manual (Affimetrix). Each array was analysed using GeneSpring (Agilent) program. Patterns were analysed to identify functional categories using Database for Annotation, Visualization and Integrated Discovery (DAVID) (http:// david.abcc.ncifcrf.gov) [27]. We used the functional annotation tool program and reported only GOTERM_BP (Biological process) that had p-values of <0.05.
Statistical analysis
All the data are representative of at least three different experiments. Statistical analysis was performed using t-test.
Supporting Information
Figure S1
TUNEL staining of wild type E8.5 embryo and Trip12mt/mt embryo at corresponding developmental stage.
(TIF)
Footnotes
Competing Interests: The authors have declared that no competing interests exist.
Funding: This research was supported by a Nuclear System to Decipher Operation Code (DECODE) (ID:17064005), and Targeted Proteins Research Program (TPRP) (ID: MPB2) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. (http://www.mext.go.jp/english/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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