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Helmlinger D, Tora L. Sharing the SAGA. Trends Biochem Sci 2017; 42:850-861. [PMID: 28964624 PMCID: PMC5660625 DOI: 10.1016/j.tibs.2017.09.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
Transcription initiation is a major regulatory step in eukaryotic gene expression. Co-activators establish transcriptionally competent promoter architectures and chromatin signatures to allow the formation of the pre-initiation complex (PIC), comprising RNA polymerase II (Pol II) and general transcription factors (GTFs). Many GTFs and co-activators are multisubunit complexes, in which individual components are organized into functional modules carrying specific activities. Recent advances in affinity purification and mass spectrometry analyses have revealed that these complexes often share functional modules, rather than containing unique components. This observation appears remarkably prevalent for chromatin-modifying and remodeling complexes. Here, we use the modular organization of the evolutionary conserved Spt-Ada-Gcn5 acetyltransferase (SAGA) complex as a paradigm to illustrate how co-activators share and combine a relatively limited set of functional tools.
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Affiliation(s)
| | - László Tora
- 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.
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2
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Sinha I, Kumar S, Poonia P, Sawhney S, Natarajan K. Functional specialization of two paralogous TAF12 variants by their selective association with SAGA and TFIID transcriptional regulatory complexes. J Biol Chem 2017; 292:6047-6055. [PMID: 28275052 PMCID: PMC5391738 DOI: 10.1074/jbc.c116.768549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
TATA box-binding protein (TBP)-associated factors (TAFs), evolutionarily conserved from yeast to humans, play a central role during transcription initiation. A subset of TAF proteins is shared in transcription factor II D (TFIID) and SAGA transcription regulatory complexes. Although higher eukaryotes contain multiple TAF variants that specify tissue- and developmental stage-specific organization of TFIID or SAGA complexes, in unicellular genomes, however, each TAF is encoded by a single gene. Surprisingly, we found that the genome of Candida albicans, the predominant human fungal pathogen, contains two paralogous TAF12 genes, CaTAF12L and CaTAF12, encoding H2B-like histone-fold domain-containing variants. Of the available fungal genome sequences, only seven other closely related diploid pathogenic Candida genomes encode the two TAF12 paralogs. Using affinity purifications from C. albicans cell extracts, we demonstrate that CaTAF12L uniquely associates with the SAGA complex and CaTAF12 associates with the TFIID complex. We further show that CaTAF12, but not CaTAF12L, is essential for C. albicans growth. Conditional depletion of the two TAF12 variant proteins caused distinct cellular and colony phenotypes. Together our results define a specialized organization of the TAF12 variants and non-redundant roles for the two TAF12 variants in the unicellular C. albicans genome.
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Affiliation(s)
- Ishani Sinha
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shambhu Kumar
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Poonia
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonal Sawhney
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishnamurthy Natarajan
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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3
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Lin Z, Wang J, Bao Y, Guo Q, Powell CA, Xu S, Chen B, Zhang M. Deciphering the transcriptomic response of Fusarium verticillioides in relation to nitrogen availability and the development of sugarcane pokkah boeng disease. Sci Rep 2016; 6:29692. [PMID: 27434999 PMCID: PMC4951700 DOI: 10.1038/srep29692] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/23/2016] [Indexed: 11/24/2022] Open
Abstract
Pokkah boeng, caused by Fusarium verticillioides, is a serious disease in sugarcane industry. The disease severity is related to the sugarcane genotype as well as environmental considerations, such as nitrogen application. The impact of the nitrogen source (ammonium sulfate, urea, or sodium nitrate) on sugarcane pokkah boeng disease and its pathogen was investigated in planta and fungal growth and sporulation production was measured in vitro. The results showed that ammonium and nitrate were beneficial to fungal mycelium growth, cell densities, and sporulation, which enhanced the disease symptoms of sugarcane pokkah boeng compared to urea fertilization. A total of 1,779 transcripts out of 13,999 annotated genes identified from global transcriptomic analysis were differentially expressed in F. verticillioides CNO-1 grown in the different sources of nitrogen. These were found to be involved in nitrogen metabolism, transport, and assimilation. Many of these genes were also associated with pathogenicity based on the PHI-base database. Several transcription factors were found to be associated with specific biological processes related to nitrogen utilization. Our results further demonstrated that nitrogen availability might play an important role in disease development by increasing fungal cell growth as well as influencing the expression of genes required for successful pathogenesis.
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Affiliation(s)
- Zhenyue Lin
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Jihua Wang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Yixue Bao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Qiang Guo
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Charles A. Powell
- Indian River Research and Education Center, IFAS, University of Florida, Fort Pierce, FL 34945, USA
| | - Shiqiang Xu
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
- Indian River Research and Education Center, IFAS, University of Florida, Fort Pierce, FL 34945, USA
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4
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Cartier A, Parent A, Labrecque P, Laroche G, Parent JL. WDR36 acts as a scaffold protein tethering a G-protein-coupled receptor, Gαq and phospholipase Cβ in a signalling complex. J Cell Sci 2011; 124:3292-304. [DOI: 10.1242/jcs.085795] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We identified the WD-repeat-containing protein, WDR36, as an interacting partner of the β isoform of thromboxane A2 receptor (TPβ) by yeast two-hybrid screening. We demonstrated that WDR36 directly interacts with the C-terminus and the first intracellular loop of TPβ by in vitro GST-pulldown assays. The interaction in a cellular context was observed by co-immunoprecipitation, which was positively affected by TPβ stimulation. TPβ–WDR36 colocalization was detected by confocal microscopy at the plasma membrane in non-stimulated HEK293 cells but the complex translocated to intracellular vesicles following receptor stimulation. Coexpression of WDR36 and its siRNA-mediated knockdown, respectively, increased and inhibited TPβ-induced Gαq signalling. Interestingly, WDR36 co-immunoprecipitated with Gαq, and promoted TPβ–Gαq interaction. WDR36 also associated with phospholipase Cβ (PLCβ) and increased the interaction between Gαq and PLCβ, but prevented sequestration of activated Gαq by GRK2. In addition, the presence of TPβ in PLCβ immunoprecipitates was augmented by expression of WDR36. Finally, disease-associated variants of WDR36 affected its ability to modulate Gαq-mediated signalling by TPβ. We report that WDR36 acts as a new scaffold protein tethering a G-protein-coupled receptor, Gαq and PLCβ in a signalling complex.
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Affiliation(s)
- Andréane Cartier
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Institut de Pharmacologie de Sherbrooke and Centre de Recherche Clinique Etienne-Lebel, Sherbrooke, QC J1H 5N4, Canada
| | - Audrey Parent
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Institut de Pharmacologie de Sherbrooke and Centre de Recherche Clinique Etienne-Lebel, Sherbrooke, QC J1H 5N4, Canada
| | - Pascale Labrecque
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Institut de Pharmacologie de Sherbrooke and Centre de Recherche Clinique Etienne-Lebel, Sherbrooke, QC J1H 5N4, Canada
| | - Geneviève Laroche
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Institut de Pharmacologie de Sherbrooke and Centre de Recherche Clinique Etienne-Lebel, Sherbrooke, QC J1H 5N4, Canada
| | - Jean-Luc Parent
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Institut de Pharmacologie de Sherbrooke and Centre de Recherche Clinique Etienne-Lebel, Sherbrooke, QC J1H 5N4, Canada
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5
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Kim SW, Kim S, Nam EJ, Jeong YW, Lee SH, Paek JH, Kim JH, Kim JW, Kim YT. Comparative Proteomic Analysis of Advanced Serous Epithelial Ovarian Carcinoma: Possible Predictors of Chemoresistant Disease. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:281-92. [DOI: 10.1089/omi.2010.0012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sang Wun Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Sunghoon Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Ji Nam
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Yong Wook Jeong
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - San Hui Lee
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Heum Paek
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Hoon Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Wook Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Kwandong University College of Medicine, Kyunggi-do, Korea
| | - Young Tae Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
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Sansó M, Vargas-Pérez I, Quintales L, Antequera F, Ayté J, Hidalgo E. Gcn5 facilitates Pol II progression, rather than recruitment to nucleosome-depleted stress promoters, in Schizosaccharomyces pombe. Nucleic Acids Res 2011; 39:6369-79. [PMID: 21515633 PMCID: PMC3159446 DOI: 10.1093/nar/gkr255] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In the fission yeast, the MAP kinase Sty1 and the transcription factor Atf1 regulate up to 400 genes in response to environmental signals, and both proteins have been shown to bind to their promoters in a stress-dependent manner. In a genetic search, we have isolated the histone H3 acetyltransferase Gcn5, a component of the SAGA complex, as being essential for oxidative stress survival and activation of those genes. Upon stress, Gcn5 is recruited to promoters and coding sequences of stress genes in a Sty1- and Atf1-dependent manner, causing both an enhanced acetylation of histone H3 and nucleosome eviction. Unexpectedly, recruitment of RNA polymerase II (Pol II) is not impaired in Δgcn5 cells. We show here that stress genes display a 400-bp long nucleosome depleted region upstream of the transcription start site even prior to activation. Stress treatment does not alter promoter nucleosome architecture, but induces eviction of the downstream nucleosomes at stress genes, which is not observed in Δgcn5 cells. We conclude that, while Pol II is recruited to nucleosome-free stress promoters in a transcription factor dependent manner, Gcn5 mediates eviction of nucleosomes positioned downstream of promoters, allowing efficient Pol II progression along the genes.
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Affiliation(s)
- Miriam Sansó
- Departament de Ciències Experimentals i de la Salut, Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, E-08003 Barcelona, Spain
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Cho SO, Lim JW, Jun JH, Kim KH, Kim H. Helicobacter pylori in a Korean isolate expressed proteins differentially in human gastric epithelial cells. Dig Dis Sci 2010; 55:1550-64. [PMID: 19672714 DOI: 10.1007/s10620-009-0908-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 07/05/2009] [Indexed: 12/19/2022]
Abstract
PURPOSE The proteins expressed in gastric epithelial cells infected with Helicobacter pylori (H. pylori) may determine the clinical outcome such as chronic gastritis, peptic ulcer, and gastric carcinoma. The present study aims to determine the differentially expressed proteins in human gastric epithelial AGS cells that were infected with H. pylori in a Korean isolate, a cagA+, vacA s1b m2 iceA1 H. pylori by proteomic analysis. The differentially expressed proteins, whose expression levels were more or less than twofold in H. pylori-infected cells, were analyzed. RESULTS Ten proteins (chromatin assembly factor-1, proliferating cell nuclear antigen, 14-3-3 protein tau, eukaryotic translation initiation factor 6, heat-shock protein 90beta, dimethylarginine dimethylaminohydrolase-1, L-lactate dehydrogenase B chain, prohibitin, triosephosphate isomerase, protein disulfide isomerase) were up-regulated while eight proteins (heat-shock gp96 precursor, nucleophosmin, ornithine aminotransferase, Ku70, L-arginine-glycine amidinotransferase, Smad anchor for receptor activation, ADP-ribosylation factor, WD repeat-containing protein isoform 1) were down-regulated by H. pylori infection in AGS cells. These proteins are related to cell proliferation, cell adhesion, carcinogenesis, cell-defense mechanisms against oxidative stress, membrane trafficking, and energy metabolism. CONCLUSIONS Oxidative stress, cell proliferation, cell adhesion, and membrane trafficking may be involved in the pathogenesis of gastric diseases including cancer associated with H. pylori in a Korean isolate.
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Affiliation(s)
- Soon Ok Cho
- Department of Pharmacology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
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8
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Helmlinger D, Marguerat S, Villén J, Gygi SP, Bähler J, Winston F. The S. pombe SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8. Genes Dev 2009; 22:3184-95. [PMID: 19056896 DOI: 10.1101/gad.1719908] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The SAGA complex is a conserved multifunctional coactivator known to play broad roles in eukaryotic transcription. To gain new insights into its functions, we performed biochemical and genetic analyses of SAGA in the fission yeast, Schizosaccharomyces pombe. Purification of the S. pombe SAGA complex showed that its subunit composition is identical to that of Saccharomyces cerevisiae. Analysis of S. pombe SAGA mutants revealed that SAGA has two opposing roles regulating sexual differentiation. First, in nutrient-rich conditions, the SAGA histone acetyltransferase Gcn5 represses ste11(+), which encodes the master regulator of the mating pathway. In contrast, the SAGA subunit Spt8 is required for the induction of ste11(+) upon nutrient starvation. Chromatin immunoprecipitation experiments suggest that these regulatory effects are direct, as SAGA is physically associated with the ste11(+) promoter independent of nutrient levels. Genetic tests suggest that nutrient levels do cause a switch in SAGA function, as spt8Delta suppresses gcn5Delta with respect to ste11(+) derepression in rich medium, whereas the opposite relationship, gcn5Delta suppression of spt8Delta, occurs during starvation. Thus, SAGA plays distinct roles in the control of the switch from proliferation to differentiation in S. pombe through the dynamic and opposing activities of Gcn5 and Spt8.
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Affiliation(s)
- Dominique Helmlinger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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9
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Nakazawa N, Nakamura T, Kokubu A, Ebe M, Nagao K, Yanagida M. Dissection of the essential steps for condensin accumulation at kinetochores and rDNAs during fission yeast mitosis. ACTA ACUST UNITED AC 2008; 180:1115-31. [PMID: 18362178 PMCID: PMC2290841 DOI: 10.1083/jcb.200708170] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The condensin complex has a fundamental role in chromosome dynamics. In this study, we report that accumulation of Schizosaccharomyces pombe condensin at mitotic kinetochores and ribosomal DNAs (rDNAs) occurs in multiple steps and is necessary for normal segregation of the sister kinetochores and rDNAs. Nuclear entry of condensin at the onset of mitosis requires Cut15/importin α and Cdc2 phosphorylation. Ark1/aurora and Cut17/Bir1/survivin are needed to dock the condensin at both the kinetochores and rDNAs. Furthermore, proteins that are necessary to form the chromatin architecture of the kinetochores (Mis6, Cnp1, and Mis13) and rDNAs (Nuc1 and Acr1) are required for condensin to accumulate specifically at these sites. Acr1 (accumulation of condensin at rDNA 1) is an rDNA upstream sequence binding protein that physically interacts with Rrn5, Rrn11, Rrn7, and Spp27 and is required for the proper accumulation of Nuc1 at rDNAs. The mechanism of condensin accumulation at the kinetochores may be conserved, as human condensin II fails to accumulate at kinetochores in hMis6 RNA interference–treated cells.
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Affiliation(s)
- Norihiko Nakazawa
- Core Research for Evolutional Science and Technology Research Program, Japan Science and Technology Corporation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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10
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Gori F, Friedman LG, Demay MB. Wdr5, a WD-40 protein, regulates osteoblast differentiation during embryonic bone development. Dev Biol 2006; 295:498-506. [PMID: 16730692 DOI: 10.1016/j.ydbio.2006.02.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 01/27/2006] [Accepted: 02/20/2006] [Indexed: 12/26/2022]
Abstract
Wdr5 accelerates osteoblast and chondrocyte differentiation in vitro, and is developmentally expressed in osteoblasts as well as in proliferating and hypertrophic chondrocytes. To investigate the role of Wdr5 during endochondral bone development, transgenic mice overexpressing Wdr5 under the control of the 2.3-kb fragment of the mouse alpha(1) I collagen promoter were generated. The transgene was specifically expressed in the osteoblasts of transgene positive mice and was absent in the growth plate. Histological analyses at embryonic day 14.5 demonstrated that the humeri of transgene positive embryos were longer than those isolated from wild-type littermates largely due to an expansion of the hypertrophic chondrocyte layer. Acceleration of osteoblast differentiation was observed with greater and more extensive expression of type I collagen and more extensive mineral deposition in the bone collar of transgene positive embryos. Acceleration of vascular invasion was also observed in transgene positive mice. Postnatal analyses of transgenic mice confirmed persistent acceleration of osteoblast differentiation. Targeted expression of Wdr5 to osteoblasts resulted in earlier activation of the canonical Wnt signaling pathway in the bone collar as well as in primary calvarial osteoblast cultures. In addition, overexpression of Wdr5 increased the expression of OPG, a target of the canonical Wnt signaling pathway. Overall, our findings suggest that Wdr5 accelerates osteoblast differentiation in association with activation of the canonical Wnt pathway.
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Affiliation(s)
- Francesca Gori
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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Caron C, Boyault C, Khochbin S. Regulatory cross-talk between lysine acetylation and ubiquitination: role in the control of protein stability. Bioessays 2005; 27:408-15. [PMID: 15770681 DOI: 10.1002/bies.20210] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It is now becoming apparent that cross-talk between two protein lysine modifications, acetylation and ubiquitination, is a critical regulatory mechanism controlling vital cellular functions. The most apparent effect is the inhibition of proteasome-mediated protein degradation by lysine acetylation. Analysis of the underlying mechanisms, however, shows that, besides a direct competition between the two lysine modifications, more complex and indirect processes also connect these two signalling pathways. These findings point to protein lysine acetylation as a potential regulator of various cellular functions involving protein ubiquitination.
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Affiliation(s)
- Cécile Caron
- Laboratoire de Biologie Moléculaie et Cellulaire de la Différenciation- INSERM U309 Equipe Chromatine et expression des gènes, Institut Albert Bonniot, Faculté de. Médecine-Pharmacie, 38706 La Tronche, France
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12
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Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L. TAF9b (formerly TAF9L) is a bona fide TAF that has unique and overlapping roles with TAF9. Mol Cell Biol 2005; 25:4638-49. [PMID: 15899866 PMCID: PMC1140618 DOI: 10.1128/mcb.25.11.4638-4649.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
TFIID plays a key role in transcription initiation of RNA polymerase II preinitiation complex assembly. TFIID is comprised of the TATA box binding protein (TBP) and 14 TBP-associated factors (TAFs). A second set of transcriptional regulatory multiprotein complexes containing TAFs has been described (called SAGA, TFTC, STAGA, and PCAF/GCN5). Using matrix-assisted laser desorption ionization mass spectrometry, we identified a novel TFTC subunit, human TAF9Like, encoded by a TAF9 paralogue gene. We show that TAF9Like is a subunit of TFIID, and thus, it will be called TAF9b. TFIID and TFTC complexes in which both TAF9 and TAF9b are present exist. In vitro and in vivo experiments indicate that the interactions between TAF9b and TAF6 or TAF9 and TAF6 histone fold pairs are similar. We observed a differential induction of TAF9 and TAF9b during apoptosis that, together with their different ability to stabilize p53, points to distinct requirements for the two proteins in gene regulation. Small interfering RNA (siRNA) knockdown of TAF9 and TAF9b revealed that both genes are essential for cell viability. Gene expression analysis of cells treated with either TAF9 or TAF9b siRNAs indicates that the two proteins regulate different sets of genes with only a small overlap. Taken together, these data demonstrate that TAF9 and TAF9b share some of their functions, but more importantly, they have distinct roles in the transcriptional regulatory process.
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Affiliation(s)
- Mattia Frontini
- Department of Transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
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13
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Tsai TC, Lee YL, Hsiao WC, Tsao YP, Chen SL. NRIP, a Novel Nuclear Receptor Interaction Protein, Enhances the Transcriptional Activity of Nuclear Receptors. J Biol Chem 2005; 280:20000-9. [PMID: 15784617 DOI: 10.1074/jbc.m412169200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcriptional regulation by members of the nuclear hormone receptor superfamily is a modular process requiring the mediation of distinct subclasses of coregulators. In this study, we isolated a novel WD40 repeat-containing gene, human nuclear receptor interaction protein (NRIP). We found NRIP interacts with either androgen or glucocorticoid receptors from in vitro and in vivo pulldown assays. Subsequently, transient transfection and luciferase activity assays suggested that NRIP was a ligand-dependent coactivator of steroid receptors (androgen and glucocorticoid) in distinct promoters. To further clarify the function of NRIP, we found an RNA interference-3-targeted NRIP gene sequence (5'-GATGATACAGCACGAGAAC-3') that could efficiently and specifically knock down endogenous and exogenous NRIP gene expression and that significantly diminished cell proliferation in prostate (LNCaP) and cervical (C33A) cells. Therefore, NRIP may play a role in enhancing the transcriptional activity of nuclear receptors and may be a critical target for developing therapeutic agents against nuclear receptor-mediated progression of prostate and cervical cancers.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Line
- Cell Line, Tumor
- Cell Proliferation
- DNA/genetics
- Female
- Humans
- In Vitro Techniques
- Male
- Mice
- Molecular Sequence Data
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/metabolism
- Neoplasms, Hormone-Dependent/pathology
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Pregnancy
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription, Genetic
- Two-Hybrid System Techniques
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/metabolism
- Uterine Cervical Neoplasms/pathology
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Affiliation(s)
- Tzung-Chieh Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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14
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Imazawa Y, Hisatake K, Mitsuzawa H, Matsumoto M, Tsukui T, Nakagawa K, Nakadai T, Shimada M, Ishihama A, Nogi Y. The Fission Yeast Protein Ker1p Is an Ortholog of RNA Polymerase I Subunit A14 in Saccharomyces cerevisiae and Is Required for Stable Association of Rrn3p and RPA21 in RNA Polymerase I. J Biol Chem 2005; 280:11467-74. [PMID: 15647272 DOI: 10.1074/jbc.m411150200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A heterodimer formed by the A14 and A43 subunits of RNA polymerase (pol) I in Saccharomyces cerevisiae is proposed to correspond to the Rpb4/Rpb7 and C17/C25 heterodimers in pol II and pol III, respectively, and to play a role(s) in the recruitment of pol I to the promoter. However, the question of whether the A14/A43 heterodimer is conserved in eukaryotes other than S. cerevisiae remains unanswered, although both Rpb4/Rpb7 and C17/C25 are conserved from yeast to human. To address this question, we have isolated a Schizosaccharomyces pombe gene named ker1+ using a yeast two-hybrid system, including rpa21+, which encodes an ortholog of A43, as bait. Although no homolog of A14 has previously been found in the S. pombe genome, functional characterization of Ker1p and alignment of Ker1p and A14 showed that Ker1p is an ortholog of A14. Disruption of ker1+ resulted in temperature-sensitive growth, and the temperature-sensitive deficit of ker1delta was suppressed by overexpression of either rpa21+ or rrn3+, which encodes the rDNA transcription factor Rrn3p, suggesting that Ker1p is involved in stabilizing the association of RPA21 and Rrn3p in pol I. We also found that Ker1p dissociated from pol I in post-log-phase cells, suggesting that Ker1p is involved in growth-dependent regulation of rDNA transcription.
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Affiliation(s)
- Yukiko Imazawa
- Department of Molecular Biology, Saitama Medical School, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan
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15
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Kimura M, Ishihama A. Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions. Nucleic Acids Res 2004; 32:6706-15. [PMID: 15616156 PMCID: PMC545442 DOI: 10.1093/nar/gkh1000] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TFIIF is a general transcription factor (GTF) that binds to RNA polymerase II (pol II) for subsequent recruitment of pol II to a promoter. TFIIF of Saccharomyces cerevisiae contains a small subunit, designated Tfg3, in addition to two conserved subunits, TFIIFalpha (Tfg1) and TFIIFbeta (Tfg2). In this study, we characterized Tfg3 of Schizosaccharomyces pombe. Using Tfg3 fused to green fluorescent protein (GFP), we found that Tfg3 is located in nuclei, and it is assembled into the C-terminal domain phosphatase (Fcp1)/TFIIF/pol II complex via interactions with TFIIFalpha and TFIIFbeta. As in the case of S.cerevisiae, Tfg3 in S.pombe forms part of another GTF, namely TFIID. The TFIID complex isolated from S.pombe that had been cultured at elevated temperatures included increased levels of Tfg3. The interaction of recombinant Tfg3 with TATA-binding protein (TBP), the central subunit of TFIID, was temperature-dependent. Moreover, a mutant of S.pombe that lacked the gene for Tfg3 was sensitive to a battery of stresses including temperature up-shift. Starting from a mutant with tfg3- mutation, we isolated five species of multicopy suppressors. Expression levels of the suppressor genes were lower in the mutant cell than in wild-type cell at an elevated temperature. Taken together, we propose that Tfg3 is involved in transcriptional regulation under stress conditions, in particular, at high temperatures.
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Affiliation(s)
- Makoto Kimura
- Gene Engineering Division, BioResource Center, RIKEN (Institute of Physical and Chemical Research), Tsukuba, Ibaraki 305-0074, Japan and Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan.
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16
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Yoon YM, Baek KH, Jeong SJ, Shin HJ, Ha GH, Jeon AH, Hwang SG, Chun JS, Lee CW. WD repeat-containing mitotic checkpoint proteins act as transcriptional repressors during interphase. FEBS Lett 2004; 575:23-9. [PMID: 15388328 DOI: 10.1016/j.febslet.2004.07.089] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Revised: 07/20/2004] [Accepted: 07/22/2004] [Indexed: 11/24/2022]
Abstract
WD repeats are implicated in protein-protein interactions and regulate a wide variety of cellular functions, including chromatin remodeling and transcription. The WD repeats of the Bub3 and Cdc20 kinetochore proteins are important for the physical interactions of these proteins with Mad2 and BubR1 to yield a kinetochore protein complex capable of delaying anaphase by inhibiting ubiquitin ligation via the anaphase-promoting complex/cyclosome. Here, we show that Bub3 and Cdc20 form a complex with histone deacetylases; this interaction appears to confer transcriptional repressor activity in a heterologous DNA-binding context. In addition, inhibition of Bub3 and Cdc20 expression significantly impairs interphase cell cycle. These results indicate that Bub3 and Cdc20 play additional roles in the integration of cell cycle arrest as transcriptional repressors.
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Affiliation(s)
- Young-Mee Yoon
- Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
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17
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Yamada T, Mizuno KI, Hirota K, Kon N, Wahls WP, Hartsuiker E, Murofushi H, Shibata T, Ohta K. Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot. EMBO J 2004; 23:1792-803. [PMID: 14988732 PMCID: PMC394230 DOI: 10.1038/sj.emboj.7600138] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Accepted: 02/02/2004] [Indexed: 12/31/2022] Open
Abstract
Histone acetyltransferases (HATs) and ATP-dependent chromatin remodeling factors (ADCRs) are involved in selective gene regulation via modulation of local chromatin configuration. Activation of the recombination hotspot ade6-M26 of Schizosaccharomyces pombe is mediated by a cAMP responsive element (CRE)-like sequence, M26, and a heterodimeric ATF/CREB transcription factor, Atf1.Pcr1. Chromatin remodeling occurs meiotically around M26. We examined the roles of HATs and ADCRs in chromatin remodeling around M26. Histones H3 and H4 around M26 were hyperacetylated in an M26- and Atf1-dependent manner early in meiosis. SpGcn5, the S. pombe homolog of Gcn5p, was required for the majority of histone H3 acetylation around M26 in vivo. Deletion of gcn5+ caused a significant delay in chromatin remodeling but only partial reduction of M26 meiotic recombination frequency. The snf22+ (a Swi2/Snf2-ADCR homologue) deletion and snf22+ gcn5+ double deletion abolished chromatin remodeling and significant reduction of meiotic recombination around M26. These results suggest that HATs and ADCRs cooperatively alter local chromatin structure, as in selective transcription activation, to activate meiotic recombination at M26 in a site-specific manner.
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Affiliation(s)
- Takatomi Yamada
- Genetic Dynamics Research Unit-Laboratory, RIKEN, Wako, Saitama, Japan
- Cellular & Molecular Biology Laboratory, RIKEN/CREST of the JST, Wako, Saitama, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ken-ichi Mizuno
- Genetic Dynamics Research Unit-Laboratory, RIKEN, Wako, Saitama, Japan
- Cellular & Molecular Biology Laboratory, RIKEN/CREST of the JST, Wako, Saitama, Japan
| | - Kouji Hirota
- Genetic Dynamics Research Unit-Laboratory, RIKEN, Wako, Saitama, Japan
- Cellular & Molecular Biology Laboratory, RIKEN/CREST of the JST, Wako, Saitama, Japan
| | - Ning Kon
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Edgar Hartsuiker
- Genome Damage and Stability Centre, University of Sussex, Falmer Brighton, UK
| | - Hiromu Murofushi
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takehiko Shibata
- Cellular & Molecular Biology Laboratory, RIKEN/CREST of the JST, Wako, Saitama, Japan
| | - Kunihiro Ohta
- Genetic Dynamics Research Unit-Laboratory, RIKEN, Wako, Saitama, Japan
- Cellular & Molecular Biology Laboratory, RIKEN/CREST of the JST, Wako, Saitama, Japan
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18
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Leurent C, Sanders SL, Demény MA, Garbett KA, Ruhlmann C, Weil PA, Tora L, Schultz P. Mapping key functional sites within yeast TFIID. EMBO J 2004; 23:719-27. [PMID: 14765106 PMCID: PMC381015 DOI: 10.1038/sj.emboj.7600111] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Accepted: 01/12/2004] [Indexed: 01/14/2023] Open
Abstract
The transcription factor TFIID, composed of the TATA box-binding protein (TBP) and 14 TBP-associated factors (TAFs), plays a key role in the regulation of gene expression by RNA polymerase II. The structure of yeast TFIID, as determined by electron microscopy and digital image analysis, is formed by three lobes, labelled A-C, connected by thin linking domains. Immunomapping revealed that TFIID contains two copies of the WD-40 repeat-containing TAF5 and that TAF5 contributes to the linkers since its C- and N-termini were found in different lobes. This property was confirmed by the finding that a recombinant complex containing TAF5 complexed with six histone fold containing TAFs was able to form a trilobed structure. Moreover, the N-terminal domain of TAF1 was mapped in lobe C, whereas the histone acetyltransferase domain resides in lobe A along with TAF7. TBP was found in the linker domain between lobes A and C in a way that the N-terminal 100 residues of TAF1 are spanned over it. The implications of these data with regard to TFIID function are discussed.
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Affiliation(s)
- Claire Leurent
- Department of transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Steven L Sanders
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA
| | - Màté A Demény
- Department of transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Krassimira A Garbett
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA
| | - Christine Ruhlmann
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Pôle API, Illkirch, France
| | - P Anthony Weil
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA
| | - Làszlò Tora
- Department of transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Patrick Schultz
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Pôle API, Illkirch, France
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1, rue Laurent Fries, BP10142, F-67404 Illkirch, France. Tel.: +33 3 90 24 4800; Fax: +33 3 88 65 3201; E-mail:
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19
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Müller F, Tora L. The multicoloured world of promoter recognition complexes. EMBO J 2004; 23:2-8. [PMID: 14685269 PMCID: PMC1271665 DOI: 10.1038/sj.emboj.7600027] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Accepted: 11/18/2003] [Indexed: 11/09/2022] Open
Abstract
The expression pattern of regulated genes changes dynamically depending on the developmental stage and the differentiation state of the cell. Transcription factors regulate cellular events at the gene expression level by communicating signals to the general transcription machinery that forms a preinitiation complex (PIC) at class II core promoters. Recent data strongly suggest that PICs are composed of different sets of factors at distinct promoters, reflecting the spatiotemporal profile of gene expression in multicellular organisms. Thus, today it is important to ask the question: how universal are the promoter recognition factors? This review will focus on findings that support the new idea that core promoter recognition by distinct factors is an additional level of transcriptional regulation and that this step is developmentally regulated.
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Affiliation(s)
- Ferenc Müller
- Institute of Toxicology and Genetics, Forschungszentrum, Karlsruhe, Germany
| | - Làszlò Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch Cedex, CU de Strasbourg, France
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20
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Mitsuzawa H, Ishihama A. RNA polymerase II transcription apparatus in Schizosaccharomyces pombe. Curr Genet 2003; 44:287-94. [PMID: 14574615 DOI: 10.1007/s00294-003-0446-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2003] [Revised: 08/27/2003] [Accepted: 09/04/2003] [Indexed: 10/26/2022]
Abstract
Eukaryotic RNA polymerase II (Pol II) transcription apparatus is a multi-protein complex consisting of the RNA polymerase II core enzyme (12 subunits), general transcription factors, the mediator, and some other specific accessory factors with regulatory functions. After genome sequencing was completed, the fission yeast Schizosaccharomyces pombe was recognized as a good model organism to study the Pol II transcription apparatus, because most genetic methods developed with the budding yeast Saccharomyces cerevisiae are applicable but the genetic systems of Sch. pombe, including transcription, are closer to those in higher eukaryotes. Recent studies on components of the Sch. pombe basal transcription machinery not only revealed a number of properties common in other eukaryotes but also illuminated some features unique to Sch. pombe. Convergence of information from both yeasts will provide us with a more general understanding of eukaryotic transcription.
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Affiliation(s)
- Hiroshi Mitsuzawa
- Department of Molecular Genetics, National Institute of Genetics, Mishima, 411-8540, Shizuoka, Japan
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21
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Mitsuzawa H, Kanda E, Ishihama A. Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts. Nucleic Acids Res 2003; 31:4696-701. [PMID: 12907709 PMCID: PMC169969 DOI: 10.1093/nar/gkg688] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2003] [Revised: 06/17/2003] [Accepted: 06/27/2003] [Indexed: 11/14/2022] Open
Abstract
Rpb4-Rpb7, a dissociable subcomplex of RNA polymerase II (pol II), is required for transcription initiation. To understand the role of Rpb7 in transcription initiation or other processes in transcription, we carried out a two-hybrid screen for proteins that interact with Rpb7 of the fission yeast Schizosaccharomyces pombe. The screen identified the S.pombe homolog of the Saccharomyces cerevisiae Nrd1, an RNA-binding protein implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by pol II. The S.pombe protein, named Seb1 for seven binding, was essential for cell viability, and bound directly to Rpb7 in vitro. Saccharomyces cerevisiae Rpb7 also interacted with Nrd1, indicating that the interaction is conserved in evolution. Glu166 and/or Asp167 of S.pombe Rpb7, residues near the C-terminus of the 172 amino acid protein, were found to be important for its interaction with Seb1. Our results suggest that Rpb7 may function to anchor a processing factor to the pol II apparatus, thereby coupling RNA processing to transcription. The role for Rpb7 is consistent with its location in the pol II complex determined by recent structural studies.
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Affiliation(s)
- Hiroshi Mitsuzawa
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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22
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Nakagawa K, Hisatake K, Imazawa Y, Ishiguro A, Matsumoto M, Pape L, Ishihama A, Nogi Y. The fission yeast RPA51 is a functional homolog of the budding yeast A49 subunit of RNA polymerase I and required for maximizing transcription of ribosomal DNA. Genes Genet Syst 2003; 78:199-209. [PMID: 12893961 DOI: 10.1266/ggs.78.199] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Saccharomyces cerevisiae A49 and mouse PAF53 are subunits specific to RNA polymerase I (Pol I) in eukaryotes. It has been known that Pol I without A49 or PAF53 maintains non-specific transcription activities but a molecular role(s) of A49 (and PAF53) remains totally unknown. We studied the fission yeast gene encoding a protein of 415 amino acids exhibiting 30% and 19% identities to A49 and PAF53, respectively. We designate the corresponding protein RPA51 and gene encoding it rpa51+ since the gene encodes a Pol I subunit and an apparent molecular mass of the protein is 51 kDa. rpa51+ is required for cell growth at lower but not at higher temperatures and is able to complement S. cerevisiae rpa49Delta mutation, indicating that RPA51 is a functionally-conserved subunit of Pol I between the budding yeast and the fission yeast. Deletion analysis of rpa51+ shows that only two-thirds of the C-terminal region are required for the function. Transcripts analysis in vivo and in vitro shows that RPA51 plays a general role for maximizing transcription of rDNA whereas it is dispensable for non-specific transcription. We also found that RPA51 associates significantly with Pol I in the stationary phase, suggesting that Pol I inactivation in the stationary phase of yeast does not result from the RPA51 dissociation.
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Affiliation(s)
- Kaori Nakagawa
- Department of Molecular Biology, Saitama Medical School, Iruma-Gun, Saitama, Japan
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23
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Seino H, Kishi T, Nishitani H, Yamao F. Two ubiquitin-conjugating enzymes, UbcP1/Ubc4 and UbcP4/Ubc11, have distinct functions for ubiquitination of mitotic cyclin. Mol Cell Biol 2003; 23:3497-505. [PMID: 12724408 PMCID: PMC164763 DOI: 10.1128/mcb.23.10.3497-3505.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell cycle events are regulated by sequential activation and inactivation of Cdk kinases. Mitotic exit is accomplished by the inactivation of mitotic Cdk kinase, which is mainly achieved by degradation of cyclins. The ubiquitin-proteasome system is involved in this process, requiring APC/C (anaphase-promoting complex/cyclosome) as a ubiquitin ligase. In Xenopus and clam oocytes, the ubiquitin-conjugating enzymes that function with APC/C have been identified as two proteins, UBC4 and UBCx/E2-C. Previously we reported that the fission yeast ubiquitin-conjugating enzyme UbcP4/Ubc11, a homologue of UBCx/E2-C, is required for mitotic transition. Here we show that the other fission yeast ubiquitin-conjugating enzyme, UbcP1/Ubc4, which is homologous to UBC4, is also required for mitotic transition in the same manner as UbcP4/Ubc11. Both ubiquitin-conjugating enzymes are essential for cell division and directly required for the degradation of mitotic cyclin Cdc13. They function nonredundantly in the ubiquitination of CDC13 because a defect in ubcP1/ubc4+ cannot be suppressed by high expression of UbcP4/Ubc11 and a defect in ubcP4/ubc11+ cannot be suppressed by high expression of UbcP1/Ubc4. In vivo analysis of the ubiquitinated state of Cdc13 shows that the ubiquitin chains on Cdc13 were short in ubcP1/ubc4 mutant cells while ubiquitinated Cdc13 was totally reduced in ubcP4/ubc11 mutant cells. Taken together, these results indicate that the two ubiquitin-conjugating enzymes play distinct and essential roles in the degradation of mitotic cyclin Cdc13, with the UbcP4/Ubc11-pathway initiating ubiquitination of Cdc13 and the UbcP1/Ubc4-pathway elongating the short ubiquitin chains on Cdc13.
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Affiliation(s)
- Hiroaki Seino
- Division of Mutagenesis, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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24
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Huang Y, McGillicuddy E, Weindel M, Dong S, Maraia RJ. The fission yeast TFIIB-related factor limits RNA polymerase III to a TATA-dependent pathway of TBP recruitment. Nucleic Acids Res 2003; 31:2108-16. [PMID: 12682361 PMCID: PMC153730 DOI: 10.1093/nar/gkg301] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The RNA polymerase (pol) III-transcribed (e.g. tRNA and 5S rRNA) genes of traditionally studied organisms rely on gene-internal promoters that precisely position the initiation factor, TFIIIB, on the upstream promoter-less DNA. This is accomplished by the ability of the TFIIIB subunit, TFIIB-related factor (Brf1), to make stable protein-protein interactions with TATA-binding protein (TBP) and place it on the promoter-less upstream DNA. Unlike traditional model organisms, Schizosaccharomyces pombe tRNA and 5S rRNA genes contain upstream TATA promoters that are required to program functional pol III initiation complexes. In this study we demonstrate that S.pombe (Sp)Brf does not form stable interactions with TBP in the absence of DNA using approaches that do reveal stable association of TBP and S.cerevisiae (Sc)Brf1. Gel mobility analyses demonstrate that a TBP-TATA DNA complex can recruit SpBrf to a Pol III promoter. Consistent with this, overproduction of SpBrf in S.pombe increases the expression of a TATA-dependent, but not a TATA-less, suppressor tRNA gene. Since previous whole genome analysis also revealed TATA elements upstream of tRNA genes in Arabidopsis, this pathway may be more widespread than appreciated previously.
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Affiliation(s)
- Ying Huang
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2753, USA
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25
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Criqui MC, de Almeida Engler J, Camasses A, Capron A, Parmentier Y, Inzé D, Genschik P. Molecular characterization of plant ubiquitin-conjugating enzymes belonging to the UbcP4/E2-C/UBCx/UbcH10 gene family. PLANT PHYSIOLOGY 2002; 130:1230-40. [PMID: 12427990 PMCID: PMC166644 DOI: 10.1104/pp.011353] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2002] [Accepted: 08/07/2002] [Indexed: 05/04/2023]
Abstract
The anaphase promoting complex or cyclosome is the ubiquitin-ligase that targets destruction box-containing proteins for proteolysis during the cell cycle. Anaphase promoting complex or cyclosome and its activator (the fizzy and fizzy-related) proteins work together with ubiquitin-conjugating enzymes (UBCs) (E2s). One class of E2s (called E2-C) seems specifically involved in cyclin B1 degradation. Although it has recently been shown that mammalian E2-C is regulated at the protein level during the cell cycle, not much is known concerning the expression of these genes. Arabidopsis encodes two genes belonging to the E2-C gene family (called UBC19 and UBC20). We found that UBC19 is able to complement fission yeast (Schizosaccharomyces pombe) UbcP4-140 mutant, indicating that the plant protein can functionally replace its yeast ortholog for protein degradation during mitosis. In situ hybridization experiments were performed to study the expression of the E2-C genes in various tissues of plants. Their transcripts were always, but not exclusively, found in tissues active for cell division. Thus, the UBC19/20 E2s may have a key function during cell cycle, but may also be involved in ubiquitylation reactions occurring during differentiation and/or in differentiated cells. Finally, we showed that a translational fusion protein between UBC19 and green fluorescent protein localized both in the cytosol and the nucleus in stable transformed tobacco (Nicotiana tabacum cv Bright Yellow 2) cells.
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Affiliation(s)
- Marie Claire Criqui
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67084 Strasbourg cedex, France
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26
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Sanders SL, Garbett KA, Weil PA. Molecular characterization of Saccharomyces cerevisiae TFIID. Mol Cell Biol 2002; 22:6000-13. [PMID: 12138208 PMCID: PMC133964 DOI: 10.1128/mcb.22.16.6000-6013.2002] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2002] [Revised: 02/27/2002] [Accepted: 05/21/2002] [Indexed: 11/20/2022] Open
Abstract
We previously defined Saccharomyces cerevisiae TFIID as a 15-subunit complex comprised of the TATA binding protein (TBP) and 14 distinct TBP-associated factors (TAFs). In this report we give a detailed biochemical characterization of this general transcription factor. We have shown that yeast TFIID efficiently mediates both basal and activator-dependent transcription in vitro and displays TATA box binding activity that is functionally distinct from that of TBP. Analyses of the stoichiometry of TFIID subunits indicated that several TAFs are present at more than 1 copy per TFIID complex. This conclusion was further supported by coimmunoprecipitation experiments with a systematic family of (pseudo)diploid yeast strains that expressed epitope-tagged and untagged alleles of the genes encoding TFIID subunits. Based on these data, we calculated a native molecular mass for monomeric TFIID. Purified TFIID behaved in a fashion consistent with this calculated molecular mass in both gel filtration and rate-zonal sedimentation experiments. Quite surprisingly, although the TAF subunits of TFIID cofractionated as a single complex, TBP did not comigrate with the TAFs during either gel filtration chromatography or rate-zonal sedimentation, suggesting that TBP has the ability to dynamically associate with the TFIID TAFs. The results of direct biochemical exchange experiments confirmed this hypothesis. Together, our results represent a concise molecular characterization of the general transcription factor TFIID from S. cerevisiae.
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Affiliation(s)
- Steven L Sanders
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615, USA
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27
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Mitsuzawa H, Ishihama A. Identification of histone H4-like TAF in Schizosaccharomyces pombe as a protein that interacts with WD repeat-containing TAF. Nucleic Acids Res 2002; 30:1952-8. [PMID: 11972332 PMCID: PMC113851 DOI: 10.1093/nar/30.9.1952] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The general transcription factor TFIID consists of the TATA-binding protein (TBP) and multiple TBP-associated factors (TAFs). We previously identified two distinct WD repeat-containing TAFs, spTAF72 and spTAF73, in the fission yeast Schizosaccharomyces pombe. Here we report the identification of another S.pombe TAF, spTAF50, which is the S.pombe homolog of histone H4-like TAFs such as human TAF80, Drosophila TAF60 and Saccharomyces cerevisiae TAF60. spTAF50 was identified in a two-hybrid screen as a protein that interacts with the C-terminal WD repeat-containing region of spTAF72. Gene disruption revealed that spTAF50 is essential for cell viability. In vitro, spTAF50 bound to spTAF72 but less efficiently to spTAF73. In S.pombe cells, spTAF50 was detected as a protein with an apparent molecular mass of approximately 50 kDa. Immunoprecipitation experiments demonstrated that spTAF50 is present in both the TFIID and SAGA-like complexes as in the case of spTAF72. These results indicate that the C-terminal region of spTAF72, which largely consists of WD repeats, interacts with spTAF50 in the TFIID and SAGA-like complexes, suggesting a role for the WD repeat domain in the interaction between TAFs.
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Affiliation(s)
- Hiroshi Mitsuzawa
- Department of Molecular Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
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Current awareness on yeast. Yeast 2001; 18:1269-76. [PMID: 11561294 DOI: 10.1002/yea.689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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