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Marcoli R, Symonds JE, Walker SP, Battershill CN, Bird S. Characterising the Physiological Responses of Chinook Salmon ( Oncorhynchus tshawytscha) Subjected to Heat and Oxygen Stress. BIOLOGY 2023; 12:1342. [PMID: 37887052 PMCID: PMC10604766 DOI: 10.3390/biology12101342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon (Oncorhynchus tshawytscha) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates.
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Affiliation(s)
- Roberta Marcoli
- Centre for Sustainable Tropical Fisheries, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
- ARC Research Hub for Supercharging Tropical Aquaculture through Genetic Solutions, James Cook University, Townsville, QLD 4811, Australia
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand;
| | - Jane E. Symonds
- Cawthron Institute, Nelson 7010, New Zealand; (J.E.S.); (S.P.W.)
| | - Seumas P. Walker
- Cawthron Institute, Nelson 7010, New Zealand; (J.E.S.); (S.P.W.)
| | | | - Steve Bird
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand;
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Chen Q, Guo Y, Zhang J, Zheng N, Wang J, Liu Y, Lu J, Zhen S, Du X, Li L, Fu J, Wang G, Gu R, Wang J, Liu Y. RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize. Nucleic Acids Res 2023; 51:7832-7850. [PMID: 37403778 PMCID: PMC10450181 DOI: 10.1093/nar/gkad571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Abstract
Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.
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Affiliation(s)
- Quanquan Chen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingmei Guo
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Nannan Zheng
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiawen Lu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Sihan Zhen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Ke F, Yu XD, Wang ZH, Gui JF, Zhang QY. Replication and transcription machinery for ranaviruses: components, correlation, and functional architecture. Cell Biosci 2022; 12:6. [PMID: 34991685 PMCID: PMC8734342 DOI: 10.1186/s13578-021-00742-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ranaviruses (family Iridoviridae) are promiscuous pathogens that can infect across species barriers in poikilotherms and can replicate in amphibian and fish cells and even in cultured mammalian cells. However, as nucleocytoplasmic large DNA viruses (NCLDVs), their replication and transcription mechanisms remain largely unknown. Here, we screened and uncovered the replication and transcription machinery of two ranaviruses, Andrias davidianus ranavirus (ADRV) and Rana grylio virus (RGV), by a combination of methods, including the isolation of proteins on nascent DNA, recombinant virus-based affinity, and NanoLuc complementation assay. RESULTS The ranavirus replication and transcription machinery was deeply dissected and identified as a complicated apparatus containing at least 30 viral and 6 host proteins. The viral proteins ADRV-47L/RGV-63R (DNA polymerase, vDPOL), ADRV-23L/RGV-91R (proliferating cell nuclear antigen, vPCNA), ADRV-85L/RGV-27R (single-stranded DNA binding protein, vSSB), ADRV-88L/RGV-24R (vhelicase/primase), etc., constitute the core replisome. Specifically, the core of the transcription complex, the viral RNA polymerase, contain the host RNAPII subunits Rpb3, Rpb6, and Rpb11, which was a first report in NCLDVs. Furthermore, correlations and interactions among these factors in the machinery were described. Significantly, the replisome core protein vDPOL (ADRV-47L) can interact with numerous viral and host proteins and could act as a linker and regulation center in viral DNA replication and transcription. Thus, these results depicted an architecture for ranavirus replication and transcription. CONCLUSIONS Up to 36 components from ranavirus and their host were found to form viral replisomes and transcription complexes using a series of precise methods, which further constructed an architecture for ranavirus replication and transcription in which vDPOL was a key central factor and various components correlated and cooperated. Therefore, it provides a cornerstone for further understanding the mechanisms of the replication and transcription of ranaviruses which can ensure the efficient production of progeny virus and adaptation to cross-species infection.
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Affiliation(s)
- Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China.,The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xue-Dong Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zi-Hao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China.,The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, 430072, China. .,The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Tenekeci S, Isik Z. Integrative Biological Network Analysis to Identify Shared Genes in Metabolic Disorders. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:522-530. [PMID: 32396100 DOI: 10.1109/tcbb.2020.2993301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Identification of common molecular mechanisms in interrelated diseases is essential for better prognoses and targeted therapies. However, complexity of metabolic pathways makes it difficult to discover common disease genes underlying metabolic disorders; and it requires more sophisticated bioinformatics models that combine different types of biological data and computational methods. Accordingly, we built an integrative network analysis model to identify shared disease genes in metabolic syndrome (MS), type 2 diabetes (T2D), and coronary artery disease (CAD). We constructed weighted gene co-expression networks by combining gene expression, protein-protein interaction, and gene ontology data from multiple sources. For 90 different configurations of disease networks, we detected the significant modules by using MCL, SPICi, and Linkcomm graph clustering algorithms. We also performed a comparative evaluation on disease modules to determine the best method providing the highest biological validity. By overlapping the disease modules, we identified 22 shared genes for MS-CAD and T2D-CAD. Moreover, 19 out of these genes were directly or indirectly associated with relevant diseases in the previous medical studies. This study does not only demonstrate the performance of different biological data sources and computational methods in disease-gene discovery, but also offers potential insights into common genetic mechanisms of the metabolic disorders.
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Berkyurek AC, Furlan G, Lampersberger L, Beltran T, Weick E, Nischwitz E, Cunha Navarro I, Braukmann F, Akay A, Price J, Butter F, Sarkies P, Miska EA. The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription. EMBO J 2021; 40:e105565. [PMID: 33533030 PMCID: PMC7917558 DOI: 10.15252/embj.2020105565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 01/03/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate germ cell development and maintain germline integrity in many animals. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. piRNA biogenesis mechanisms are diverse and remain poorly understood. Here, we identify the RNA polymerase II (RNA Pol II) core subunit RPB-9 as required for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We show that rpb-9 initiates heritable piRNA-mediated gene silencing at two DNA transposon families and at a subset of somatic genes in the germline. We provide genetic and biochemical evidence that RPB-9 is required for piRNA biogenesis by recruiting the Integrator complex at piRNA genes, hence promoting transcriptional termination. We conclude that, as a part of its rapid evolution, the piRNA pathway has co-opted an ancient machinery for high-fidelity transcription.
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Affiliation(s)
- Ahmet C Berkyurek
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Giulia Furlan
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Lisa Lampersberger
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Toni Beltran
- MRC London Institute of Medical SciencesLondonUK
- Institute of Clinical SciencesImperial College LondonLondonUK
| | - Eva‐Maria Weick
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Present address:
Structural Biology ProgramSloan Kettering InstituteMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Emily Nischwitz
- Quantitative ProteomicsInstitute of Molecular BiologyMainzGermany
| | - Isabela Cunha Navarro
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Fabian Braukmann
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Alper Akay
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Present address:
School of Biological SciencesUniversity of East AngliaNorwich, NorfolkUK
| | - Jonathan Price
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Falk Butter
- Quantitative ProteomicsInstitute of Molecular BiologyMainzGermany
| | - Peter Sarkies
- MRC London Institute of Medical SciencesLondonUK
- Institute of Clinical SciencesImperial College LondonLondonUK
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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Poreba E, Durzynska J. Nuclear localization and actions of the insulin-like growth factor 1 (IGF-1) system components: Transcriptional regulation and DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108307. [PMID: 32430099 DOI: 10.1016/j.mrrev.2020.108307] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022]
Abstract
Insulin-like growth factor (IGF) system stimulates growth, proliferation, and regulates differentiation of cells in a tissue-specific manner. It is composed of two insulin-like growth factors (IGF-1 and IGF-2), six insulin-like growth factor-binding proteins (IGFBPs), and two insulin-like growth factor receptors (IGF-1R and IGF-2R). IGF actions take place mostly through the activation of the plasma membrane-bound IGF-Rs by the circulating ligands (IGFs) released from the IGFBPs that stabilize their levels in the serum. This review focuses on the IGF-1 part of the system. The IGF-1 gene, which is expressed mainly in the liver as well as in other tissues, comprises six alternatively spliced exons that code for three protein isoforms (pro-IGF-1A, pro-IGF-1B, and pro-IGF-1C), which are processed to mature IGF-1 and E-peptides. The IGF-1R undergoes autophosphorylation, resulting in a signaling cascade involving numerous cytoplasmic proteins such as AKT and MAPKs, which regulate the expression of target genes. However, a more complex picture of the axis has recently emerged with all its components being translocated to the nuclear compartment. IGF-1R takes part in the regulation of gene expression by forming transcription complexes, modifying the activity of chromatin remodeling proteins, and participating in DNA damage tolerance mechanisms. Four IGFBPs contain a nuclear localization signal (NLS), which targets them to the nucleus, where they regulate gene expression (IGFBP-2, IGFBP-3, IGFBP-5, IGFBP-6) and DNA damage repair (IGFBP-3 and IGFBP-6). Last but not least, the IGF-1B isoform has been reported to be localized in the nuclear compartment. However, no specific molecular actions have been assigned to the nuclear pro-IGF-1B or its derivative EB peptide. Therefore, further studies are needed to shed light on their nuclear activity. These recently uncovered nuclear actions of different components of the IGF-1 axis are relevant in cancer cell biology and are discussed in this review.
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Affiliation(s)
- Elzbieta Poreba
- Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Julia Durzynska
- Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Lynham J, Houry WA. The Multiple Functions of the PAQosome: An R2TP- and URI1 Prefoldin-Based Chaperone Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:37-72. [DOI: 10.1007/978-3-030-00737-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Heterozygous deletion of chromosome 17p renders prostate cancer vulnerable to inhibition of RNA polymerase II. Nat Commun 2018; 9:4394. [PMID: 30349055 PMCID: PMC6197287 DOI: 10.1038/s41467-018-06811-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022] Open
Abstract
Heterozygous deletion of chromosome 17p (17p) is one of the most frequent genomic events in human cancers. Beyond the tumor suppressor TP53, the POLR2A gene encoding the catalytic subunit of RNA polymerase II (RNAP2) is also included in a ~20-megabase deletion region of 17p in 63% of metastatic castration-resistant prostate cancer (CRPC). Using a focused CRISPR-Cas9 screen, we discovered that heterozygous loss of 17p confers a selective dependence of CRPC cells on the ubiquitin E3 ligase Ring-Box 1 (RBX1). RBX1 activates POLR2A by the K63-linked ubiquitination and thus elevates the RNAP2-mediated mRNA synthesis. Combined inhibition of RNAP2 and RBX1 profoundly suppress the growth of CRPC in a synergistic manner, which potentiates the therapeutic effectivity of the RNAP2 inhibitor, α-amanitin-based antibody drug conjugate (ADC). Given the limited therapeutic options for CRPC, our findings identify RBX1 as a potentially therapeutic target for treating human CRPC harboring heterozygous deletion of 17p.
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Han J, Park SH, Kim DJ, Kim H, Choi YH, Lee JH, Park SC, Chung J. Antibodies to the DNA-directed RNA polymerase II subunit RPB1 occur with highest frequency in centenarians. IMMUNITY & AGEING 2016; 13:8. [PMID: 27006680 PMCID: PMC4802847 DOI: 10.1186/s12979-016-0064-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/14/2016] [Indexed: 11/29/2022]
Abstract
Background Recently, phage display technology has made it possible to define the circulating repertoire of humoral immunity. This study was designed to define the circulating antibodies specific to centenarians. Results We used a phage-displayed combinatorial peptide library to screen for peptides (YSATLRY and YSPTLFY) that preferentially react with the IgG fraction of centenarians aged 100–105 years. Centenarian sera binds to YSATLRY and YSPTLFY with higher frequency than that of healthy volunteers aged 60–79 years or healthy volunteers younger than or equal to 43 years of age. We prepared polyclonal antibodies to YSATLRY from human sera to immunoprecipitate the native antigen, which was identified as the carboxy-terminal domain (CTD) of DNA-directed RNA polymerase II subunit RPB1. The RBP1 CTD contains multiple YSPTSPS repeats, which are significantly homologous to YSATLRY and YSPTLFY. The immunoprecipitated RPB1 had significantly slower mobility than did RPB1 in cell lysates, and the polyclonal antibodies reacted with CTD peptide, depending on the phosphorylation pattern. Therefore, it appears that the polyclonal antibodies preferentially bind to highly phosphorylated RPB1. We also confirmed that human monoclonal antibodies reactive to both YSATLRY and YSPTLFY bound to the phosphorylated YSPTSPS motif. Conclusions This study showed that centenarians possess IgG antibodies that are reactive to YSATLRY and YSPTLFY, mimicking the phosphorylated form of the YSPTSPS motif (CTD of RPB1), at a much higher frequency than that of the average population. Electronic supplementary material The online version of this article (doi:10.1186/s12979-016-0064-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jungwon Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380 South Korea ; Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 00380 South Korea
| | - So-Hyun Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380 South Korea ; Present Address: Seoul Animal Medical Center, Gyenggi-do, 12790 South Korea
| | - Dong-Jo Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380 South Korea ; Present Address: Celltrion, Incheon, 22014 South Korea
| | - Hyori Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 00380 South Korea
| | - Yoon-Ho Choi
- Department of Medicine, Center for Health Promotion, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351 South Korea
| | - Jong-Hyuk Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380 South Korea
| | - Sang Chul Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380 South Korea ; Present Address: Daegu Gyeongbuk Institute of Science and Technology, Deagu, 42988 South Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380 South Korea ; Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 00380 South Korea ; Cancer Research Institute, Seoul National University College of Medicine, Seoul, 00380 South Korea
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Chen L, Guan L, Qian P, Xu F, Wu Z, Wu Y, He K, Gou X, Li J, Hou S. NRPB3, the third largest subunit of RNA polymerase II, is essential for stomatal patterning and differentiation in Arabidopsis. Development 2016; 143:1600-11. [PMID: 26989174 PMCID: PMC4909857 DOI: 10.1242/dev.129098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 03/03/2016] [Indexed: 12/22/2022]
Abstract
Stomata are highly specialized epidermal structures that control transpiration and gas exchange between plants and the environment. Signal networks underlying stomatal development have been previously uncovered but much less is known about how signals involved in stomatal development are transmitted to RNA polymerase II (Pol II or RPB), which plays a central role in the transcription of mRNA coding genes. Here, we identify a partial loss-of-function mutation of the third largest subunit of nuclear DNA-dependent Pol II (NRPB3) that exhibits an increased number of stomatal lineage cells and paired stomata. Phenotypic and genetic analyses indicated that NRPB3 is not only required for correct stomatal patterning, but is also essential for stomatal differentiation. Protein-protein interaction assays showed that NRPB3 directly interacts with two basic helix-loop-helix (bHLH) transcription factors, FAMA and INDUCER OF CBF EXPRESSION1 (ICE1), indicating that NRPB3 serves as an acceptor for signals from transcription factors involved in stomatal development. Our findings highlight the surprisingly conserved activating mechanisms mediated by the third largest subunit of Pol II in eukaryotes. Summary: RNA polymerase II subunit NRPB3 interacts with stomatal bHLH transcription factors FAMA and ICE1, connecting the stomatal development pathway to the general transcription machinery.
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Affiliation(s)
- Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Liping Guan
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Pingping Qian
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Fan Xu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhongliang Wu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yujun Wu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Kai He
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Xiaoping Gou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jia Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Suiwen Hou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
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Srivastava R, Ahn SH. Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function. Biotechnol Adv 2015; 33:856-72. [PMID: 26241863 DOI: 10.1016/j.biotechadv.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/08/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022]
Abstract
At the onset of transcription, many protein machineries interpret the cellular signals that regulate gene expression. These complex signals are mostly transmitted to the indispensable primary proteins involved in transcription, RNA polymerase II (RNAPII) and histones. RNAPII and histones are so well coordinated in this cellular function that each cellular signal is precisely allocated to specific machinery depending on the stage of transcription. The carboxy-terminal domain (CTD) of RNAPII in eukaryotes undergoes extensive posttranslational modification, called the 'CTD code', that is indispensable for coupling transcription with many cellular processes, including mRNA processing. The posttranslational modification of histones, known as the 'histone code', is also critical for gene transcription through the reversible and dynamic remodeling of chromatin structure. Notably, the histone code is closely linked with the CTD code, and their combinatorial effects enable the delicate regulation of gene transcription. This review elucidates recent findings regarding the CTD modifications of RNAPII and their coordination with the histone code, providing integrative pathways for the fine-tuned regulation of gene expression and cellular function.
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Affiliation(s)
- Rakesh Srivastava
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seong Hoon Ahn
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea.
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12
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Zhang J, Pan YF, Ding ZW, Yang GZ, Tan YX, Yang C, Jiang TY, Liu LJ, Zhang B, Han T, Cao D, Yang T, Yang N, Wu MC, Dong LW, Wang HY. RMP promotes venous metastases of hepatocellular carcinoma through promoting IL-6 transcription. Oncogene 2014; 34:1575-83. [DOI: 10.1038/onc.2014.84] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/31/2014] [Accepted: 02/25/2014] [Indexed: 02/07/2023]
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13
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Tycon MA, Daddysman MK, Fecko CJ. RNA polymerase II subunits exhibit a broad distribution of macromolecular assembly states in the interchromatin space of cell nuclei. J Phys Chem B 2013; 118:423-33. [PMID: 24354435 DOI: 10.1021/jp4082933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nearly all cellular processes are enacted by multi-subunit protein complexes, yet the assembly mechanism of most complexes is not well understood. The anthropomorphism "protein recruitment" that is used to describe the concerted binding of proteins to accomplish a specific function conceals significant uncertainty about the underlying physical phenomena and chemical interactions governing the formation of macromolecular complexes. We address this deficiency by investigating the diffusion dynamics of two RNA polymerase II subunits, Rpb3 and Rpb9, in regions of live Drosophila cell nuclei that are devoid of chromatin binding sites. Using FRAP microscopy, we demonstrate that both unengaged subunits are incorporated into a broad distribution of complexes, with sizes ranging from free (unincorporated) proteins to those that have been predicted for fully assembled gene transcription units. In live cells, Rpb3 exhibits regions of stability at both size extremes connected by a continuous distribution of complexes. Corresponding measurements on cellular extracts reveal a distribution that retains peaks at the extremes but not in between, suggesting that partially assembled complexes are less stable. We propose that the broad distribution of macromolecular species allows for mechanistic flexibility in the assembly of transcription complexes.
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Affiliation(s)
- Michael A Tycon
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-3290, United States
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14
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Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
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15
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Lavallée-Adam M, Rousseau J, Domecq C, Bouchard A, Forget D, Faubert D, Blanchette M, Coulombe B. Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res 2012; 12:272-81. [PMID: 23157168 DOI: 10.1021/pr300778b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Affinity purification combined with tandem mass spectrometry (AP-MS/MS) is a well-established method used to discover interaction partners for a given protein of interest. Because most AP-MS/MS approaches are performed using the soluble fraction of whole cell extracts (WCE), information about the cellular compartments where the interactions occur is lost. More importantly, classical AP-MS/MS often fails to identify interactions that take place in the nonsoluble fraction of the cell, for example, on the chromatin or membranes; consequently, protein complexes that are less soluble are underrepresented. In this paper, we introduce a method called multiple cell compartment AP-MS/MS (MCC-AP-MS/MS), which identifies the interactions of a protein independently in three fractions of the cell: the cytoplasm, the nucleoplasm, and the chromatin. We show that this fractionation improves the sensitivity of the method when compared to the classical affinity purification procedure using soluble WCE while keeping a very high specificity. Using three proteins known to localize in various cell compartments as baits, the CDK9 subunit of transcription elongation factor P-TEFb, the RNA polymerase II (RNAP II)-associated protein 4 (RPAP4), and the largest subunit of RNAP II, POLR2A, we show that MCC-AP-MS/MS reproducibly yields fraction-specific interactions. Finally, we demonstrate that this improvement in sensitivity leads to the discovery of novel interactions of RNAP II carboxyl-terminal domain (CTD) interacting domain (CID) proteins with POLR2A.
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Affiliation(s)
- Mathieu Lavallée-Adam
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3A 2B4, Canada
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16
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Reich C, Zeller M, Milkereit P, Hausner W, Cramer P, Tschochner H, Thomm M. The archaeal RNA polymerase subunit P and the eukaryotic polymerase subunit Rpb12 are interchangeable in vivo and in vitro. Mol Microbiol 2008; 71:989-1002. [PMID: 19183282 PMCID: PMC2680338 DOI: 10.1111/j.1365-2958.2008.06577.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The general subunit of all three eukaryotic RNA polymerases, Rpb12, and subunit P of the archaeal enzyme show sequence similarities in their N-terminal zinc ribbon and some highly conserved residues in the C-terminus. We report here that archaeal subunit P under the control of a strong yeast promoter could complement the lethal phenotype of a RPB12 deletion mutant and that subunit Rpb12 from yeast can functionally replace subunit P during reconstitution of the archaeal RNA polymerase. The ΔP enzyme is unable to form stable open complexes, but can efficiently extend a dinucleotide on a premelted template or RNA on an elongation scaffold. This suggests that subunit P is directly or indirectly involved in promoter opening. The activity of the ΔP enzyme can be rescued by the addition of Rpb12 or subunit P to transcription reactions. Mutation of cysteine residues in the zinc ribbon impair the activity of the enzyme in several assays and this mutated form of P is rapidly replaced by wild-type P in transcription reactions. The conserved zinc ribbon in the N-terminus seems to be important for proper interaction of the complete subunit with other RNA polymerase subunits and a 17-amino-acid C-terminal peptide is sufficient to support all basic RNA polymerase functions in vitro.
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Affiliation(s)
- Christoph Reich
- Lehrstuhl für Mikrobiologie, Universitat Regensburg, Regensburg, Germany
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17
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Jung CR, Choi S, Im DS. The NS5A protein of hepatitis C virus represses gene expression of hRPB10alpha, a common subunit of host RNA polymerases, through interferon regulatory factor-1 binding site. Virus Res 2007; 129:155-65. [PMID: 17714821 DOI: 10.1016/j.virusres.2007.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 07/09/2007] [Accepted: 07/12/2007] [Indexed: 11/22/2022]
Abstract
The nonstructural (NS) 5A protein of hepatitis C virus (HCV) plays important roles in both viral RNA replication and modulation of the physiology of the host cell. Here we report that NS5A repressed gene expression of hRPB10alpha, a common subunit of host RNA polymerases (Pol), in hepatoma cell lines and Huh-7 cells harboring HCV replicon. Analysis of the hRPB10alpha promoter region revealed that interferon regulatory factor-1 binding element (IRF-E) was essential for its transcription. The IRF-E was responsible for the NS5A-mediated repression of the hRPB10alpha transcription and its induction by IRF-1 that is known to be induced by interferon-alpha. Electrophoretic mobility shift assay showed that IRF-1 bound to the IRF-E and the binding reduced when NS5A was expressed. NS5A appeared to negatively regulate IRF-1 expression, which might be partly responsible for the decrease of hRPB10alpha expression. NS5A expression moderately decreased promoter-independent Pol activity in vitro. Transcription of adenoviral genes that are dependent on Pol II or III and propagation of adenoviral genome were impaired in HeLa cells with stable NS5A expression. The results suggest that NS5A may partly modulate host cell transcription by the down-regulation of hRPB10alpha.
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Affiliation(s)
- Cho-Rok Jung
- Gene Therapy Research Unit, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong, Daejeon 305-806, Republic of Korea
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18
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Chernukhin I, Shamsuddin S, Kang SY, Bergström R, Kwon YW, Yu W, Whitehead J, Mukhopadhyay R, Docquier F, Farrar D, Morrison I, Vigneron M, Wu SY, Chiang CM, Loukinov D, Lobanenkov V, Ohlsson R, Klenova E. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 2007; 27:1631-48. [PMID: 17210645 PMCID: PMC1820452 DOI: 10.1128/mcb.01993-06] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. "Serial" chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the beta-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.
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Affiliation(s)
- Igor Chernukhin
- Department of Biological Sciences, Central Campus, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
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19
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Hu X, Malik S, Negroiu CC, Hubbard K, Velalar CN, Hampton B, Grosu D, Catalano J, Roeder RG, Gnatt A. A Mediator-responsive form of metazoan RNA polymerase II. Proc Natl Acad Sci U S A 2006; 103:9506-11. [PMID: 16769904 PMCID: PMC1480437 DOI: 10.1073/pnas.0603702103] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA polymerase II (Pol II), whose 12 subunits are conserved across eukaryotes, is at the heart of the machinery responsible for transcription of mRNA. Although associated general transcription factors impart promoter specificity, responsiveness to gene- and tissue-selective activators additionally depends on the multiprotein Mediator coactivator complex. We have isolated from tissue extracts a distinct and abundant mammalian Pol II subpopulation that contains an additional tightly associated polypeptide, Gdown1. Our results establish that Gdown1-containing Pol II, designated Pol II(G), is selectively dependent on and responsive to Mediator. Thus, in an in vitro assay with general transcription factors, Pol II lacking Gdown1 displays unfettered levels of activator-dependent transcription in the presence or absence of Mediator. In contrast, Pol II(G) is dramatically less efficient in responding to activators in the absence of Mediator yet is highly and efficiently responsive to activators in the presence of Mediator. Our results reveal a transcriptional control mechanism in which Mediator-dependent regulation is enforced by means of Gdown1, which likely restricts Pol II function only to be reversed by Mediator.
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Affiliation(s)
- Xiaopeng Hu
- *Department of Pharmacology and Experimental Therapeutics
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | | | - Kyle Hubbard
- *Department of Pharmacology and Experimental Therapeutics
| | | | | | - Dan Grosu
- *Department of Pharmacology and Experimental Therapeutics
| | | | - Robert G. Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Averell Gnatt
- *Department of Pharmacology and Experimental Therapeutics
- Marlene and Stewart Greenebaum Cancer Center and Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201; and
- To whom correspondence should be addressed. E-mail:
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20
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Kang X, Hu Y, Li Y, Guo X, Jiang X, Lai L, Xia B, Jin C. Structural, Biochemical, and Dynamic Characterizations of the hRPB8 Subunit of Human RNA Polymerases. J Biol Chem 2006; 281:18216-26. [PMID: 16632472 DOI: 10.1074/jbc.m513241200] [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] [Indexed: 11/06/2022] Open
Abstract
The RPB8 subunit is present in all three types of eukaryotic RNA polymerases and is highly conserved during evolution. It is an essential subunit required for the transcription of nuclear genes, but the detailed mechanism including its interactions with different subunits and oligonucleotides remains largely unclear. Herein, we report the three-dimensional structure of human RPB8 (hRPB8) at high resolution determined by NMR spectroscopy. The protein fold comprises an eight-stranded beta-barrel, six short helices, and a large unstructured Omega-loop. The overall structure of hRPB8 is similar to that of yRPB8 from Saccharomyces cerevisiae and belongs to the oligonucleotide/oligosaccharide-binding fold. However, several features of the tertiary structures are notably different between the two proteins. In particular, hRPB8 has a more clustered positively charged binding interface with the largest subunit RPB1 of the RNA polymerases. We employed biochemical methods to detect its interactions with different single-stranded DNA sequences. In addition, single-stranded DNA titration experiments were performed to identify the residues involved in nonspecific binding with different DNA sequences. Furthermore, we characterized the millisecond time scale conformational flexibility of hRPB8 upon its binding to single-stranded DNA. The current results demonstrate that hRPB8 interacts with single-stranded DNA nonspecifically and adopts significant conformational changes, and the hRPB8/single-stranded DNA complex is a fast exchanging system. The solution structure in conjunction with the biochemical and dynamic studies reveal new aspects of this subunit in the molecular assembly and the biological function of the human nuclear RNA polymerases.
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Affiliation(s)
- Xue Kang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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21
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Hamard PJ, Dalbies-Tran R, Hauss C, Davidson I, Kedinger C, Chatton B. A functional interaction between ATF7 and TAF12 that is modulated by TAF4. Oncogene 2005; 24:3472-83. [PMID: 15735663 DOI: 10.1038/sj.onc.1208565] [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: 11/09/2022]
Abstract
The ATF7 proteins, which are members of the cyclic AMP responsive binding protein (CREB)/activating transcription factor (ATF) family of transcription factors, display quite versatile properties: they can interact with the adenovirus E1a oncoprotein, mediating part of its transcriptional activity; they heterodimerize with the Jun, Fos or related transcription factors, likely modulating their DNA-binding specificity; they also recruit to the promoter a stress-induced protein kinase (JNK2). In the present study, we investigate the functional relationships of ATF7 with hsTAF12 (formerly hsTAF(II)20/15), which has originally been identified as a component of the general transcription factor TFIID. We show that overexpression of hsTAF12 potentiates ATF7-induced transcriptional activation through direct interaction with ATF7, suggesting that TAF12 is a functional partner of ATF7. In support of this conclusion, chromatin immunoprecipitation experiments confirm the interaction of ATF7 with TAF12 on an ATF7-responsive promoter, in the absence of any artificial overexpression of both proteins. We also show that the TAF12-dependent transcriptional activation is competitively inhibited by TAF4. Although both TAF12 isoforms (TAF12-1 and -2, formerly TAF(II)20 and TAF(II)15) interact with the ATF7 activation region through their histone-fold domain, only the largest, hsTAF12-1, mediates transcriptional activation through its N-terminal region.
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Affiliation(s)
- Pierre-Jacques Hamard
- Ecole Supérieure de Biotechnologie de Strasbourg, Université Louis Pasteur, Parc d'innovation, UMR7100 CNRS-ULP, Bd. Sebastien Brant-BP10413, 67412 Strasbourg, Illkirch Cedex, France
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22
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Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem 2004; 73:1051-87. [PMID: 15189167 DOI: 10.1146/annurev.biochem.73.011303.073950] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One way to understand cells and circumscribe the function of proteins is through molecular networks. These networks take a variety of forms including webs of protein-protein interactions, regulatory circuits linking transcription factors and targets, and complex pathways of metabolic reactions. We first survey experimental techniques for mapping networks (e.g., the yeast two-hybrid screens). We then turn our attention to computational approaches for predicting networks from individual protein features, such as correlating gene expression levels or analyzing sequence coevolution. All the experimental techniques and individual predictions suffer from noise and systematic biases. These problems can be overcome to some degree through statistical integration of different experimental datasets and predictive features (e.g., within a Bayesian formalism). Next, we discuss approaches for characterizing the topology of networks, such as finding hubs and analyzing subnetworks in terms of common motifs. Finally, we close with perspectives on how network analysis represents a preliminary step toward a systems approach for modeling cells.
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Affiliation(s)
- Yu Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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23
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Takramah D, Seiffert BM, Schaller S, Vigneron M, Häcker G. Baculovirus P35 interacts with a subunit of human RNA polymerase II and can enhance promoter activity in human cells. J Gen Virol 2003; 84:3011-3019. [PMID: 14573806 DOI: 10.1099/vir.0.19395-0] [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: 11/18/2022] Open
Abstract
The early protein P35 from the baculovirus Autographa californica nucleopolyhedrovirus is a direct inhibitor of caspases and can block apoptosis in a wide variety of systems. In addition, it has been linked to the regulation of viral gene expression, shut-down of protein synthesis in infected insect cells and malignant transformation of mouse fibroblasts. By yeast-two-hybrid screening we identified the RPB11a subunit of human RNA polymerase II as an interaction partner of P35. Specificity of the interaction was confirmed by affinity blotting. By immunocytology, P35 was in part found in the nucleus of transfected cells. Homology searches further revealed that P35 has structural similarity with RPB3, the subunit of RNA polymerase II that has been demonstrated to interact directly with RPB11a. When transfected into human colon carcinoma cells, P35 was able to enhance the activity of E-cadherin and beta-actin promoters by about a factor of two as measured by luciferase reporter assay. P35 and hRPB11a together enhanced the E-cadherin activity about three- to fourfold. These data suggest an additional role for P35 in the regulation of cellular transcription.
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Affiliation(s)
- David Takramah
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstr. 9, D-81675 Munich, Germany
| | - Barbara M Seiffert
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstr. 9, D-81675 Munich, Germany
| | - Sophie Schaller
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (CNRS/INSERM/ULP), Illkirch, France
| | - Marc Vigneron
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (CNRS/INSERM/ULP), Illkirch, France
| | - Georg Häcker
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstr. 9, D-81675 Munich, Germany
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24
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Lee DK, Li M, Chang C. The second largest subunit of RNA polymerase II interacts with and enhances transactivation of androgen receptor. Biochem Biophys Res Commun 2003; 302:162-9. [PMID: 12593864 DOI: 10.1016/s0006-291x(03)00126-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AR may communicate with the general transcription machinery on the core promoter to exert its function as a transcriptional modulator. Our previous reports demonstrated that AR interacted with TFIIH and positive transcription elongation factor b (P-TEFb), and that phosphorylation of the carboxy-terminal domain in the largest subunit of RNA polymerase II might play important roles in AR-mediated transcription. These results suggest that AR may modulate gene expression by enhancing the efficiency of transcriptional elongation. Here we further demonstrate that co-expression of the second largest subunit of RNA polymerase II (RPB2) enhances AR transactivation. However, co-expression of the other subunits of RNA polymerase II or TFIIB did not show preferential enhancement of AR-mediated transcription. Furthermore, co-transfection of RPB2 with ER showed little effect on enhancement of ER transactivation. Together, AR may be able to interact with TFIIH, P-TEFb, and RPB2 to enhance transcription from AR target genes, such as prostate specific antigen that may play important roles in the prostate cancer progression.
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Affiliation(s)
- Dong Kun Lee
- George Whipple Laboratory for Cancer Research, Department of Pathology, Urology, and the Cancer Center, University of Rochester Medical Center, 601 Elmwood Avenue, Box 626, Rochester, NY 14642, USA
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25
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Abstract
The androgen-androgen receptor (AR) signaling pathway plays a key role in proper development and function of male reproductive organs. Like other transcriptional regulators, AR may communicate with the general transcription machinery on the core promoter to exert its function as a transcriptional modulator. The molecular communication between AR and the general transcription machinery may be achieved either by the direct protein-protein interaction between AR and the general transcription machinery or by the indirect interaction mediated by coregulators. Analyses of AR-mediated transcription suggest that the orchestrated interaction of AR with the transcription factors IIF (TFIIF) and IIH (TFIIH), and positive transcription elongation factor b (P-TEFb), may increase efficiency of transcriptional elongation from the androgen target genes, such as prostate specific antigen (PSA). Based on studies so far, AR may regulate transcription not by enhanced assembly of preinitiation transcription complex but by regulating promoter clearance and elongation stage of transcription.
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Affiliation(s)
- Dong Kun Lee
- George Whipple Laboratory for Cancer Research, Department of Pathology, and the Cancer Center, 601 Elmwood Avenue, P.O. Box 626, Rochester 14642, NY, USA
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26
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Edwards AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, Gerstein M. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet 2002; 18:529-36. [PMID: 12350343 DOI: 10.1016/s0168-9525(02)02763-4] [Citation(s) in RCA: 212] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Currently, there is a major effort to map protein-protein interactions on a genome-wide scale. The utility of the resulting interaction networks will depend on the reliability of the experimental methods and the coverage of the approaches. Known macromolecular complexes provide a defined and objective set of protein interactions with which to compare biochemical and genetic data for validation. Here, we show that a significant fraction of the protein-protein interactions in genome-wide datasets, as well as many of the individual interactions reported in the literature, are inconsistent with the known 3D structures of three recent complexes (RNA polymerase II, Arp2/3 and the proteasome). Furthermore, comparison among genome-wide datasets, and between them and a larger (but less well resolved) group of 174 complexes, also shows marked inconsistencies. Finally, individual interaction datasets, being inherently noisy, are best used when integrated together, and we show how simple Bayesian approaches can combine them, significantly decreasing error rate.
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Affiliation(s)
- Aled M Edwards
- Banting and Best Department of Medical Research, University of Toronto, C.H. Best Institute, 112 College St, Toronto, Ontario, Canada M5G 1L6
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27
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Werner F, Weinzierl ROJ. A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol Cell 2002; 10:635-46. [PMID: 12408830 DOI: 10.1016/s1097-2765(02)00629-9] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA polymerases (RNAPs) are core components of the cellular transcriptional machinery. Progress with functional studies of eukaryotic RNAPs has been delayed by the fact that it has not yet been possible to assemble active enzymes from individual subunits. Archaeal RNAPs are directly comparable to eukaryotic RNAPII in terms of primary sequence homology and quaternary structure. Here we report the successful in vitro assembly of a recombinant archaeal RNAP from purified subunits. The recombinant enzyme displays full activity in transcription assays and is capable, in the presence of two other basal factors, of promoter-specific transcription. The assembly of mutant enzymes yielded several unexpected insights into the structural and functional contributions of various subunits toward overall RNAP activity.
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Affiliation(s)
- Finn Werner
- Department of Biological Sciences, Imperial College of Science, Technology and Medicine, London, United Kingdom
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28
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Durrin LK, Krontiris TG. The thymocyte-specific MAR binding protein, SATB1, interacts in vitro with a novel variant of DNA-directed RNA polymerase II, subunit 11. Genomics 2002; 79:809-17. [PMID: 12036295 DOI: 10.1006/geno.2002.6772] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A yeast two-hybrid screen of a Jurkat (T cell) derived cDNA library, using SATB1 (a matrix attachment region binding protein) as the bait, yielded four independent isolates of a novel variant of the DNA directed RNA polymerase II, subunit 11 (RPB11). Absence of lysine-17 from the amino terminus of this variant cannot be explained by alternative mRNA splicing. Instead, allele-specific PCR, combined with GenBank database searches, suggests that a recent gene duplication event has resulted in distinct loci encoding three variant forms of RPB11. Differential splicing of mRNA transcripts accounts for unique carboxy termini among the RPB11 proteins. The exclusive association of SATB1 with one form of RPB11 is influenced primarily by the N-terminal amino acid disparity, as deletion of the entire C terminus does not alter interaction affinity. Association of RPB11 with SATB1 maps between amino acids 58 and 222 of SATB1, a region that includes a PDZ-like dimerization motif.
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Affiliation(s)
- Linda K Durrin
- Division of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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Dumay-Odelot H, Acker J, Arrebola R, Sentenac A, Marck C. Multiple roles of the tau131 subunit of yeast transcription factor IIIC (TFIIIC) in TFIIIB assembly. Mol Cell Biol 2002; 22:298-308. [PMID: 11739742 PMCID: PMC134217 DOI: 10.1128/mcb.22.1.298-308.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast transcription factor IIIC (TFIIIC) plays a key role in assembling the transcription initiation factor TFIIIB on class III genes after TFIIIC-DNA binding. The second largest subunit of TFIIIC, tau131, is thought to initiate TFIIIB assembly by interacting with Brf1/TFIIIB70. In this work, we have analyzed a TFIIIC mutant (tau131-DeltaTPR2) harboring a deletion in tau131 removing the second of its 11 tetratricopeptide repeats. Remarkably, this thermosensitive mutation was selectively suppressed in vivo by overexpression of B"/TFIIIB90, but not Brf1 or TATA-binding protein. In vitro, the mutant factor preincubated at restrictive temperature bound DNA efficiently but lost transcription factor activity. The in vitro transcription defect was abolished at high concentrations of B" but not Brf1. Copurification experiments of baculovirus-expressed proteins confirmed a direct physical interaction between tau131 and B". tau131, therefore, appears to be involved in the recruitment of both Brf1 and B".
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Affiliation(s)
- Hélène Dumay-Odelot
- Service de Biochimie et de Génétique Moléculaire, CEA/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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30
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Grandemange S, Schaller S, Yamano S, Du Manoir S, Shpakovski GV, Mattei MG, Kedinger C, Vigneron M. A human RNA polymerase II subunit is encoded by a recently generated multigene family. BMC Mol Biol 2001; 2:14. [PMID: 11747469 PMCID: PMC61041 DOI: 10.1186/1471-2199-2-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2001] [Accepted: 11/30/2001] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The sequences encoding the yeast RNA polymerase II (RPB) subunits are single copy genes. RESULTS While those characterized so far for the human (h) RPB are also unique, we show that hRPB subunit 11 (hRPB11) is encoded by a multigene family, mapping on chromosome 7 at loci p12, q11.23 and q22. We focused on two members of this family, hRPB11a and hRPB11b: the first encodes subunit hRPB11a, which represents the major RPB11 component of the mammalian RPB complex; the second generates polypeptides hRPB11balpha and hRPB11bbeta through differential splicing of its transcript and shares homologies with components of the hPMS2L multigene family related to genes involved in mismatch-repair functions (MMR). Both hRPB11a and b genes are transcribed in all human tissues tested. Using an inter-species complementation assay, we show that only hRPB11balpha is functional in yeast. In marked contrast, we found that the unique murine homolog of RPB11 gene maps on chromosome 5 (band G), and encodes a single polypeptide which is identical to subunit hRPB11a. CONCLUSIONS The type hRPB11b gene appears to result from recent genomic recombination events in the evolution of primates, involving sequence elements related to the MMR apparatus.
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Affiliation(s)
- Sylvie Grandemange
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Sophie Schaller
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Shigeru Yamano
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Stanislas Du Manoir
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP-7, 117997 Moscow, Russia
| | - Marie-Geneviève Mattei
- U.491/INSERM, Faculté de médecine Timone, 27 bd Jean Moulin, F-13385 Marseille Cedex 5, France
| | - Claude Kedinger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
| | - Marc Vigneron
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS / INSERM / ULP) BP 163, F-67404 ILLKIRCH Cedex, France
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31
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Zhou H, Lee KA. An hsRPB4/7-dependent yeast assay for trans-activation by the EWS oncogene. Oncogene 2001; 20:1519-24. [PMID: 11313895 DOI: 10.1038/sj.onc.1204135] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2000] [Revised: 11/27/2000] [Accepted: 11/29/2000] [Indexed: 11/09/2022]
Abstract
Chromosomal fusions of the N-terminal region of the Ewings Sarcoma Oncogene (EWS-Activation-Domain, EAD) to the DNA-binding domains of a variety of cellular transcription factors, produce oncogenic proteins (EWS-fusion proteins (EFPs)) that cause a variety of malignancies. The EAD can act as a potent transcriptional activation domain and is required for the oncogenic activity of EFPs. Previous studies demonstrating a physical interaction between the EAD and the human RNA Polymerase II subunit hsRPB7 suggest a crucial role for RPB7 and its partner, RPB4, in EAD function. Homologues of hsRPB4/7 exist in S. cerevisiae, and here we describe an RPB4/7-dependent yeast assay for EAD-mediated trans-activation. Conditional yeast strains lacking RPB4 are defective for trans-activation by a Gal4/EAD fusion protein at the permissive temperature. Introduction of hsRPB4 alone is unable to rescue trans-activation, while a combination of hsRPB4 and hsRPB7 significantly rescues activity. These findings provide the first functional evidence for a direct role of the RPB4/7 complex in EAD-mediated trans-activation. In addition, the yeast assay provides a tractable system for further molecular analysis of EAD and RPB4/7 action.
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Affiliation(s)
- H Zhou
- Department of Biology, Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, SAR., China
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32
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Abstract
Protein interactions among RNA polymerase small subunits from the archaeon Methanococcus jannaschii were investigated using affinity pulldown assays in pairwise and higher-order combinations. In the most extensive study of archaeal RNA polymerase subunit interactions to date, including 37 pairs of proteins, 10 ternary combinations, and three quaternary combinations, we found evidence for pairwise interactions of subunit D with subunits L and N, and a ternary complex of subunits D, L and N. No other small subunit interactions occurred. These results are consistent with interactions observed in a crystal structure of eukaryotic RNA polymerase II and support a common archaeal/eukaryal RNA polymerase architecture. We further propose that subunit E" is not an integral member of archaeal RNA polymerases. Finally, we discuss the relative accuracy of the various methods that have been used to predict protein-protein interactions in RNA polymerase.
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Affiliation(s)
- A A Best
- Department of Microbiology, University of Illinois, B103 Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave., Urbana, IL 61801, USA
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33
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Werner F, Eloranta JJ, Weinzierl RO. Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic Acids Res 2000; 28:4299-305. [PMID: 11058130 PMCID: PMC113124 DOI: 10.1093/nar/28.21.4299] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The archaeal and eukaryotic evolutionary domains diverged from each other approximately 2 billion years ago, but many of the core components of their transcriptional and translational machineries still display a readily recognizable degree of similarity in their primary structures. The F and P subunits present in archaeal RNA polymerases were only recently identified in a purified archaeal RNA polymerase preparation and, on the basis of localized sequence homologies, tentatively identified as archaeal versions of the eukaryotic RPB4 and RPB12 RNA polymerase subunits, respectively. We prepared recombinant versions of the F and P subunits from Methanococcus jannaschii and used them in in vitro and in vivo protein interaction assays to demonstrate that they interact with other archaeal subunits in a manner predicted from their eukaryotic counterparts. The overall structural conservation of the M. jannaschii F subunit, although not readily recognizable on the primary amino acid sequence level, is sufficiently high to allow the formation of an archaeal-human F-RPB7 hybrid complex.
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Affiliation(s)
- F Werner
- Department of Biochemistry, Imperial College of Science, Technology and Medicine, Exhibition Road, London SW7 2AY, UK
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34
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Masutomi K, Kaneko S, Hayashi N, Yamashita T, Shirota Y, Kobayashi K, Murakami S. Telomerase activity reconstituted in vitro with purified human telomerase reverse transcriptase and human telomerase RNA component. J Biol Chem 2000; 275:22568-73. [PMID: 10811633 DOI: 10.1074/jbc.m000622200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Telomerase is a specialized reverse transcriptase that catalyzes elongation of the telomeric tandem repeat, TTAGGG, by addition of this sequence to the ends of existing telomeres. Human telomerase reverse transcriptase (hTERT) has been identified as a catalytic enzyme involved in telomere elongation that requires telomerase RNA, human telomerase RNA component (hTR), as an RNA template. We established a new method to express and purify soluble insect-expressed recombinant hTERT. The partially purified FLAG-hTERT retained the catalytic activity of telomerase in a complementation assay in vitro to exhibit telomerase activity in telomerase-negative TIG3 cell extract and in a reconstitution assay with FLAG-hTERT and purified hTR in vitro. FLAG-hTERT (D712A) with a mutation in the VDV motif exhibited no telomerase activity, confirming the authentic catalytic activity of FLAG-hTERT. The reconstituted complex of FLAG-hTERT and hTR in vitro was detected by electrophoretic mobility shift assay, and its activity was stimulated by more than 30-fold by TIG3 cell extract. This suggested that some cellular component(s) in the extract facilitated the reconstituted telomerase activity in vitro. Geldanamycin had no effect on the reconstituted activity but partially reduced the stimulated activity of the reconstituted telomerase by the TIG3 cell extract, suggesting that Hsp90 may contribute to the stimulatory effect of the cellular components.
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Affiliation(s)
- K Masutomi
- Department of Molecular Biology, Division of Molecular Oncology, Cancer Research Institute and the First Department of Internal Medicine, Medical School, Kanazawa University, Kanazawa 920-0934, Japan
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35
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Mackereth CD, Arrowsmith CH, Edwards AM, McIntosh LP. Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum. Proc Natl Acad Sci U S A 2000; 97:6316-21. [PMID: 10841539 PMCID: PMC18600 DOI: 10.1073/pnas.97.12.6316] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA polymerase subunit RPB10 displays a high level of conservation across archaea and eukarya and is required for cell viability in yeast. Structure determination of this RNA polymerase subunit from Methanobacterium thermoautotrophicum reveals a topology, which we term a zinc-bundle, consisting of three alpha-helices stabilized by a zinc ion. The metal ion is bound within an atypical CX(2)CX(n)CC sequence motif and serves to bridge an N-terminal loop with helix 3. This represents an example of two adjacent zinc-binding Cys residues within an alpha-helix conformation. Conserved surface features of RPB10 include discrete regions of neutral, acidic, and basic residues, the latter being located around the zinc-binding site. One or more of these regions may contribute to the role of this subunit as a scaffold protein within the polymerase holoenzyme.
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Affiliation(s)
- C D Mackereth
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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36
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Fanciulli M, Bruno T, Di Padova M, De Angelis R, Iezzi S, Iacobini C, Floridi A, Passananti C. Identification of a novel partner of RNA polymerase II subunit 11, Che-1, which interacts with and affects the growth suppression function of Rb. FASEB J 2000; 14:904-12. [PMID: 10783144 DOI: 10.1096/fasebj.14.7.904] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
hRPB11 is a core subunit of RNA polymerase II (pol II) specifically down-regulated on doxorubicin (dox) treatment. Levels of this protein profoundly affect cell differentiation, cell proliferation, and tumorigenicity in vivo. Here we describe Che-1, a novel human protein that interacts with hRPB11. Che-1 possesses a domain of high homology with Escherichia coli RNA polymerase final sigma-factor 70 and SV40 large T antigen. In addition, we report that Che-1 interacts with the retinoblastoma susceptibility gene (Rb) by two distinct domains. Functionally, we demonstrate that Che-1 represses the growth suppression function of Rb, counteracting the inhibitory action of Rb on the trans-activation function of E2F1. These results identify a novel protein that binds Rb and the core of pol II, and suggest that Che-1 may be part of transcription regulatory complex.
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Affiliation(s)
- M Fanciulli
- Cell Metabolism and Pharmacokinetics Laboratory, Regina Elena Cancer Institute, 00158 Rome, Italy
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37
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De Graeve F, Bahr A, Chatton B, Kedinger C. A murine ATFa-associated factor with transcriptional repressing activity. Oncogene 2000; 19:1807-19. [PMID: 10777215 DOI: 10.1038/sj.onc.1203492] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The ATFa proteins, which are members of the CREB/ATF family of transcription factors, have previously been shown to interact with the adenovirus E1a oncoprotein and to mediate its transcriptional activity; they heterodimerize with Jun, Fos or related transcription factors, possibly altering their DNA-binding specificity; they also stably bind JNK2, a stress-induced protein kinase. Here we report the identification and characterization of a novel protein isolated in a yeast two-hybrid screen using the N-terminal half of ATFa as a bait. This 1306-residue protein (mAM, for mouse ATFa-associated Modulator) is rather acidic (pHi 4.5) and contains high proportions of Ser/Thr (21%) and Pro (11%) residues. It colocalizes and interacts with ATFa in mammalian cells, contains a bipartite nuclear localization signal and possesses an ATPase activity. Transfection experiments show that mAM is able to downregulate transcriptional activity, in an ATPase-independent manner. Our results indicate that mAM interacts with several components of the basal transcription machinery (TFIIE and TFIIH), including RNAPII itself. Together, these findings suggest that mAM may be involved in the fine-tuning of ATFa-regulated gene expression, by interfering with the assembly or stability of specific preinitiation transcription complexes.
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Affiliation(s)
- F De Graeve
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, Communauté Urbaine de Strasbourg, France
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38
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BRCA1 interaction with RNA polymerase II reveals a role for hRPB2 and hRPB10alpha in activated transcription. Proc Natl Acad Sci U S A 2000; 97. [PMID: 10725406 PMCID: PMC16207 DOI: 10.1073/pnas.070452397] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The functions of most of the 12 subunits of the RNA polymerase II (Pol II) enzyme are unknown. In this study, we demonstrate that two of the subunits, hRPB2 and hRPB10alpha, mediate the regulated stimulation of transcription. We find that the transcriptional coactivator BRCA1 interacts directly with the core Pol II complex in vitro. We tested whether single subunits from Pol II would compete with the intact Pol II complex to inhibit transcription stimulated by BRCA1. Excess purified Pol II subunits hRPB2 or hRPB10alpha blocked BRCA1- and VP16-dependent transcriptional activation in vitro with minimal effect on basal transcription. No other Pol II subunits tested inhibited activated transcription in these assays. Furthermore, hRPB10alpha, but not hRPB2, blocked Sp1-dependent activation.
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39
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Schlegel BP, Green VJ, Ladias JA, Parvin JD. BRCA1 interaction with RNA polymerase II reveals a role for hRPB2 and hRPB10 in activated transcription. Proc Natl Acad Sci U S A 2000; 97:3148-53. [PMID: 10725406 PMCID: PMC16207 DOI: 10.1073/pnas.97.7.3148] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The functions of most of the 12 subunits of the RNA polymerase II (Pol II) enzyme are unknown. In this study, we demonstrate that two of the subunits, hRPB2 and hRPB10alpha, mediate the regulated stimulation of transcription. We find that the transcriptional coactivator BRCA1 interacts directly with the core Pol II complex in vitro. We tested whether single subunits from Pol II would compete with the intact Pol II complex to inhibit transcription stimulated by BRCA1. Excess purified Pol II subunits hRPB2 or hRPB10alpha blocked BRCA1- and VP16-dependent transcriptional activation in vitro with minimal effect on basal transcription. No other Pol II subunits tested inhibited activated transcription in these assays. Furthermore, hRPB10alpha, but not hRPB2, blocked Sp1-dependent activation.
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Affiliation(s)
- B P Schlegel
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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40
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Kimura M, Ishihama A. Involvement of multiple subunit-subunit contacts in the assembly of RNA polymerase II. Nucleic Acids Res 2000; 28:952-9. [PMID: 10648788 PMCID: PMC102587 DOI: 10.1093/nar/28.4.952] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA polymerase II from the fission yeast Schizo-saccharomyces pombe consists of 12 species of subunits, Rpb1-Rpb12. We expressed these subunits, except Rpb4, simultaneously in cultured insect cells with baculovirus expression vectors. For the isolation of subunit complexes formed in the virus-infected cells, a glutathione S -transferase (GST) sequence was fused to the rpb3 cDNA to produce GST-Rpb3 fusion protein and a decahistidine-tag sequence was inserted into the rpb1 cDNA to produce Rpb1H protein. After successive affinity chromatography on glutathione and Ni(2+)columns, complexes consisting of the seven subunits, Rpb1H, Rpb2, GST-Rpb3, Rpb5, Rpb7, Rpb8 and Rpb11, were identified. Omission of the GST-Rpb3 expression resulted in reduced assembly of the Rpb11 into the complex. Direct interaction between Rpb3 and the other six subunits was detected by pairwise coexpression experiments. Coexpression of various combinations of a few subunits revealed that Rpb11 enhances Rpb3-Rpb8 interaction and consequently Rpb8 enhances Rpb1-Rpb3 interaction to some extent. We propose a mechanism in which the assembly of RNA poly-merase II is stabilized through multiple subunit-subunit contacts.
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Affiliation(s)
- M Kimura
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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41
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Jones E, Kimura H, Vigneron M, Wang Z, Roeder RG, Cook PR. Isolation and characterization of monoclonal antibodies directed against subunits of human RNA polymerases I, II, and III. Exp Cell Res 2000; 254:163-72. [PMID: 10623476 DOI: 10.1006/excr.1999.4739] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human nuclei contain three different RNA polymerases: polymerases I, II, and III. Each polymerase is a multi-subunit enzyme with 12-17 subunits. The localization of these subunits is limited by the paucity of antibodies suitable for immunofluorescence. We now describe eight different monoclonal antibodies that react specifically with RPB6 (also known as RPA20, RPB14.4, or RPC20), RPB8 (RPA18, RPB17, or RPC18), RPC32, or RPC39 and which are suitable for such studies. Each antibody detects one specific band in immunoblots of nuclear extracts; each also immunoprecipitates large complexes containing many other subunits. When used for immunofluorescence, antibodies against the subunits shared by all three polymerases (i.e., RPB6, RPB8) gave a few bright foci in nucleoli and nucleoplasm, as well as many fainter nucleoplasmic foci; all the bright foci were generally distinct from speckles containing Sm antigen. Antibodies against the two subunits found only in polymerase III (i.e., RPC32, RPC39) gave a few bright and many faint nucleoplasmic foci, but no nucleolar foci. Growth in two transcriptional inhibitors-5, 6-dichloro-1-beta-d-ribofuranosylbenzimidazole and actinomycin D-led to the redistribution of each subunit in a characteristic manner.
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Affiliation(s)
- E Jones
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
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42
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Bertolotti A, Bell B, Tora L. The N-terminal domain of human TAFII68 displays transactivation and oncogenic properties. Oncogene 1999; 18:8000-10. [PMID: 10637511 DOI: 10.1038/sj.onc.1203207] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In Ewing tumor, the (11;22) chromosomal translocation produces a chimeric molecule composed of the amino-terminal domain of EWS fused to the carboxyl-terminal DNA-binding domain of FLI-1. Previously, we have identified a novel protein TAFII68, which is highly similar to EWS and another closely related protein TLS (also called FUS). We demonstrate that the N-terminus of TAFII68 efficiently stimulates transcription when fused to two different DNA binding domains and that overexpression of TAFII68-FLI-1 chimeras in NIH3T3 cells leads to oncogenic transformation. We have also investigated the molecular mechanisms which could account for the transcriptional activation and the oncogenic transformation potential of the N-termini of TAFII68 and EWS. Thus, we have tested whether the artificial recruitment of components of the preinitiation complex (PIC) or a histone acetyltransferase (HAT) could bypass the requirement for the activation domains of either EWS or TAFII68. Recruitment of individual components of the transcription machinery or the GCN5 HAT is not sufficient to promote activation from FLI-1 responsive genes either in transfection experiments or in oncogenic transformation assays. These results suggest that the TAFII68 or EWS activation domains enhance a step after PIC formation in the transcriptional activation process.
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Affiliation(s)
- A Bertolotti
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163 - 67404 Illkirch Cedex, CU de Strasbourg, France
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43
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Bardoni B, Schenck A, Mandel JL. A novel RNA-binding nuclear protein that interacts with the fragile X mental retardation (FMR1) protein. Hum Mol Genet 1999; 8:2557-66. [PMID: 10556305 DOI: 10.1093/hmg/8.13.2557] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Silenced expression of the FMR1 gene is responsible for the fragile X syndrome. The FMR1 gene codes for an RNA binding protein (FMRP), which can shuttle between the nucleus and the cytoplasm and is found associated to polysomes in the cytoplasm. By two-hybrid assay in yeast, we identified a novel protein interacting with FMRP: nuclear FMRP interacting protein (NUFIP). NUFIP mRNA expression is strikingly similar to that of the FMR1 gene in neurones of cortex, hippocampus and cerebellum. At the subcellular level, NUFIP colocalizes with nuclear isoforms of FMRP in a dot-like pattern. NUFIP presents a C2H2 zinc finger motif and a nuclear localization signal, but has no homology to known proteins and shows RNA binding activity in vitro. NUFIP does not interact with the FMRP homologues encoded by the FXR1 and FXR2 genes. Thus, these results indicate a specific nuclear role for FMRP.
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Affiliation(s)
- B Bardoni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, CU de Strasbourg, France.
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44
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Schaller S, Grandemange S, Shpakovski GV, Golemis EA, Kedinger C, Vigneron M. Interactions between the full complement of human RNA polymerase II subunits. FEBS Lett 1999; 461:253-7. [PMID: 10567706 DOI: 10.1016/s0014-5793(99)01441-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
As an approach to elucidating the rules governing the assembly of human RNA polymerase II (hRPB), interactions between its subunits have been systematically analyzed. Eleven of the 12 expected hRPB subunits have previously been tested for reciprocal interactions (J. Biol. Chem. 272 (1997) 16815-16821). We now report the results obtained for the last subunit (hRPB4; Mol. Cell. Biol. 18 (1998) 1935-1945) and propose an essentially complete picture of the potential interactions occurring within hRPB. Finally, complementation experiments in yeast indicated that hRPB4 expression efficiently cured both heat and cold-sensitivity of RPB4-lacking strains, supporting the existence of conserved functional subunit interactions.
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Affiliation(s)
- S Schaller
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS/INSERM/ULP), BP 163, 67404, Illkirch, France
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45
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Flores A, Briand JF, Gadal O, Andrau JC, Rubbi L, Van Mullem V, Boschiero C, Goussot M, Marck C, Carles C, Thuriaux P, Sentenac A, Werner M. A protein-protein interaction map of yeast RNA polymerase III. Proc Natl Acad Sci U S A 1999; 96:7815-20. [PMID: 10393904 PMCID: PMC22144 DOI: 10.1073/pnas.96.14.7815] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure of the yeast RNA polymerase (pol) III was investigated by exhaustive two-hybrid screening using a library of random genomic fragments fused to the Gal4 activation domain. This procedure allowed us to identify contacts between individual polypeptides, localize the contact domains, and deduce a protein-protein interaction map of the multisubunit enzyme. In all but one case, pol III subunits were able to interact in vivo with one or sometimes two partner subunits of the enzyme or with subunits of TFIIIC. Four subunits that are common to pol I, II, and III (ABC27, ABC14.5, ABC10alpha, and ABC10beta), two that are common to pol I and III (AC40 and AC19), and one pol III-specific subunit (C11) can associate with defined regions of the two large subunits. These regions overlapped with highly conserved domains. C53, a pol III-specific subunit, interacted with a 37-kDa polypeptide that copurifies with the enzyme and therefore appears to be a unique pol III subunit (C37). Together with parallel interaction studies based on dosage-dependent suppression of conditional mutants, our data suggest a model of the pol III preinitiation complex.
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Affiliation(s)
- A Flores
- Service de Biochimie et Génétique Moléculaire, Bât. 142, Commissariat à l'Energie Atomique/Saclay, F-91191 Gif-sur-Yvette Cedex, France
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46
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Woychik NA. Fractions to functions: RNA polymerase II thirty years later. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:311-7. [PMID: 10384295 DOI: 10.1101/sqb.1998.63.311] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- N A Woychik
- Department of Molecular Genetics and Microbiology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway 08854, USA
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47
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Bruno T, Corbi N, Di Padova M, De Angelis R, Floridi A, Passananti C, Fanciulli M. The RNA polymerase II core subunit 11 interacts with keratin 19, a component of the intermediate filament proteins. FEBS Lett 1999; 453:273-7. [PMID: 10405159 DOI: 10.1016/s0014-5793(99)00733-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have previously cloned the human RNA polymerase II subunit 11, as a doxorubicin sensitive gene product. We suggested multiple tasks for this subunit, including structural and regulatory roles. With the aim to clarify the human RNA polymerase II subunit 11 function, we have identified its interacting protein partners using the yeast two-hybrid system. Here, we show that human RNA polymerase II subunit 11 specifically binds keratin 19, a component of the intermediate filament protein family, which is expressed in a tissue and differentiation-specific manner. In particular, keratin 19 is a part of the nuclear matrix intermediate filaments. We provide evidence that human RNA polymerase II subunit 11 interacts with keratin 19 via its N-terminal alpha motif, the same motif necessary for its interaction with the human RNA polymerase II core subunit 3. We found that keratin 19 contains two putative leucine zipper domains sharing peculiar homology with the alpha motif of human RNA polymerase II subunit 3. Finally, we demonstrate that keratin 19 can compete for binding human RNA polymerase II subunit 11/human RNA polymerase II subunit 3 in vitro, suggesting a possible regulatory role for this molecule in RNA polymerase II assembly/activity.
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Affiliation(s)
- T Bruno
- Cell Metabolism and Pharmacokinetics Laboratory, Regina Elena Cancer Institute, Rome, Italy
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48
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Thiru A, Hodach M, Eloranta JJ, Kostourou V, Weinzierl RO, Matthews S. RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes. J Mol Biol 1999; 287:753-60. [PMID: 10191143 DOI: 10.1006/jmbi.1999.2638] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The archaeal H and eukaryotic RPB5 RNA polymerase subunits are highly homologous and are likely to play a fundamental role in transcription that extends from archaea to humans. We report the structure of subunit H, in solution, from the archaeon Methanococcus jannaschii using multidimensional nuclear magnetic resonance. The structure reveals a novel fold containing a four-stranded mixed beta sheet that is flanked on one side by three short helices. The dominant feature is beta-ribbon motif, which presents a hydrophobic, basic surface, and defines a general RNA polymerase architectural scaffold.
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Affiliation(s)
- A Thiru
- Department of Biochemistry, Imperial College of Science Technology and Medicine, Exhibition Road, London, South Kensington, SW7 2AY, UK
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49
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Sheffer A, Varon M, Choder M. Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol Cell Biol 1999; 19:2672-80. [PMID: 10082533 PMCID: PMC84060 DOI: 10.1128/mcb.19.4.2672] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rpb4 and Rpb7 are two yeast RNA polymerase II (Pol II) subunits whose mechanistic roles have recently started to be deciphered. Although previous data suggest that Rpb7 can stably interact with Pol II only as a heterodimer with Rpb4, RPB7 is essential for viability, whereas RPB4 is essential only during some stress conditions. To resolve this discrepancy and to gain a better understanding of the mode of action of Rpb4, we took advantage of the inability of cells lacking RPB4 (rpb4Delta, containing Pol IIDelta4) to grow above 30 degrees C and screened for genes whose overexpression could suppress this defect. We thus discovered that overexpression of RPB7 could suppress the inability of rpb4Delta cells to grow at 34 degrees C (a relatively mild temperature stress) but not at higher temperatures. Overexpression of RPB7 could also partially suppress the cold sensitivity of rpb4Delta strains and fully suppress their inability to survive a long starvation period (stationary phase). Notably, however, overexpression of RPB4 could not override the requirement for RPB7. Consistent with the growth phenotype, overexpression of RPB7 could suppress the transcriptional defect characteristic of rpb4Delta cells during the mild, but not during a more severe, heat shock. We also demonstrated, through two reciprocal coimmunoprecipitation experiments, a stable interaction of the overproduced Rpb7 with Pol IIDelta4. Nevertheless, fewer Rpb7 molecules interacted with Pol IIDelta4 than with wild-type Pol II. Thus, a major role of Rpb4 is to augment the interaction of Rpb7 with Pol II. We suggest that Pol IIDelta4 contains a small amount of Rpb7 that is sufficient to support transcription only under nonstress conditions. When RPB7 is overexpressed, more Rpb7 assembles with Pol IIDelta4, enough to permit appropriate transcription also under some stress conditions.
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Affiliation(s)
- A Sheffer
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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50
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Miyao T, Woychik NA. RNA polymerase subunit RPB5 plays a role in transcriptional activation. Proc Natl Acad Sci U S A 1998; 95:15281-6. [PMID: 9860960 PMCID: PMC28034 DOI: 10.1073/pnas.95.26.15281] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mutation in RPB5 (rpb5-9), an essential RNA polymerase subunit assembled into RNA polymerases I, II, and III, revealed a role for this subunit in transcriptional activation. Activation by GAL4-VP16 was impaired upon in vitro transcription with mutant whole-cell extracts. In vivo experiments using inducible reporter plasmids and Northern analysis support the in vitro data and demonstrate that RPB5 influences activation at some, but not all, promoters. Remarkably, this mutation maps to a conserved region of human RPB5 implicated by others to play a role in activation. Chimeric human-yeast RPB5 containing this conserved region now can function in place of its yeast counterpart. The defects noted with rpb5-9 are similar to those seen in truncation mutants of the RPB1-carboxyl terminal domain (CTD). We demonstrate that RPB5 and the RPB1-CTD have overlapping roles in activation because the double mutant is synthetically lethal and has exacerbated activation defects at the GAL1/10 promoter. These studies demonstrate that there are multiple activation targets in RNA polymerase II and that RPB5 and the CTD have similar roles in activation.
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Affiliation(s)
- T Miyao
- University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Department of Molecular Genetics and Microbiology, 675 Hoes Lane, Piscataway, NJ 08854-5635, USA
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