1
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Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P. Three-step mechanism of promoter escape by RNA polymerase II. Mol Cell 2024; 84:1699-1710.e6. [PMID: 38604172 DOI: 10.1016/j.molcel.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/04/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024]
Abstract
The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.
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Affiliation(s)
- Yumeng Zhan
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frauke Grabbe
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Elisa Oberbeckmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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2
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Muniesa-Vargas A, Davó-Martínez C, Ribeiro-Silva C, van der Woude M, Thijssen KL, Haspels B, Häckes D, Kaynak ÜU, Kanaar R, Marteijn JA, Theil AF, Kuijten MMP, Vermeulen W, Lans H. Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure. Nat Commun 2024; 15:3490. [PMID: 38664429 PMCID: PMC11045817 DOI: 10.1038/s41467-024-47935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
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Affiliation(s)
- Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ben Haspels
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ülkem U Kaynak
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Maayke M P Kuijten
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
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3
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Hoag A, Duan M, Mao P. The role of Transcription Factor IIH complex in nucleotide excision repair. Environ Mol Mutagen 2024; 65 Suppl 1:72-81. [PMID: 37545038 PMCID: PMC10903506 DOI: 10.1002/em.22568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/05/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
DNA damage occurs throughout life from a variety of sources, and it is imperative to repair damage in a timely manner to maintain genome stability. Thus, DNA repair mechanisms are a fundamental part of life. Nucleotide excision repair (NER) plays an important role in the removal of bulky DNA adducts, such as cyclobutane pyrimidine dimers from ultraviolet light or DNA crosslinking damage from platinum-based chemotherapeutics, such as cisplatin. A main component for the NER pathway is transcription factor IIH (TFIIH), a multifunctional, 10-subunit protein complex with crucial roles in both transcription and NER. In transcription, TFIIH is a component of the pre-initiation complex and is important for promoter opening and the phosphorylation of RNA Polymerase II (RNA Pol II). During repair, TFIIH is important for DNA unwinding, recruitment of downstream repair factors, and verification of the bulky lesion. Several different disease states can arise from mutations within subunits of the TFIIH complex. Most strikingly are xeroderma pigmentosum (XP), XP combined with Cockayne syndrome (CS), and trichothiodystrophy (TTD). Here, we summarize the recruitment and functions of TFIIH in the two NER subpathways, global genomic (GG-NER) and transcription-coupled NER (TC-NER). We will also discuss how TFIIH's roles in the two subpathways lead to different genetic disorders.
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Affiliation(s)
- Allyson Hoag
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
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4
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Kitamura K, Hoshino T, Okabe A, Fukuyo M, Rahmutulla B, Tanaka N, Kobayashi S, Tanaka T, Shida T, Ueda M, Minamoto T, Matsubara H, Kaneda A, Ishii H, Matsushita K. The Link of mRNA and rRNA Transcription by PUF60/FIR through TFIIH/P62 as a Novel Therapeutic Target for Cancer. Int J Mol Sci 2023; 24:17341. [PMID: 38139171 PMCID: PMC10743661 DOI: 10.3390/ijms242417341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The interaction between mRNA and ribosomal RNA (rRNA) transcription in cancer remains unclear. RNAP I and II possess a common N-terminal tail (NTT), RNA polymerase subunit RPB6, which interacts with P62 of transcription factor (TF) IIH, and is a common target for the link between mRNA and rRNA transcription. The mRNAs and rRNAs affected by FUBP1-interacting repressor (FIR) were assessed via RNA sequencing and qRT-PCR analysis. An FIR, a c-myc transcriptional repressor, and its splicing form FIRΔexon2 were examined to interact with P62. Protein interaction was investigated via isothermal titration calorimetry measurements. FIR was found to contain a highly conserved region homologous to RPB6 that interacts with P62. FIRΔexon2 competed with FIR for P62 binding and coactivated transcription of mRNAs and rRNAs. Low-molecular-weight chemical compounds that bind to FIR and FIRΔexon2 were screened for cancer treatment. A low-molecular-weight chemical, BK697, which interacts with FIRΔexon2, inhibited tumor cell growth with rRNA suppression. In this study, a novel coactivation pathway for cancer-related mRNA and rRNA transcription through TFIIH/P62 by FIRΔexon2 was proposed. Direct evidence in X-ray crystallography is required in further studies to show the conformational difference between FIR and FIRΔexon2 that affects the P62-RBP6 interaction.
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Affiliation(s)
- Kouichi Kitamura
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Tyuji Hoshino
- Department of Molecular Design, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan;
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Nobuko Tanaka
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
| | - Sohei Kobayashi
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
- Department of Medical Technology and Sciences, Health and Sciences, International University of Health and Welfare, Chiba 286-8686, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Takashi Shida
- Research Team for Promoting Independence and Mental Health, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo 173-0015, Japan;
| | - Mashiro Ueda
- Master’s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba 305-8575, Japan;
| | - Toshinari Minamoto
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan;
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; (A.O.); (M.F.); (B.R.); (A.K.)
| | - Hideshi Ishii
- Medical Data Science, Center of Medical Innovation and Translational Research (CoMIT), Osaka University, Osaka 565-0871, Japan;
| | - Kazuyuki Matsushita
- Department of Laboratory Medicine, Chiba University Hospital, Chiba 260-8677, Japan; (K.K.); (N.T.); (S.K.)
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5
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Theil AF, Häckes D, Lans H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst) 2023; 132:103568. [PMID: 37977600 DOI: 10.1016/j.dnarep.2023.103568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/19/2023]
Abstract
The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands.
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6
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He F, Bravo M, Fan L. Helicases required for nucleotide excision repair: structure, function and mechanism. Enzymes 2023; 54:273-304. [PMID: 37945175 DOI: 10.1016/bs.enz.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway conserved from bacteria to humans. Various DNA helicases, a group of enzymes capable of separating DNA duplex into two strands through ATP binding and hydrolysis, are required by NER to unwind the DNA duplex around the lesion to create a repair bubble and for damage verification and removal. In prokaryotes, UvrB helicase is required for repair bubble formation and damage verification, while UvrD helicase is responsible for the removal of the excised damage containing single-strand (ss) DNA fragment. In addition, UvrD facilitates transcription-coupled repair (TCR) by backtracking RNA polymerase stalled at the lesion. In eukaryotes, two helicases XPB and XPD from the transcription factor TFIIH complex fulfill the helicase requirements of NER. Interestingly, homologs of all these four helicases UvrB, UvrD, XPB, and XPD have been identified in archaea. This review summarizes our current understanding about the structure, function, and mechanism of these four helicases.
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Affiliation(s)
- Feng He
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Marco Bravo
- Department of Biochemistry, University of California, Riverside, CA, United States
| | - Li Fan
- Department of Biochemistry, University of California, Riverside, CA, United States.
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7
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Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature 2023; 617:170-175. [PMID: 37076618 PMCID: PMC10416759 DOI: 10.1038/s41586-023-05959-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts1. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases2. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported3-7. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
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Affiliation(s)
- Jinseok Kim
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Chia-Lung Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- School of Life Sciences, Anhui University, Hefei, China
| | - Yanxiang Cui
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Filip M Golebiowski
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- Roche Polska, Warsaw, Poland
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Fumio Hanaoka
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe, Japan.
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.
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8
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Khalid F, Phan T, Qiang M, Maity P, Lasser T, Wiese S, Penzo M, Alupei M, Orioli D, Scharffetter-Kochanek K, Iben S. TFIIH mutations can impact on translational fidelity of the ribosome. Hum Mol Genet 2023; 32:1102-1113. [PMID: 36308430 PMCID: PMC10026254 DOI: 10.1093/hmg/ddac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/11/2022] [Accepted: 10/25/2022] [Indexed: 11/14/2022] Open
Abstract
TFIIH is a complex essential for transcription of protein-coding genes by RNA polymerase II, DNA repair of UV-lesions and transcription of rRNA by RNA polymerase I. Mutations in TFIIH cause the cancer prone DNA-repair disorder xeroderma pigmentosum (XP) and the developmental and premature aging disorders trichothiodystrophy (TTD) and Cockayne syndrome. A total of 50% of the TTD cases are caused by TFIIH mutations. Using TFIIH mutant patient cells from TTD and XP subjects we can show that the stress-sensitivity of the proteome is reduced in TTD, but not in XP. Using three different methods to investigate the accuracy of protein synthesis by the ribosome, we demonstrate that translational fidelity of the ribosomes of TTD, but not XP cells, is decreased. The process of ribosomal synthesis and maturation is affected in TTD cells and can lead to instable ribosomes. Isolated ribosomes from TTD patients show an elevated error rate when challenged with oxidized mRNA, explaining the oxidative hypersensitivity of TTD cells. Treatment of TTD cells with N-acetyl cysteine normalized the increased translational error-rate and restored translational fidelity. Here we describe a pathomechanism that might be relevant for our understanding of impaired development and aging-associated neurodegeneration.
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Affiliation(s)
- Fatima Khalid
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
| | - Tamara Phan
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
| | - Mingyue Qiang
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
| | - Pallab Maity
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
| | - Theresa Lasser
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit of Mass Spectrometry and Proteomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Marius Alupei
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
| | - Donata Orioli
- Institute of Molecular Genetics, Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | | | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University Medical Center, 89081 Ulm, Germany
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9
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Compe E, Pangou E, Le May N, Elly C, Braun C, Hwang JH, Coin F, Sumara I, Choi KW, Egly JM. Phosphorylation of XPD drives its mitotic role independently of its DNA repair and transcription functions. Sci Adv 2022; 8:eabp9457. [PMID: 35977011 PMCID: PMC9385140 DOI: 10.1126/sciadv.abp9457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The helicase XPD is known as a key subunit of the DNA repair/transcription factor TFIIH. However, here, we report that XPD, independently to other TFIIH subunits, can localize with the motor kinesin Eg5 to mitotic spindles and the midbodies of human cells. The XPD/Eg5 partnership is promoted upon phosphorylation of Eg5/T926 by the kinase CDK1, and conversely, it is reduced once Eg5/S1033 is phosphorylated by NEK6, a mitotic kinase that also targets XPD at T425. The phosphorylation of XPD does not affect its DNA repair and transcription functions, but it is required for Eg5 localization, checkpoint activation, and chromosome segregation in mitosis. In XPD-mutated cells derived from a patient with xeroderma pigmentosum, the phosphomimetic form XPD/T425D or even the nonphosphorylatable form Eg5/S1033A specifically restores mitotic chromosome segregation errors. These results thus highlight the phospho-dependent mitotic function of XPD and reveal how mitotic defects might contribute to XPD-related disorders.
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Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Evanthia Pangou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Cycle Cellulaire et Signalisation de l’Ubiquitine, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404, Strasbourg, France
| | - Nicolas Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Clémence Elly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Ji-Hyun Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Cycle Cellulaire et Signalisation de l’Ubiquitine, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404, Strasbourg, France
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Expression et Réparation du Génome, Equipe labellisée Ligue contre le Cancer, CNRS/INSERM/Université de Strasbourg, BP 163, Illkirch Cedex, C. U., 67404 Strasbourg, France
- College of Medicine, National Taiwan Institute, Taipei 10051, Taiwan
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10
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Meng Y, Feng R, Yang Z, Liu T, Huo T, Jiang H. Oxidative stress induced by realgar in neurons: p38 MAPK and ERK1/2 perturb autophagy and induce the p62-Keap1-Nrf2 feedback loop to activate the Nrf2 signalling pathway. J Ethnopharmacol 2022; 282:114582. [PMID: 34492322 DOI: 10.1016/j.jep.2021.114582] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Due to the modernization of traditional Chinese medicine (TCM) and the influence of traditional medication habits (TCM has no toxicity or side effects), arsenic poisoning incidents caused by the abuse of realgar and realgar-containing Chinese patent medicines have occurred occasionally. However, the potential mechanism of central nervous system toxicity of realgar remains unclear. AIM OF THE STUDY This study aimed to clarify the specific mechanism of realgar-induced neurotoxicity. MATERIALS AND METHODS In this study, the roles of ERK1/2 and p38 MAPK in realgar-induced neuronal autophagy and overactivation of the nuclear factor erythroid-derived factor 2-related factor (Nrf2) signalling pathways was investigated in vivo and in vitro. RESULTS The arsenic in realgar passed through the blood-brain barrier and accumulated in the brain, resulting in damage to neurons, synapses and myelin sheaths in the cerebral cortex and a decrease in the total antioxidant capacity. The specific mechanism is that the excessive activation of Nrf2 is regulated by the upstream signalling molecules ERK1/2 and p38MAPK. At the same time, p38 MAPK and ERK1/2 interfere with autophagy, thereby promoting autophagy initiation but causing subsequent dysfunctional autophagic degradation and inducing the p62-Keap1-Nrf2 feedback loop to promote Nrf2 signalling pathway activation and nerve cell apoptosis. CONCLUSIONS This study confirmed the role of the signalling molecules p38 MAPK and ERK1/2 in perturbing autophagy and inducing the p62-Keap1-Nrf2 feedback loop to activate the Nrf2 signalling pathway in realgar-induced neurotoxicity.
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Affiliation(s)
- Yuan Meng
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Rui Feng
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Zhao Yang
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Tingting Liu
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Taoguang Huo
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Hong Jiang
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China; The Key Laboratory of Liaoning Province on Toxic and Biological Effects of Arsenic, Shenyang, Liaoning, People's Republic of China.
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11
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Zhao T, Vvedenskaya IO, Lai WKM, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae. eLife 2021; 10:e71013. [PMID: 34652274 PMCID: PMC8589449 DOI: 10.7554/elife.71013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40-120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.
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Affiliation(s)
- Tingting Zhao
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - William KM Lai
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Shrabani Basu
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Craig D Kaplan
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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12
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Tomko EJ, Luyties O, Rimel JK, Tsai CL, Fuss JO, Fishburn J, Hahn S, Tsutakawa SE, Taatjes DJ, Galburt EA. The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning. J Mol Biol 2021; 433:166813. [PMID: 33453189 PMCID: PMC8327364 DOI: 10.1016/j.jmb.2021.166813] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
The general transcription factor TFIIH contains three ATP-dependent catalytic activities. TFIIH functions in nucleotide excision repair primarily as a DNA helicase and in Pol II transcription initiation as a dsDNA translocase and protein kinase. During initiation, the XPB/Ssl2 subunit of TFIIH couples ATP hydrolysis to dsDNA translocation facilitating promoter opening and the kinase module phosphorylates Pol II to facilitate the transition to elongation. These functions are conserved between metazoans and yeast; however, yeast TFIIH also drives transcription start-site scanning in which Pol II scans downstream DNA to locate productive start-sites. The ten-subunit holo-TFIIH from S. cerevisiae has a processive dsDNA translocase activity required for scanning and a structural role in scanning has been ascribed to the three-subunit TFIIH kinase module. Here, we assess the dsDNA translocase activity of ten-subunit holo- and core-TFIIH complexes (i.e. seven subunits, lacking the kinase module) from both S. cerevisiae and H. sapiens. We find that neither holo nor core human TFIIH exhibit processive translocation, consistent with the lack of start-site scanning in humans. Furthermore, in contrast to holo-TFIIH, the S. cerevisiae core-TFIIH also lacks processive translocation and its dsDNA-stimulated ATPase activity was reduced ~5-fold to a level comparable to the human complexes, potentially explaining the reported upstream shift in start-site observed in vitro in the absence of the S. cerevisiae kinase module. These results suggest that neither human nor S. cerevisiae core-TFIIH can translocate efficiently, and that the S. cerevisiae kinase module functions as a processivity factor to allow for robust transcription start-site scanning.
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Affiliation(s)
- Eric J Tomko
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olivia Luyties
- Dept. of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Jenna K Rimel
- Dept. of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jill O Fuss
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James Fishburn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Hahn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Eric A Galburt
- Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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13
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Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, Geverts B, Plummer DA, Bezstarosti K, Theil AF, Mitter R, Houtsmuller AB, Vermeulen W, Demmers JAA, Li S, van Vugt MATM, Lans H, Bernards R, Svejstrup JQ, Ray Chaudhuri A, Wyrick JJ, Marteijn JA. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 2021; 23:608-619. [PMID: 34108662 PMCID: PMC7611218 DOI: 10.1038/s41556-021-00692-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023]
Abstract
Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA polymerase II, causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions. However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR-Cas9 screen, we identified the elongation factor ELOF1 as an important factor in the transcription stress response following DNA damage. We show that ELOF1 has an evolutionarily conserved role in transcription-coupled nucleotide excision repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair transcription-blocking lesions and resume transcription. Additionally, ELOF1 modulates transcription to protect cells against transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage via two distinct mechanisms.
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Affiliation(s)
- Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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14
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Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, He Y. Structure of the human Mediator-bound transcription preinitiation complex. Science 2021; 372:52-56. [PMID: 33707221 PMCID: PMC8117670 DOI: 10.1126/science.abg3074] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 12/24/2022]
Abstract
Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.
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Affiliation(s)
- R Abdella
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - A Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - S Chen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - C J Inouye
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - R Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Y He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA
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15
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Hohrman K, Gonçalves D, Morano KA, Johnson JL. Disrupting progression of the yeast Hsp90 folding pathway at different transition points results in client-specific maturation defects. Genetics 2021; 217:iyab009. [PMID: 33789348 PMCID: PMC8045699 DOI: 10.1093/genetics/iyab009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/11/2021] [Indexed: 11/12/2022] Open
Abstract
The protein molecular chaperone Hsp90 (Heat shock protein, 90 kilodalton) plays multiple roles in the biogenesis and regulation of client proteins impacting myriad aspects of cellular physiology. Amino acid alterations located throughout Saccharomyces cerevisiae Hsp90 have been shown to result in reduced client activity and temperature-sensitive growth defects. Although some Hsp90 mutants have been shown to affect activity of particular clients more than others, the mechanistic basis of client-specific effects is unknown. We found that Hsp90 mutants that disrupt the early step of Hsp70 and Sti1 interaction, or show reduced ability to adopt the ATP-bound closed conformation characterized by Sba1 and Cpr6 interaction, similarly disrupt activity of three diverse clients, Utp21, Ssl2, and v-src. In contrast, mutants that appear to alter other steps in the folding pathway had more limited effects on client activity. Protein expression profiling provided additional evidence that mutants that alter similar steps in the folding cycle cause similar in vivo consequences. Our characterization of these mutants provides new insight into how Hsp90 and cochaperones identify and interact with diverse clients, information essential for designing pharmaceutical approaches to selectively inhibit Hsp90 function.
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Affiliation(s)
- Kaitlyn Hohrman
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Davi Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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16
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Masuda HP, Nakabashi M, Morgante PG, Kajihara D, de Setta N, Menck CFM, Van Sluys MA. Evidence for sub-functionalization of tandemly duplicated XPB nucleotide excision repair genes in Arabidopsis thaliana. Gene 2020; 754:144818. [PMID: 32485308 DOI: 10.1016/j.gene.2020.144818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022]
Abstract
Plants are continuously exposed to agents that can generate DNA lesions. Nucleotide Excision Repair (NER) is one of the repair pathways employed by plants to protect their genome, including from sunlight. The Xeroderma Pigmentosum type B (XPB) protein is a DNA helicase shown to be involved in NER and is also an essential subunitof the Transcription Factor IIH (TFIIH) complex. XPB was found to be a single copy gene in eukaryotes, but found as a tandem duplication in the plant Arabidopsis thaliana, AtXPB1 and AtXPB2. We aimed to investigate whether the XPB in tandem duplication was common within members of the Brassicaceae. We analyzed genomic DNA of species from different tribes of the family and the results indicate that the tandem duplication occurred in Camelineae tribe ancestor, of which A. thaliana belongs, at approximately 8 million years ago. Further experiments were devised to study possible functional roles for the A. thaliana AtXPB paralogs. A non-coincident expression profile of the paralogs was observed in various plant organs, developmental and cell cycle stages. AtXPB2 expression was observed in proliferating cells and clustered with the transcription of other components of the TFIIH such as p44, p52 and XPD/UVH6 along the cell cycle. AtXPB1 gene transcription, on the other hand, was enhanced specifically after UV-B irradiation in leaf trichomes. Altogether, our results reported herein suggest a functional specialization for the AtXPB paralogs: while the AtXPB2 paralog may have a role in cell proliferation and repair as XPB of other eukaryotes, the AtXPB1 paralog is most likely implicated in repair functions in highly specialized A. thaliana cells.
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Affiliation(s)
- Hana Paula Masuda
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Myna Nakabashi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Patricia G Morgante
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Universidade Estadual Paulista (UNESP), Campus de Registro São Paulo, SP, Brazil
| | - Daniela Kajihara
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Laboratório de Biologia Vascular, Instituto do Coração (InCor) da Faculdade de Medicina, Universidade de São Paulo, SP, Brazil
| | - Nathalia de Setta
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | | | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil.
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17
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Zurita M, Murillo-Maldonado JM. Drosophila as a Model Organism to Understand the Effects during Development of TFIIH-Related Human Diseases. Int J Mol Sci 2020; 21:ijms21020630. [PMID: 31963603 PMCID: PMC7013941 DOI: 10.3390/ijms21020630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/20/2022] Open
Abstract
Human mutations in the transcription and nucleotide excision repair (NER) factor TFIIH are linked with three human syndromes: xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS). In particular, different mutations in the XPB, XPD and p8 subunits of TFIIH may cause one or a combination of these syndromes, and some of these mutations are also related to cancer. The participation of TFIIH in NER and transcription makes it difficult to interpret the different manifestations observed in patients, particularly since some of these phenotypes may be related to problems during development. TFIIH is present in all eukaryotic cells, and its functions in transcription and DNA repair are conserved. Therefore, Drosophila has been a useful model organism for the interpretation of different phenotypes during development as well as the understanding of the dynamics of this complex. Interestingly, phenotypes similar to those observed in humans caused by mutations in the TFIIH subunits are present in mutant flies, allowing the study of TFIIH in different developmental processes. Furthermore, studies performed in Drosophila of mutations in different subunits of TFIIH that have not been linked to any human diseases, probably because they are more deleterious, have revealed its roles in differentiation and cell death. In this review, different achievements made through studies in the fly to understand the functions of TFIIH during development and its relationship with human diseases are analysed and discussed.
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18
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Nogales E, Greber BJ. High-resolution cryo-EM structures of TFIIH and their functional implications. Curr Opin Struct Biol 2019; 59:188-194. [PMID: 31600675 PMCID: PMC6951423 DOI: 10.1016/j.sbi.2019.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/27/2019] [Accepted: 08/25/2019] [Indexed: 01/26/2023]
Abstract
Eukaryotic transcription factor IIH (TFIIH) is a 500 kDa-multiprotein complex that harbors two SF2-family DNA-dependent ATPase/helicase subunits and the kinase activity of Cyclin-dependent kinase 7. TFIIH serves as a general transcription factor for transcription initiation by eukaryotic RNA polymerase II and plays an important role in nucleotide excision DNA repair. Aiming to understand the molecular mechanisms of its function and regulation in two key cellular pathways, the high-resolution structure of TFIIH has been pursued for decades. Recent breakthroughs, largely enabled by methodological advances in cryo-electron microscopy, have finally revealed the structure of TFIIH and its interactions in the context of the Pol II-pre-initiation complex, and provide a first glimpse of a TFIIH-containing assembly in DNA repair. Here, we review and discuss these recent structural insights and their functional implications.
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Affiliation(s)
- Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
| | - Basil J Greber
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
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19
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Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nat Struct Mol Biol 2019; 26:397-406. [PMID: 31110295 PMCID: PMC6642811 DOI: 10.1038/s41594-019-0220-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/29/2019] [Indexed: 12/11/2022]
Abstract
Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly's global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE-p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.
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Affiliation(s)
- Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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20
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Sandoz J, Nagy Z, Catez P, Caliskan G, Geny S, Renaud JB, Concordet JP, Poterszman A, Tora L, Egly JM, Le May N, Coin F. Functional interplay between TFIIH and KAT2A regulates higher-order chromatin structure and class II gene expression. Nat Commun 2019; 10:1288. [PMID: 30894545 PMCID: PMC6426930 DOI: 10.1038/s41467-019-09270-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
The TFIIH subunit XPB is involved in combined Xeroderma Pigmentosum and Cockayne syndrome (XP-B/CS). Our analyses reveal that XPB interacts functionally with KAT2A, a histone acetyltransferase (HAT) that belongs to the hSAGA and hATAC complexes. XPB interacts with KAT2A-containing complexes on chromatin and an XP-B/CS mutation specifically elicits KAT2A-mediated large-scale chromatin decondensation. In XP-B/CS cells, the abnormal recruitment of TFIIH and KAT2A to chromatin causes inappropriate acetylation of histone H3K9, leading to aberrant formation of transcription initiation complexes on the promoters of several hundred genes and their subsequent overexpression. Significantly, this cascade of events is similarly sensitive to KAT2A HAT inhibition or to the rescue with wild-type XPB. In agreement, the XP-B/CS mutation increases KAT2A HAT activity in vitro. Our results unveil a tight connection between TFIIH and KAT2A that controls higher-order chromatin structure and gene expression and provide new insights into transcriptional misregulation in a cancer-prone DNA repair-deficient disorder.
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Affiliation(s)
- Jérémy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Zita Nagy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Philippe Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Gizem Caliskan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Sylvain Geny
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Jean-Baptiste Renaud
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Nicolas Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France.
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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21
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Abstract
Transcription factor IIH (TFIIH) is a multiprotein complex involved in both eukaryotic transcription and DNA repair, revealing a tight connection between these two processes. Composed of 10 subunits, it can be resolved into a 7-subunits core complex with the XPB translocase and the XPD helicase, and the 3-subunits kinase complex CAK, which also exists as a free complex with a distinct function. Initially identified as basal transcription factor, TFIIH also participates in transcription regulation and plays a key role in nucleotide excision repair (NER) for opening DNA at damaged sites, lesion verification and recruitment of additional repair factors. Our understanding of TFIIH function in eukaryotic cells has greatly benefited from studies of the genetic rare diseases xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD), that are not only characterized by cancer and aging predispositions but also by neurological and developmental defects. Although much remains unknown about TFIIH function, significant progresses have been done regarding the structure of the complex, the functions of its catalytic subunits and the multiple roles of the regulatory core-TFIIH subunits. This review provides a non-exhaustive survey of key discoveries on the structure and function of this pivotal factor, which can be considered as a promising target for therapeutic strategies.
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Affiliation(s)
- Olga Kolesnikova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Laura Radu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
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22
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Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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23
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Lu H, Yu D, Hansen AS, Ganguly S, Liu R, Heckert A, Darzacq X, Zhou Q. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature 2018; 558:318-323. [PMID: 29849146 PMCID: PMC6475116 DOI: 10.1038/s41586-018-0174-3] [Citation(s) in RCA: 347] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 05/02/2018] [Indexed: 12/15/2022]
Abstract
Hyperphosphorylation of the C-terminal domain (CTD) of the RPB1 subunit of human RNA polymerase (Pol) II is essential for transcriptional elongation and mRNA processing1-3. The CTD contains 52 heptapeptide repeats of the consensus sequence YSPTSPS. The highly repetitive nature and abundant possible phosphorylation sites of the CTD exert special constraints on the kinases that catalyse its hyperphosphorylation. Positive transcription elongation factor b (P-TEFb)-which consists of CDK9 and cyclin T1-is known to hyperphosphorylate the CTD and negative elongation factors to stimulate Pol II elongation1,4,5. The sequence determinant on P-TEFb that facilitates this action is currently unknown. Here we identify a histidine-rich domain in cyclin T1 that promotes the hyperphosphorylation of the CTD and stimulation of transcription by CDK9. The histidine-rich domain markedly enhances the binding of P-TEFb to the CTD and functional engagement with target genes in cells. In addition to cyclin T1, at least one other kinase-DYRK1A 6 -also uses a histidine-rich domain to target and hyperphosphorylate the CTD. As a low-complexity domain, the histidine-rich domain also promotes the formation of phase-separated liquid droplets in vitro, and the localization of P-TEFb to nuclear speckles that display dynamic liquid properties and are sensitive to the disruption of weak hydrophobic interactions. The CTD-which in isolation does not phase separate, despite being a low-complexity domain-is trapped within the cyclin T1 droplets, and this process is enhanced upon pre-phosphorylation by CDK7 of transcription initiation factor TFIIH1-3. By using multivalent interactions to create a phase-separated functional compartment, the histidine-rich domain in kinases targets the CTD into this environment to ensure hyperphosphorylation and efficient elongation of Pol II.
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Affiliation(s)
- Huasong Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dan Yu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sourav Ganguly
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rongdiao Liu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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24
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Kim YD, Hwang SL, Lee EJ, Kim HM, Chung MJ, Elfadl AK, Lee SE, Nedumaran B, Harris RA, Jeong KS. Melatonin ameliorates alcohol-induced bile acid synthesis by enhancing miR-497 expression. J Pineal Res 2017; 62. [PMID: 28095641 DOI: 10.1111/jpi.12386] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/11/2017] [Indexed: 12/12/2022]
Abstract
Alcoholic liver disease is a major cause of chronic liver disease worldwide, and cannabinoid receptor type 1 (CB1R) is involved in a diverse metabolic diseases. B-cell translocation gene 2 (BTG2) and yin yang 1 (YY1) are a potent regulator of biological conditions. Melatonin plays a crucial role in regulating diverse physiological functions and metabolic homeostasis. MicroRNAs are key regulators of various biological processes. Herein, we demonstrate that melatonin improves bile acid synthesis in the liver of alcohol-fed mice by controlling miR-497 expression. The level of bile acid and the expression of Cb1r, Btg2, Yy1, and bile acid synthetic enzymes were significantly elevated in the livers of Lieber-DeCarli alcohol-fed mice. The overexpression of Btg2 enhanced Yy1 gene expression and bile acid production, whereas disrupting the CB1R-BTG2-YY1 cascade protected against the bile acid synthesis caused by alcohol challenge. We identified an alcohol-mediated YY1 binding site on the cholesterol 7α-hydroxylase (Cyp7a1) gene promoter using promoter deletion analysis and chromatin immunoprecipitation assays. Notably, melatonin attenuated the alcohol-stimulated induction of Btg2, Yy1 mRNA levels and bile acid production by promoting miR-497. Overexpression of a miR-497 mimic dramatically diminished the increase of Btg2 and Yy1 gene expression as well as bile acid production by alcohol, whereas this phenomenon was reversed by miR-497 inhibitor. These results demonstrate that the upregulation of miR-497 by melatonin represses alcohol-induced bile acid synthesis by attenuating the BTG2-YY1 signaling pathway. The melatonin-miR497 signaling network may provide novel therapeutic targets for the treatment of hepatic metabolic dysfunction caused by the alcohol-dependent pathway.
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Affiliation(s)
- Yong Deuk Kim
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
- Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, Korea
- School of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Seung-Lark Hwang
- School of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Eun-Joo Lee
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
- Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, Korea
| | - Hyeong-Mi Kim
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
- Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, Korea
| | - Myung-Jin Chung
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
- Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, Korea
| | - Ahmed K Elfadl
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
- Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, Korea
| | - Sung-Eun Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Balachandar Nedumaran
- Department of Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Robert A Harris
- Roudebush VA Medical Center and the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kyu-Shik Jeong
- Department of Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
- Stem Cell Therapeutic Research Institute, Kyungpook National University, Daegu, Korea
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25
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Abstract
Two papers in this issue of Molecular Cell provide insights into how the multisubunit Mediator coactivator complex dynamically links enhancer-bound activators to the RNA polymerase II machinery at the core promoter.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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26
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Abstract
XPD, as part of the TFIIH complex, has classically been linked to the damage verification step of nucleotide excision repair (NER). However, recent data indicate that XPD, due to its iron-sulfur center interacts with the iron sulfur cluster assembly proteins, and may interact with other proteins in the cell to mediate a diverse set of biological functions including cell cycle regulation, mitosis, and mitochondrial function. In this perspective, after first reviewing the function and some of the key disease causing variants that affect XPD's interaction with TFIIH and the CDK-activating kinase complex (CAK), we investigate these intriguing cellular roles of XPD and highlight important unanswered questions that provide a fertile ground for further scientific exploration.
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Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States.
| | - Jochen Kuper
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, Wuerzburg, Germany.
| | - Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, Wuerzburg, Germany.
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27
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Kuschal C, Botta E, Orioli D, Digiovanna JJ, Seneca S, Keymolen K, Tamura D, Heller E, Khan SG, Caligiuri G, Lanzafame M, Nardo T, Ricotti R, Peverali FA, Stephens R, Zhao Y, Lehmann AR, Baranello L, Levens D, Kraemer KH, Stefanini M. GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy. Am J Hum Genet 2016; 98:627-42. [PMID: 26996949 DOI: 10.1016/j.ajhg.2016.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/10/2016] [Indexed: 12/24/2022] Open
Abstract
The general transcription factor IIE (TFIIE) is essential for transcription initiation by RNA polymerase II (RNA pol II) via direct interaction with the basal transcription/DNA repair factor IIH (TFIIH). TFIIH harbors mutations in two rare genetic disorders, the cancer-prone xeroderma pigmentosum (XP) and the cancer-free, multisystem developmental disorder trichothiodystrophy (TTD). The phenotypic complexity resulting from mutations affecting TFIIH has been attributed to the nucleotide excision repair (NER) defect as well as to impaired transcription. Here, we report two unrelated children showing clinical features typical of TTD who harbor different homozygous missense mutations in GTF2E2 (c.448G>C [p.Ala150Pro] and c.559G>T [p.Asp187Tyr]) encoding the beta subunit of transcription factor IIE (TFIIEβ). Repair of ultraviolet-induced DNA damage was normal in the GTF2E2 mutated cells, indicating that TFIIE was not involved in NER. We found decreased protein levels of the two TFIIE subunits (TFIIEα and TFIIEβ) as well as decreased phosphorylation of TFIIEα in cells from both children. Interestingly, decreased phosphorylation of TFIIEα was also seen in TTD cells with mutations in ERCC2, which encodes the XPD subunit of TFIIH, but not in XP cells with ERCC2 mutations. Our findings support the theory that TTD is caused by transcriptional impairments that are distinct from the NER disorder XP.
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Affiliation(s)
- Christiane Kuschal
- Dermatology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Elena Botta
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Donata Orioli
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - John J Digiovanna
- Dermatology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Seneca
- Center for Medical Genetics, Research Group Reproduction and Genetics, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Kathelijn Keymolen
- Center for Medical Genetics, Research Group Reproduction and Genetics, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Deborah Tamura
- Dermatology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Elizabeth Heller
- Dermatology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sikandar G Khan
- Dermatology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Giuseppina Caligiuri
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Manuela Lanzafame
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Tiziana Nardo
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Roberta Ricotti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Fiorenzo A Peverali
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Robert Stephens
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA; Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Yongmei Zhao
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Alan R Lehmann
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Laura Baranello
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kenneth H Kraemer
- Dermatology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Miria Stefanini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy.
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28
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Tajedin L, Tarique M, Tuteja R. Plasmodium falciparum XPD translocates in 5' to 3' direction, is expressed throughout the blood stages, and interacts with p44. Protoplasma 2015; 252:1487-1504. [PMID: 25708921 DOI: 10.1007/s00709-015-0779-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
XPD helicase, a TFIIH subunit, is essential for several processes including transcription, NER, cell cycle regulation, and apoptosis in eukaryotes. Another component of TFIIH, namely p44, is among the well-known interacting partners of XPD and is vital in regulating the helicase activities of latter. However, none of the above mentioned proteins have been functionally characterized in Plasmodium falciparum. Consequently, in this study, we performed detailed studies on XPD and its interacting partner, p44, from P. falciparum 3D7 strain. Accordingly, we expressed and purified recombinant PfXPD and its fragments and Pfp44 proteins and characterized the enzymatic activities of PfXPD and its fragments. The in vivo stage-specific expression and subcellular localizations of PfXPD and Pfp44 proteins were studied using the specific antibodies in the intraerythrocytic developmental stages of P. falciparum 3D7 strain. Our results suggest that PfXPD displays the characteristic ssDNA-dependent ATPase and 5'-3' DNA helicase activities. We also report the existence of two high molecular weight forms of p44 in P. falciparum 3D7 strain. Both PfXPD and Pfp44 colocalize in the nucleus and interact with each other, which suggest that they are most likely components of the same complex apparently, TFIIH. Furthermore, during trophozoite and schizont stages, both proteins exhibit a distinct cytoplasmic distribution pattern which implies that PfXPD and Pfp44 might also be involved in other functions. These studies will aid in understanding the basic biology of malaria parasite.
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Affiliation(s)
- Leila Tajedin
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Mohammed Tarique
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India.
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Schmitt DR, Kuper J, Elias A, Kisker C. The structure of the TFIIH p34 subunit reveals a von Willebrand factor A like fold. PLoS One 2014; 9:e102389. [PMID: 25013903 PMCID: PMC4094531 DOI: 10.1371/journal.pone.0102389] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/19/2014] [Indexed: 11/19/2022] Open
Abstract
RNA polymerase II dependent transcription and nucleotide excision repair are mediated by a multifaceted interplay of subunits within the general transcription factor II H (TFIIH). A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these vital cellular processes. The importance of this complex becomes further evident in the context of severe diseases like xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy, that arise from single point mutations in TFIIH subunits. Here we describe the structure of the p34 subunit of the TFIIH complex from the eukaryotic thermophilic fungus Chaetomium thermophilum. The structure revealed that p34 contains a von Willebrand Factor A (vWA) like domain, a fold which is generally known to be involved in protein-protein interactions. Within TFIIH p34 strongly interacts with p44, a positive regulator of the helicase XPD. Putative protein-protein interfaces are analyzed and possible binding sites for the p34-p44 interaction suggested.
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Affiliation(s)
- Dominik R. Schmitt
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Agnes Elias
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Wuerzburg, Germany
- * E-mail:
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30
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Kunihiro S, Kowata H, Kondou Y, Takahashi S, Matsui M, Berberich T, Youssefian S, Hidema J, Kusano T. Overexpression of rice OsREX1-S, encoding a putative component of the core general transcription and DNA repair factor IIH, renders plant cells tolerant to cadmium- and UV-induced damage by enhancing DNA excision repair. Planta 2014; 239:1101-1111. [PMID: 24563249 DOI: 10.1007/s00425-014-2042-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/03/2014] [Indexed: 06/03/2023]
Abstract
Screening of 40,000 Arabidopsis FOX (Full-length cDNA Over-eXpressor gene hunting system) lines expressing rice full-length cDNAs brings us to identify four cadmium (Cd)-tolerant lines, one of which carried OsREX1-S as a transgene. OsREX1-S shows the highest levels of identity to Chlamydomonas reinhardtii REX1-S (referred to as CrREX1-S, in which REX denotes Required for Excision) and to yeast and human TFB5s (RNA polymerase II transcription factor B5), both of which are components of the general transcription and DNA repair factor, TFIIH. Transient expression of OsREX1-S consistently localized the protein to the nucleus of onion cells. The newly generated transgenic Arabidopsis plants expressing OsREX1-S reproducibly displayed enhanced Cd tolerance, confirming that the Cd-tolerance of the initial identified line was conferred solely by OsREX1-S expression. Furthermore, transgenic Arabidopsis plants expressing OsREX1-S exhibited ultraviolet-B (UVB) tolerance by reducing the amounts of cyclobutane pyrimidine dimers produced by UVB radiation. Moreover, those transgenic OsREX1-S Arabidopsis plants became resistant to bleomycin (an inducer of DNA strand break) and mitomycin C (DNA intercalating activity), compared to wild type. Our results indicate that OsREX1-S renders host plants tolerant to Cd, UVB radiation, bleomycin and mitomycin C through the enhanced DNA excision repair.
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Affiliation(s)
- Shuta Kunihiro
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
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31
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Wong KH, Jin Y, Struhl K. TFIIH phosphorylation of the Pol II CTD stimulates mediator dissociation from the preinitiation complex and promoter escape. Mol Cell 2014; 54:601-12. [PMID: 24746699 DOI: 10.1016/j.molcel.2014.03.024] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 02/19/2014] [Accepted: 03/07/2014] [Indexed: 11/30/2022]
Abstract
The transition between transcriptional initiation and elongation by RNA polymerase (Pol) II is associated with phosphorylation of its C-terminal tail (CTD). Depletion of Kin28, the TFIIH subunit that phosphorylates the CTD, does not affect elongation but causes Pol II occupancy profiles to shift upstream in a FACT-independent manner indicative of a defect in promoter escape. Stronger defects in promoter escape are linked to stronger effects on preinitiation complex formation and transcription, suggesting that impairment in promoter escape results in premature dissociation of general factors and Pol II near the promoter. Kin28 has a stronger effect on genes whose transcription is dependent on SAGA as opposed to TFIID. Strikingly, Kin28 depletion causes a dramatic increase in Mediator at the core promoter. These observations suggest that TFIIH phosphorylation of the CTD causes Mediator dissociation, thereby permitting rapid promoter escape of Pol II from the preinitiation complex.
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Affiliation(s)
- Koon Ho Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Yi Jin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Chabot PR, Raiola L, Lussier-Price M, Morse T, Arseneault G, Archambault J, Omichinski JG. Structural and functional characterization of a complex between the acidic transactivation domain of EBNA2 and the Tfb1/p62 subunit of TFIIH. PLoS Pathog 2014; 10:e1004042. [PMID: 24675874 PMCID: PMC3968163 DOI: 10.1371/journal.ppat.1004042] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/15/2014] [Indexed: 11/30/2022] Open
Abstract
Infection with the Epstein-Barr virus (EBV) can lead to a number of human diseases including Hodgkin's and Burkitt's lymphomas. The development of these EBV-linked diseases is associated with the presence of nine viral latent proteins, including the nuclear antigen 2 (EBNA2). The EBNA2 protein plays a crucial role in EBV infection through its ability to activate transcription of both host and viral genes. As part of this function, EBNA2 associates with several host transcriptional regulatory proteins, including the Tfb1/p62 (yeast/human) subunit of the general transcription factor IIH (TFIIH) and the histone acetyltransferase CBP(CREB-binding protein)/p300, through interactions with its C-terminal transactivation domain (TAD). In this manuscript, we examine the interaction of the acidic TAD of EBNA2 (residues 431-487) with the Tfb1/p62 subunit of TFIIH and CBP/p300 using nuclear magnetic resonance (NMR) spectroscopy, isothermal titration calorimeter (ITC) and transactivation studies in yeast. NMR studies show that the TAD of EBNA2 binds to the pleckstrin homology (PH) domain of Tfb1 (Tfb1PH) and that residues 448-471 (EBNA2₄₄₈₋₄₇₁) are necessary and sufficient for this interaction. NMR structural characterization of a Tfb1PH-EBNA2₄₄₈₋₄₇₁ complex demonstrates that the intrinsically disordered TAD of EBNA2 forms a 9-residue α-helix in complex with Tfb1PH. Within this helix, three hydrophobic amino acids (Trp458, Ile461 and Phe462) make a series of important interactions with Tfb1PH and their importance is validated in ITC and transactivation studies using mutants of EBNA2. In addition, NMR studies indicate that the same region of EBNA2 is also required for binding to the KIX domain of CBP/p300. This study provides an atomic level description of interactions involving the TAD of EBNA2 with target host proteins. In addition, comparison of the Tfb1PH-EBNA2₄₄₈₋₄₇₁ complex with structures of the TAD of p53 and VP16 bound to Tfb1PH highlights the versatility of intrinsically disordered acidic TADs in recognizing common target host proteins.
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Affiliation(s)
- Philippe R. Chabot
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
| | - Luca Raiola
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
| | - Mathieu Lussier-Price
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
| | - Thomas Morse
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
| | - Genevieve Arseneault
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
| | - Jacques Archambault
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
| | - James G. Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Succursale Centre-Ville, Montréal, Québec, Canada
- * E-mail:
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Bogolyubov DS, Batalova FM, Kiselyov AM, Stepanova IS. Nuclear structures in Tribolium castaneum oocytes. Cell Biol Int 2013; 37:1061-79. [PMID: 23686847 DOI: 10.1002/cbin.10135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/21/2013] [Indexed: 12/12/2022]
Abstract
The first ultrastructural and immunomorphological characteristics of the karyosphere (karyosome) and extrachromosomal nuclear bodies in the red flour beetle, Tribolium castaneum, are presented. The karyosphere forms early in the diplotene stage of meiotic prophase by the gathering of all oocyte chromosomes in a limited nuclear volume. Using the BrUTP assay, T. castaneum oocyte chromosomes united in the karyosphere maintain their transcriptional activity until the end of oocyte growth. Hyperphosphorylated RNA polymerase II and basal transcription factors (TFIID and TFIIH) were detected in the perichromatin region of the karyosphere. The T. castaneum karyosphere has an extrachromosomal capsule that separates chromosomes from the rest of the nucleoplasm. Certain structural proteins (F-actin, lamin B) were found in the capsule. Unexpectedly, the karyosphere capsule in T. castaneum oocytes was found to be enriched in TMG-capped snRNAs, which suggests that the capsule is not only a structural support for the karyosphere, but may be involved in biogenesis of snRNPs. We also identified the counterparts of 'universal' extrachromosomal nuclear domains, Cajal bodies (CBs) and interchromatin granule clusters (IGCs). Nuclear bodies containing IGC marker protein SC35 display some features unusual for typical IGCs. SC35 domains in T. castaneum oocytes are predominantly fibrillar complex bodies that do not contain trimethyl guanosine (TMG)-capped small nuclear (sn) RNAs. Microinjections of 2'-O-methyl (U)22 probes into the oocytes allowed revealing poly(A)+ RNAs in these nuclear domains. Several proteins related to mRNA export (heterogeneous ribonucleoprotein core protein A1, export adapters Y14 and Aly and export receptor NXF1) were also detected there. We believe that unusual SC35 nuclear domains of T. castaneum oocytes are possibly involved in mRNP but not snRNP biogenesis.
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Affiliation(s)
- Dmitry S Bogolyubov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia.
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Zhu Q, Wani G, Sharma N, Wani A. Lack of CAK complex accumulation at DNA damage sites in XP-B and XP-B/CS fibroblasts reveals differential regulation of CAK anchoring to core TFIIH by XPB and XPD helicases during nucleotide excision repair. DNA Repair (Amst) 2012; 11:942-50. [PMID: 23083890 DOI: 10.1016/j.dnarep.2012.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 09/05/2012] [Accepted: 09/10/2012] [Indexed: 11/15/2022]
Abstract
Transcription factor II H (TFIIH) is composed of core TFIIH and Cdk-activating kinase (CAK) complexes. Besides transcription, TFIIH also participates in nucleotide excision repair (NER), verifying DNA lesions through its helicase components XPB and XPD. The assembly state of TFIIH is known to be affected by truncation mutations in xeroderma pigmentosum group G/Cockayne syndrome (XP-G/CS). Here, we showed that CAK component MAT1 was rapidly recruited to UV-induced DNA damage sites, co-localizing with core TFIIH component p62, and dispersed from the damage sites upon completion of DNA repair. While the core TFIIH-CAK association remained intact, MAT1 failed to accumulate at DNA damage sites in fibroblasts harboring XP-B or XP-B/CS mutations. Nevertheless, MAT1, XPD and XPC as well as XPG were able to accumulate at damage sites in XP-D fibroblasts, in which the core TFIIH-CAK association also remained intact. Interestingly, XPG recruitment was impaired in XP-B/CS fibroblasts derived from patients with mild phenotype, but persisted in XP-B/CS fibroblasts from severely affected patients resulting in a nonfunctional preincision complex. An examination of steady-state levels of RNA polymerase II (RNAPII) indicated that UV-induced RNAPII phosphorylation was dramatically reduced in XP-B/CS fibroblasts. These results demonstrated that the CAK rapidly disassociates from the core TFIIH upon assembly of nonfunctional preincision complex in XP-B and XP-B/CS cells. The persistency of nonfunctional preincision complex correlates with the severity exhibited by XP-B patients. The results suggest that XPB and XPD helicases differentially regulate the anchoring of CAK to core TFIIH during damage verification step of NER.
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Affiliation(s)
- Qianzheng Zhu
- Department of Radiology, The Ohio State University, Columbus, OH 43210, USA.
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35
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Balasingham SV, Zegeye ED, Homberset H, Rossi ML, Laerdahl JK, Bohr VA, Tønjum T. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB. PLoS One 2012; 7:e36960. [PMID: 22615856 PMCID: PMC3353954 DOI: 10.1371/journal.pone.0036960] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 04/11/2012] [Indexed: 11/23/2022] Open
Abstract
XPB, also known as ERCC3 and RAD25, is a 3′→5′ DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA) surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3′→5′ DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg2+/Mn2+. Consistent with the 3′→5′ polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3′ overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3′ DNA tail, it was not active on substrates containing a 3′ RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.
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Affiliation(s)
- Seetha V. Balasingham
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ephrem Debebe Zegeye
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Marie L. Rossi
- Laboratory of Molecular Gerontology, NIH Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Jon K. Laerdahl
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, NIH Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- * E-mail:
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36
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Abstract
Nucleotide excision repair (NER) is a DNA repair pathway that is responsible for removing a variety of lesions caused by harmful UV light, chemical carcinogens, and environmental mutagens from DNA. NER involves the concerted action of over 30 proteins that sequentially recognize a lesion, excise it in the form of an oligonucleotide, and fill in the resulting gap by repair synthesis. ERCC1-XPF and XPG are structure-specific endonucleases responsible for carrying out the incisions 5' and 3' to the damage respectively, culminating in the release of the damaged oligonucleotide. This review focuses on the recent work that led to a greater understanding of how the activities of ERCC1-XPF and XPG are regulated in NER to prevent unwanted cuts in DNA or the persistence of gaps after incision that could result in harmful, cytotoxic DNA structures.
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Affiliation(s)
| | - Barbara Orelli
- Department of Pharmacological Sciences, Stony Brook, NY 11794-3400
| | - Orlando D. Schärer
- Department of Pharmacological Sciences, Stony Brook, NY 11794-3400
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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Kainov DE, Selth LA, Svejstrup JQ, Egly JM, Poterzsman A. Interacting partners of the Tfb2 subunit from yeast TFIIH. DNA Repair (Amst) 2010; 9:33-9. [PMID: 19897425 DOI: 10.1016/j.dnarep.2009.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 10/03/2009] [Accepted: 10/06/2009] [Indexed: 11/29/2022]
Abstract
TFIIH is an evolutionary conserved eukaryotic multi-protein complex composed of ten subunits. It is involved in transcription, cell cycle regulation, RNA splicing and the nucleotide excision DNA repair pathway (NER). Depending on the process in which it is functioning, the composition of TFIIH varies and activities of its subunits are differentially regulated. Here we focused on interplay between the Ssl2, Tfb2 and Tfb5 subunits of TFIIH from Saccharomyces cerevisiae. We found that Tfb2 bridges the Ssl2 helicase and the NER-specific Tfb5 subunit. Moreover, the Tfb5-interacting domain of Tfb2 also binds nucleic acids (NA), although the addition of Tfb5 triggers dissociation of NA from Tfb2. In yeast cells, deletion of TFB5 is more detrimental to NER than loss of the Tfb5/NA-interacting domain of Tfb2, while combining these mutations resulted in suppression of the UV sensitivity of tfb5Delta. The implications of our findings in regards to TFIIH function and group A trichothiodystrophy, an inherited disease associated with mutations in the human TFB5 gene, are discussed.
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Affiliation(s)
- Denis E Kainov
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
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Giglia-Mari G, Theil AF, Mari PO, Mourgues S, Nonnekens J, Andrieux LO, de Wit J, Miquel C, Wijgers N, Maas A, Fousteri M, Hoeijmakers JHJ, Vermeulen W. Differentiation driven changes in the dynamic organization of Basal transcription initiation. PLoS Biol 2009; 7:e1000220. [PMID: 19841728 PMCID: PMC2754661 DOI: 10.1371/journal.pbio.1000220] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 09/07/2009] [Indexed: 01/01/2023] Open
Abstract
A novel mouse model reveals that the dynamic behavior of transcription factors can vary considerably between different cells of an organism. Studies based on cell-free systems and on in vitro–cultured living cells support the concept that many cellular processes, such as transcription initiation, are highly dynamic: individual proteins stochastically bind to their substrates and disassemble after reaction completion. This dynamic nature allows quick adaptation of transcription to changing conditions. However, it is unknown to what extent this dynamic transcription organization holds for postmitotic cells embedded in mammalian tissue. To allow analysis of transcription initiation dynamics directly into living mammalian tissues, we created a knock-in mouse model expressing fluorescently tagged TFIIH. Surprisingly and in contrast to what has been observed in cultured and proliferating cells, postmitotic murine cells embedded in their tissue exhibit a strong and long-lasting transcription-dependent immobilization of TFIIH. This immobilization is both differentiation driven and development dependent. Furthermore, although very statically bound, TFIIH can be remobilized to respond to new transcriptional needs. This divergent spatiotemporal transcriptional organization in different cells of the soma revisits the generally accepted highly dynamic concept of the kinetic framework of transcription and shows how basic processes, such as transcription, can be organized in a fundamentally different fashion in intact organisms as previously deduced from in vitro studies. The accepted model of eukaryotic mRNA production is that transcription factors spend most of their time diffusing throughout the cell nucleus, encountering gene promoters (their substrate) in a random fashion and binding to them for a very short time. A similar modus operandi has been accepted as a paradigm for interactions within most of the chromatin-associated enzymatic processes (transcription, replication, DNA damage response). However, it is not known whether such behavior is indeed a common characteristic for all cells in the organism. To answer this question, we generated a knock-in mouse that expresses in all cells a fluorescently tagged transcription factor (TFIIH) that functions in both transcription initiation and DNA repair. This new tool, when combined with quantitative imaging techniques, allowed us to monitor the mobility of this transcription factor in virtually all living tissues. In this study, we show that, in contrast to the aforementioned paradigm, in highly differentiated postmitotic cells such as neurons, hepatocytes, and cardiac myocytes, TFIIH is effectively immobilized on the chromatin during transcription, whereas in proliferative cells, TFIIH has the same dynamic behavior as in cultured cells. Our study also points out that results obtained from in vitro or cultured cell systems cannot always be directly extrapolated to the whole organism. More importantly, this raises a question for researchers in the transcription field: why do some cells opt for a dynamic framework for transcription, whereas others exhibit a static one?
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Affiliation(s)
- Giuseppina Giglia-Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
- * E-mail: (GG-M); (WV)
| | - Arjan F. Theil
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Pierre-Olivier Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Sophie Mourgues
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Julie Nonnekens
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Jan de Wit
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Nils Wijgers
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Maria Fousteri
- Department of Toxicogenetics, LUMC, Leiden, The Netherlands
| | | | - Wim Vermeulen
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- * E-mail: (GG-M); (WV)
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Abstract
The mammalian circadian system synchronizes organisms' daily cyclical physiology from gene expression to gross behavioral patterns. A new study from our group suggests that DNA repair is also intimately linked to circadian rhythm. Since the repair of DNA lesions contributes to the resistance of chemotherapy with DNA damaging agents such as cisplatin, understanding the fundamental molecular mechanism regulating DNA repair pathways is important for cancer therapy. Here we review the significance of the connection linking the circadian clock with nucleotide excision repair and discuss potential implications for chemotherapy.
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Affiliation(s)
- Tae-Hong Kang
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
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Gentile A, Ditt RF, Dias FO, Da Silva MJ, Dornelas MC, Menossi M. Characterization of ScMat1, a putative TFIIH subunit from sugarcane. Plant Cell Rep 2009; 28:663-672. [PMID: 19148648 DOI: 10.1007/s00299-008-0663-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Revised: 11/27/2008] [Accepted: 12/09/2008] [Indexed: 05/27/2023]
Abstract
The general transcription factor TFIIH is a multiprotein complex with different enzymatic activities such as helicase, protein kinase and DNA repair. MAT1 (ménage à trois 1) is one of the TFIIH subunits that has kinase activity and it is the third subunit of the cyclin-dependent kinase (CDK)-activating kinase (CAK), CDK7- cyclin H. The main objective of this work was to characterize ScMAT1, a sugarcane gene encoding a MAT1 homolog. Northern blots and in situ hybridization results showed that ScMAT1 was expressed in sugarcane mature leaf, leaf roll and inflorescence, and it was not differentially expressed in any of the other tissues analyzed such us bud and roots. In addition, ScMAT1 was not differentially expressed during different stress conditions and treatment with hormones. In situ hybridization analyses also showed that ScMAT1 was expressed in different cell types during leaf development. In order to identify proteins that interact with ScMAT1, a yeast two hybrid assay with ScMAT1 as bait was used to screen a sugarcane leaf cDNA library. The screening of yeast two hybrids yielded 14 positive clones. One of them is a cytochrome p450 family protein involved in oxidative degradation of toxic compounds. Other clones isolated are also related to plant responses to stress. To determine the subcellular localization of ScMAT1, a ScMAT1-GFP fusion was assayed in onion epidermal cell and the fluorescence was localized to the nucleus, in agreement with the putative role of ScMAT1 as a basal transcription factor.
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Affiliation(s)
- Agustina Gentile
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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Aguilar-Fuentes J, Fregoso M, Herrera M, Reynaud E, Braun C, Egly JM, Zurita M. p8/TTDA overexpression enhances UV-irradiation resistance and suppresses TFIIH mutations in a Drosophila trichothiodystrophy model. PLoS Genet 2008; 4:e1000253. [PMID: 19008953 PMCID: PMC2576456 DOI: 10.1371/journal.pgen.1000253] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 10/03/2008] [Indexed: 11/25/2022] Open
Abstract
Mutations in certain subunits of the DNA repair/transcription factor complex TFIIH are linked to the human syndromes xeroderma pigmentosum (XP), Cockayne's syndrome (CS), and trichothiodystrophy (TTD). One of these subunits, p8/TTDA, interacts with p52 and XPD and is important in maintaining TFIIH stability. Drosophila mutants in the p52 (Dmp52) subunit exhibit phenotypic defects similar to those observed in TTD patients with defects in p8/TTDA and XPD, including reduced levels of TFIIH. Here, we demonstrate that several Dmp52 phenotypes, including lethality, developmental defects, and sterility, can be suppressed by p8/TTDA overexpression. TFIIH levels were also recovered in rescued flies. In addition, p8/TTDA overexpression suppressed a lethal allele of the Drosophila XPB homolog. Furthermore, transgenic flies overexpressing p8/TTDA were more resistant to UV irradiation than were wild-type flies, apparently because of enhanced efficiency of cyclobutane-pyrimidine-dimers and 6–4 pyrimidine-pyrimidone photoproducts repair. This study is the first using an intact higher-animal model to show that one subunit mutant can trans-complement another subunit in a multi-subunit complex linked to human diseases. TFIIH participates in RNA polymerase II transcription, nucleotide excision repair, and control of the cell cycle. In humans, certain mutations in the XPB and XPD subunits of TFIIH generate the syndromes trichothiodystrophy (TTD), xeroderma pigmentosum (XP), and Cockayne's syndrome (CS). In contrast, mutations in the p8/TTDA subunit have been linked only to TTD. Cells derived from TTD patients with defects in p8/TTDA have reduced levels of TFIIH. Therefore, it has been proposed that the main function of p8/TTDA is to stabilize and maintain steady-state levels of TFIIH. In Drosophila, mutations in Dmp52 and haywire genes generate phenotypes that share similarities with those associated with mutations in their human counterparts, including reduced TFIIH levels. We report that p8/TTDA overexpression suppressed accumulated developmental defects associated with mutations in the Dmp52 and haywire genes. We also provide evidence suggesting that the rescue of these defects is, in part, because of the recovery of normal TFIIH levels in mutant flies. These results indicate that overexpression of p8/TTDA trans-complemented mutations in other TFIIH subunits and suppressed defects accumulated during fly development. The overexpression of p8/TTDA in wild-type flies increased their UV irradiation resistance, apparently because of more efficient nucleotide excision repair.
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Affiliation(s)
- Javier Aguilar-Fuentes
- Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Mariana Fregoso
- Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Mariana Herrera
- Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Enrique Reynaud
- Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, C.U. de Strasbourg, France
| | - Jean Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, C.U. de Strasbourg, France
| | - Mario Zurita
- Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
- * E-mail:
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Chiganças V, Lima-Bessa KM, Stary A, Menck CFM, Sarasin A. Defective transcription/repair factor IIH recruitment to specific UV lesions in trichothiodystrophy syndrome. Cancer Res 2008; 68:6074-83. [PMID: 18676829 DOI: 10.1158/0008-5472.can-07-6695] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most trichothiodystrophy (TTD) patients present mutations in the xeroderma pigmentosum D (XPD) gene, coding for a subunit of the transcription/repair factor IIH (TFIIH) complex involved in nucleotide excision repair (NER) and transcription. After UV irradiation, most TTD/XPD patients are more severely affected in the NER of cyclobutane pyrimidine dimers (CPD) than of 6-4-photoproducts (6-4PP). The reasons for this differential DNA repair defect are unknown. Here we report the first study of NER in response to CPDs or 6-4PPs separately analyzed in primary fibroblasts. This was done by using heterologous photorepair; recombinant adenovirus vectors carrying photolyases enzymes that repair CPD or 6-4PP specifically by using the energy of light were introduced in different cell lines. The data presented here reveal that some TTD/XPD mutations affect the recruitment of TFIIH specifically to CPDs, but not to 6-4PPs. This deficiency is further confirmed by the inability of TTD/XPD cells to recruit, specifically for CPDs, NER factors that arrive in a TFIIH-dependent manner later in the NER pathway. For 6-4PPs, we show that TFIIH complexes carrying an NH(2)-terminal XPD mutated protein are also deficient in recruitment of NER proteins downstream of TFIIH. Treatment with the histone deacetylase inhibitor trichostatin A allows the recovery of TFIIH recruitment to CPDs in the studied TTD cells and, for COOH-terminal XPD mutations, increases the repair synthesis and survival after UV, suggesting that this defect can be partially related with accessibility of DNA damage in closed chromatin regions.
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Affiliation(s)
- Vanessa Chiganças
- Laboratory of Genetic Stability and Oncogenesis, Centre National de la Recherche Scientifique, Formation de Recherche en Evolution 2939, Institut Gustave Roussy, Université Paris-Sud, Villejuif, France.
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Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F, Werner M. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol Cell 2008; 31:337-46. [PMID: 18691966 DOI: 10.1016/j.molcel.2008.06.021] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 02/10/2008] [Accepted: 06/01/2008] [Indexed: 11/18/2022]
Abstract
In vitro, without Mediator, the association of general transcription factors (GTF) and RNA polymerase II (Pol II) in preinitiation complexes (PIC) occurs in an orderly fashion. In this work, we explore the in vivo function of Mediator in GTF recruitment to PIC. A direct interaction between Med11 Mediator head subunit and Rad3 TFIIH subunit was identified. We explored the significance of this interaction and those of Med11 with head module subunits Med17 and Med22 and found that impairing these interactions could differentially affect the recruitment of TFIIH, TFIIE, and Pol II in the PIC. A med11 mutation that altered promoter occupancy by the TFIIK kinase module of TFIIH genome-wide also reduced Pol II CTD serine 5 phosphorylation. We conclude that the Mediator head module plays a critical role in TFIIH and TFIIE recruitment to the PIC. We identify steps in PIC formation that suggest a branched assembly pathway.
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Abstract
The structure of the Rad4/Rad23 protein, shown in a recent issue of Nature (Min and Pavletich, 2007), reveals how structurally diverse lesions are recognized in eukaryotic nucleotide excision repair: by probing for accessible nondamaged DNA opposite the lesion.
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Affiliation(s)
- Orlando D Schärer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11974-3400, USA.
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Lewis AE, Rusten M, Hoivik EA, Vikse EL, Hansson ML, Wallberg AE, Bakke M. Phosphorylation of steroidogenic factor 1 is mediated by cyclin-dependent kinase 7. Mol Endocrinol 2007; 22:91-104. [PMID: 17901130 PMCID: PMC5419630 DOI: 10.1210/me.2006-0478] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The nuclear receptor steroidogenic factor-1 (SF1) is critical for development and function of steroidogenic tissues. Posttranslational modifications are known to influence the transcriptional capacity of SF1, and it was previously demonstrated that serine 203 is phosphorylated. In this paper we report that serine 203 is phosphorylated by a cyclin-dependent kinase 7 (CDK7)-mediated process. As part of the CDK-activating kinase complex, CDK7 is a component of the basal transcription factor TFIIH, and phosphorylation of SF1 as well as SF1-dependent transcription was clearly reduced in cells carrying a mutation that renders the CDK-activating kinase complex unable to interact with the TFIIH core. Coimmunoprecipitation analyses revealed that SF1 and CDK7 reside in the same complex, and kinase assays demonstrated that immunoprecipitated CDK7 and purified TFIIH phosphorylate SF1 in vitro. The CDK inhibitor roscovitine blocked phosphorylation of SF1, and an inactive form of CDK7 repressed the phosphorylation level and the transactivation capacity of SF1. Structural studies have identified phosphoinositides as potential ligands for SF1. Interestingly, we found that mutations designed to block phospholipid binding dramatically decreased the level of SF1 phosphorylation. Together our results suggest a connection between ligand occupation and phosphorylation and association with the basic transcriptional machinery, indicating an intricate regulation of SF1 transactivation.
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Affiliation(s)
- Aurélia E Lewis
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
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Ding B, Ruggiero C, Chen X, Li S. Tfb5 is partially dispensable for Rad26 mediated transcription coupled nucleotide excision repair in yeast. DNA Repair (Amst) 2007; 6:1661-9. [PMID: 17644494 PMCID: PMC2096704 DOI: 10.1016/j.dnarep.2007.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 06/08/2007] [Indexed: 11/18/2022]
Abstract
Nucleotide excision repair (NER) is a conserved DNA repair mechanism capable of removing a variety of helix-distorting DNA lesions. A specialized NER pathway, called transcription coupled NER (TC-NER), refers to preferential repair in the transcribed strand of an actively transcribed gene. To be distinguished from TCR-NER, the genome-wide NER process is termed as global genomic NER (GG-NER). In Saccharomyces cerevisiae, GG-NER is dependent on Rad7, whereas TC-NER is mediated by Rad26, the homolog of the human Cockayne syndrome group B protein, and by Rpb9, a non-essential subunit of RNA polymerase II. Tfb5, the tenth subunit of the transcription/repair factor TFIIH, is implicated in one group of the human syndrome trichothiodystrophy. Here, we show that Tfb5 plays different roles in different NER pathways in yeast. No repair takes place in the non-transcribed strand of a gene in tfb5 cells, or in both strands of a gene in rad26 rpb9 tfb5 cells, indicating that Tfb5 is essential for GG-NER. However, residual repair occurs in the transcribed strand of a gene in tfb5 cells, suggesting that Tfb5 is important, but not absolutely required for TC-NER. Interestingly, substantial repair occurs in the transcribed strand of a gene in rad7 tfb5 and rad7 rpb9 tfb5 cells, indicating that, in the absence of GG-NER, Tfb5 is largely dispensable for Rad26 mediated TC-NER. Furthermore, we show that no repair takes place in the transcribed strand of a gene in rad7 rad26 tfb5 cells, suggesting that Tfb5 is required for Rpb9 mediated TC-NER. Taken together, our results indicate that Tfb5 is partially dispensable for Rad26 mediated TC-NER, especially in GG-NER deficient cells. However, this TFIIH subunit is required for other NER pathways.
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Affiliation(s)
| | | | | | - Shisheng Li
- *Corresponding Author [225-578-9102(Phone)/225-578-9895(FAX)/ ]
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Ito S, Kuraoka I, Chymkowitch P, Compe E, Takedachi A, Ishigami C, Coin F, Egly JM, Tanaka K. XPG stabilizes TFIIH, allowing transactivation of nuclear receptors: implications for Cockayne syndrome in XP-G/CS patients. Mol Cell 2007; 26:231-43. [PMID: 17466625 DOI: 10.1016/j.molcel.2007.03.013] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 12/25/2006] [Accepted: 03/05/2007] [Indexed: 11/26/2022]
Abstract
Mutations in the human XPG gene give rise to an inherited photosensitive disorder, xeroderma pigmentosum (XP) associated with Cockayne syndrome (XP-G/CS). The clinical features of CS in XP-G/CS patients are difficult to explain on the basis of a defect in nucleotide excision repair (NER). We found that XPG forms a stable complex with TFIIH, which is active in transcription and NER. Mutations in XPG found in XP-G/CS patient cells that prevent the association with TFIIH also resulted in the dissociation of CAK and XPD from the core TFIIH. As a consequence, the phosphorylation and transactivation of nuclear receptors were disturbed in XP-G/CS as well as xpg(-/-) MEF cells and could be restored by expression of wild-type XPG. These results provide an insight into the role of XPG in the stabilization of TFIIH and the regulation of gene expression and provide an explanation of some of the clinical features of XP-G/CS.
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Affiliation(s)
- Shinsuke Ito
- Laboratories for Organismal Biosystems, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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Friedberg EC, Wood RD. New insights into the combined Cockayne/xeroderma pigmentosum complex: human XPG protein can function in transcription factor stability. Mol Cell 2007; 26:162-4. [PMID: 17466619 DOI: 10.1016/j.molcel.2007.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A new study provides evidence supporting a function for XPG protein in maintaining the integrity and function of TFIIH (Ito et al. [2007], this issue of Molecular Cell). This observation likely explains some of the clinical features of individuals with both defective DNA repair and development.
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Affiliation(s)
- Errol C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072, USA.
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Ren P, Rosas IO, Macdonald SD, Wu HP, Billings EM, Gochuico BR. Impairment of alveolar macrophage transcription in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2007; 175:1151-7. [PMID: 17332483 PMCID: PMC1899274 DOI: 10.1164/rccm.200607-958oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 03/01/2007] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Alveolar macrophages are inflammatory cells that may contribute to the pathogenesis of idiopathic pulmonary fibrosis (IPF), which is characterized by excessive alveolar aggregation of cells and extracellular matrix proteins. OBJECTIVES To identify potential molecular mechanisms of IPF. METHODS To examine large-scale gene expression, messenger RNA isolated from alveolar macrophages and peripheral blood mononuclear cells from subjects with IPF and normal volunteers was hybridized to cDNA filters. MEASUREMENTS AND MAIN RESULTS We showed that in IPF there is global down-regulation of gene expression in alveolar macrophages but not in blood monocytes. Nuclear run-on and pulse-chase studies showed that alveolar macrophages had significantly reduced transcription (p < 0.01). No significant difference in RNA degradation was found between subjects with IPF and normal volunteers. Western blot analyses revealed that concentrations of transcription factor II-H, a general transcription factor, were significantly lower in alveolar macrophages from subjects with IPF than in those from normal volunteers (p = 0.012). CONCLUSIONS Impaired transcription in IPF is associated with decreased concentrations of transcription factor II-H in alveolar macrophages and may alter the intraalveolar milieu in IPF.
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Affiliation(s)
- Ping Ren
- Pulmonary--Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Bour G, Lalevée S, Rochette-Egly C. Protein kinases and the proteasome join in the combinatorial control of transcription by nuclear retinoic acid receptors. Trends Cell Biol 2007; 17:302-9. [PMID: 17467991 DOI: 10.1016/j.tcb.2007.04.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 03/14/2007] [Accepted: 04/20/2007] [Indexed: 01/06/2023]
Abstract
Nuclear retinoic acid receptors (RARs) are transcriptional transregulators that control the expression of specific subsets of genes in a ligand-dependent manner. The basic mechanism for switching on gene transcription by agonist-liganded RARs involves their binding at specific response elements located in target genes. It also involves interactions with coregulatory protein complexes, the assembly of which is directed by the C-terminal ligand-binding domain of RARs. In addition to this scenario, several recent studies highlighted a fundamental role for the N-terminal domain in the transcriptional activity of RARs, following phosphorylation by the CDK7 kinase of the general transcription factor TFIIH and by p38MAPK. It has also emerged that the ubiquitin-proteasome system has a key role in RAR-mediated transcription. Here, we review new insights into how N-terminal domain and the proteasome pathway can influence the dynamics of RAR transcriptional activity.
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Affiliation(s)
- Gaétan Bour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Cell Biology and Signal Transduction, BP10142/Inserm, U596/CNRS, UMR7104, Illkirch, France
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