1
|
Zuñiga-Hernandez J, Meneses C, Bastias M, Allende ML, Glavic A. Drosophila DAxud1 Has a Repressive Transcription Activity on Hsp70 and Other Heat Shock Genes. Int J Mol Sci 2023; 24:ijms24087485. [PMID: 37108646 PMCID: PMC10138878 DOI: 10.3390/ijms24087485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Drosophila melanogaster DAxud1 is a transcription factor that belongs to the Cysteine Serine Rich Nuclear Protein (CSRNP) family, conserved in metazoans, with a transcriptional transactivation activity. According to previous studies, this protein promotes apoptosis and Wnt signaling-mediated neural crest differentiation in vertebrates. However, no analysis has been conducted to determine what other genes it might control, especially in connection with cell survival and apoptosis. To partly answer this question, this work analyzes the role of Drosophila DAxud1 using Targeted-DamID-seq (TaDa-seq), which allows whole genome screening to determine in which regions it is most frequently found. This analysis confirmed the presence of DAxud1 in groups of pro-apoptotic and Wnt pathway genes, as previously described; furthermore, stress resistance genes that coding heat shock protein (HSP) family genes were found as hsp70, hsp67, and hsp26. The enrichment of DAxud1 also identified a DNA-binding motif (AYATACATAYATA) that is frequently found in the promoters of these genes. Surprisingly, the following analyses demonstrated that DAxud1 exerts a repressive role on these genes, which are necessary for cell survival. This is coupled with the pro-apoptotic and cell cycle arrest roles of DAxud1, in which repression of hsp70 complements the maintenance of tissue homeostasis through cell survival modulation.
Collapse
Affiliation(s)
- Jorge Zuñiga-Hernandez
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
| | - Claudio Meneses
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
- Millennium Nucleus Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Macarena Bastias
- Centro de Biotecnología vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
| | - Alvaro Glavic
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
| |
Collapse
|
2
|
Fu I, Mu H, Geacintov NE, Broyde S. Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair. Nucleic Acids Res 2022; 50:6837-6853. [PMID: 35713557 PMCID: PMC9262607 DOI: 10.1093/nar/gkac496] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 01/19/2023] Open
Abstract
In nucleotide excision repair (NER), the xeroderma pigmentosum D helicase (XPD) scans DNA searching for bulky lesions, stalls when encountering such damage to verify its presence, and allows repair to proceed. Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6-4) pyrimidone UV photoproduct (6-4PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215-221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.
Collapse
Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Hong Mu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- To whom correspondence should be addressed. Tel: +1 212 998 8231;
| |
Collapse
|
3
|
Hwang JH, Vuong LT, Choi KW. Crumbs, Galla and Xpd are required for Kinesin-5 regulation in mitosis and organ growth in Drosophila. J Cell Sci 2020; 133:jcs246801. [PMID: 32501288 DOI: 10.1242/jcs.246801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Xeroderma Pigmentosum D (XPD, also known as ERCC2) is a multi-functional protein involved in transcription, DNA repair and chromosome segregation. In Drosophila, Xpd interacts with Crumbs (Crb) and Galla to regulate mitosis during embryogenesis. It is unknown how these proteins are linked to mitosis. Here, we show that Crb, Galla-2 and Xpd regulate nuclear division in the syncytial embryo by interacting with Klp61F, the Drosophila mitotic Kinesin-5 associated with bipolar spindles. Crb, Galla-2 and Xpd physically interact with Klp61F and colocalize to mitotic spindles. Knockdown of any of these proteins results in similar mitotic defects. These phenotypes are restored by overexpression of Klp61F, suggesting that Klp61F is a major effector. Mitotic defects of galla-2 RNAi are suppressed by Xpd overexpression but not vice versa. Depletion of Crb, Galla-2 or Xpd results in a reduction of Klp61F levels. Reducing proteasome function restores Klp61F levels and suppresses mitotic defects caused by knockdown of Crb, Galla-2 or Xpd. Furthermore, eye growth is regulated by Xpd and Klp61F. Hence, we propose that Crb, Galla-2 and Xpd interact to maintain the level of Klp61F during mitosis and organ growth.
Collapse
Affiliation(s)
- Ji-Hyun Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Linh Thuong Vuong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| |
Collapse
|
4
|
Pavlova GA, Popova JV, Andreyeva EN, Yarinich LA, Lebedev MO, Razuvaeva AV, Dubatolova TD, Oshchepkova AL, Pellacani C, Somma MP, Pindyurin AV, Gatti M. RNAi-mediated depletion of the NSL complex subunits leads to abnormal chromosome segregation and defective centrosome duplication in Drosophila mitosis. PLoS Genet 2019; 15:e1008371. [PMID: 31527906 PMCID: PMC6772098 DOI: 10.1371/journal.pgen.1008371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/01/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
The Drosophila Nonspecific Lethal (NSL) complex is a major transcriptional regulator of housekeeping genes. It contains at least seven subunits that are conserved in the human KANSL complex: Nsl1/Wah (KANSL1), Dgt1/Nsl2 (KANSL2), Rcd1/Nsl3 (KANSL3), Rcd5 (MCRS1), MBD-R2 (PHF20), Wds (WDR5) and Mof (MOF/KAT8). Previous studies have shown that Dgt1, Rcd1 and Rcd5 are implicated in centrosome maintenance. Here, we analyzed the mitotic phenotypes caused by RNAi-mediated depletion of Rcd1, Rcd5, MBD-R2 or Wds in greater detail. Depletion of any of these proteins in Drosophila S2 cells led to defects in chromosome segregation. Consistent with these findings, Rcd1, Rcd5 and MBD-R2 RNAi cells showed reduced levels of both Cid/CENP-A and the kinetochore component Ndc80. In addition, RNAi against any of the four genes negatively affected centriole duplication. In Wds-depleted cells, the mitotic phenotypes were similar but milder than those observed in Rcd1-, Rcd5- or MBD-R2-deficient cells. RT-qPCR experiments and interrogation of published datasets revealed that transcription of many genes encoding centromere/kinetochore proteins (e.g., cid, Mis12 and Nnf1b), or involved in centriole duplication (e.g., Sas-6, Sas-4 and asl) is substantially reduced in Rcd1, Rcd5 and MBD-R2 RNAi cells, and to a lesser extent in wds RNAi cells. During mitosis, both Rcd1-GFP and Rcd5-GFP accumulate at the centrosomes and the telophase midbody, MBD-R2-GFP is enriched only at the chromosomes, while Wds-GFP accumulates at the centrosomes, the kinetochores, the midbody, and on a specific chromosome region. Collectively, our results suggest that the mitotic phenotypes caused by Rcd1, Rcd5, MBD-R2 or Wds depletion are primarily due to reduced transcription of genes involved in kinetochore assembly and centriole duplication. The differences in the subcellular localizations of the NSL components may reflect direct mitotic functions that are difficult to detect at the phenotypic level, because they are masked by the transcription-dependent deficiency of kinetochore and centriolar proteins. The Drosophila Nonspecific Lethal (NSL) complex is a conserved protein assembly that controls transcription of more than 4,000 housekeeping genes. We analyzed the mitotic functions of four genes, Rcd1, Rcd5, MBD-R2 and wds, encoding NSL subunits. Inactivation of these genes by RNA interference (RNAi) resulted in defects in both chromosome segregation and centrosome duplication. Our analyses indicate that RNAi against Rcd1, Rcd5 or MBD-R2 reduces transcription of genes involved in centromere/kinetochore assembly and centriole replication. During interphase, Rcd1, Rcd5, MBD-R2 and Wds are confined to the nucleus, as expected for transcription factors. However, during mitosis each of these proteins relocates to specific mitotic structures. Our results suggest that the four NSL components work together as a complex to stimulate transcription of genes encoding important mitotic determinants. However, the different localization of the proteins during mitosis suggests that they might have acquired secondary “moonlighting” functions that directly contribute to the mitotic process.
Collapse
Affiliation(s)
- Gera A. Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Julia V. Popova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
| | - Evgeniya N. Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Lyubov A. Yarinich
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Mikhail O. Lebedev
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Alyona V. Razuvaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana D. Dubatolova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Anastasiya L. Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Novosibirsk, Russia
| | - Claudia Pellacani
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Maria Patrizia Somma
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Alexey V. Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail: (AVP); (MG)
| | - Maurizio Gatti
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- * E-mail: (AVP); (MG)
| |
Collapse
|
5
|
Cruz-Becerra G, Valerio-Cabrera S, Juárez M, Bucio-Mendez A, Zurita M. TFIIH localization is highly dynamic during zygotic genome activation in Drosophila, and its depletion causes catastrophic mitosis. J Cell Sci 2018; 131:jcs.211631. [PMID: 29643118 DOI: 10.1242/jcs.211631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
In Drosophila, zygotic genome activation occurs in pre-blastoderm embryos during rapid mitotic divisions. How the transcription machinery is coordinated to achieve this goal in a very brief time span is still poorly understood. Transcription factor II H (TFIIH) is fundamental for transcription initiation by RNA polymerase II (RNAPII). Herein, we show the in vivo dynamics of TFIIH at the onset of transcription in Drosophila embryos. TFIIH shows an oscillatory behaviour between the nucleus and cytoplasm. TFIIH foci are observed from interphase to metaphase, and colocalize with those for RNAPII phosphorylated at serine 5 (RNAPIIS5P) at prophase, suggesting that transcription occurs during the first mitotic phases. Furthermore, embryos with defects in subunits of either the CAK or the core subcomplexes of TFIIH show catastrophic mitosis. Although, transcriptome analyses show altered expression of several maternal genes that participate in mitosis, the global level of RNAPIIS5P in TFIIH mutant embryos is similar to that in the wild type, therefore, a direct role for TFIIH in mitosis cannot be ruled out. These results provide important insights regarding the role of a basal transcription machinery component when the zygotic genome is activated.
Collapse
Affiliation(s)
- Grisel Cruz-Becerra
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Sarai Valerio-Cabrera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Mandy Juárez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Alyeri Bucio-Mendez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| |
Collapse
|
6
|
Sameer AS, Nissar S. XPD-The Lynchpin of NER: Molecule, Gene, Polymorphisms, and Role in Colorectal Carcinogenesis. Front Mol Biosci 2018; 5:23. [PMID: 29616226 PMCID: PMC5869190 DOI: 10.3389/fmolb.2018.00023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/27/2018] [Indexed: 01/17/2023] Open
Abstract
In mammals the bulky DNA adduct lesions known to result in deleterious phenotypes are acted upon and removed from the genomic DNA by nucleotide excision repair (NER) pathway. TFIIH multi-protein complex with its important helicase–Xeroderma Pigmentosum Protein (XPD) serves as the pivotal factor for opening up of the damaged lesion DNA site and carry out the repair process. The initial damage verification step of the TFIIH is in part dependent upon the helicase activity of XPD. Besides, XPD is also actively involved in the initiation steps of transcription and in the regulation of the cell cycle and apoptosis. In this review, we will be exploring the new insights in scientific research on the functioning of the NER pathway, the role of TFIIH as the central complex of NER, the pivotal helicase XPD as the lynchpin of NER and the effects of various single nucleotide polymorphisms (SNPs) of XPD on its functioning and their consequent role in colorectal carcinogenesis.
Collapse
Affiliation(s)
- Aga Syed Sameer
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Saniya Nissar
- Department of Biochemistry, Kashmir University, Srinagar, India
| |
Collapse
|
7
|
Pan W, Song D, He W, Lu H, Lan Y, Tong J, Gao F, Zhao K. The matrix protein of vesicular stomatitis virus inhibits host-directed transcription of target genes via interaction with the TFIIH subunit p8. Vet Microbiol 2017; 208:82-88. [DOI: 10.1016/j.vetmic.2017.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/16/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
|
8
|
Alekseev S, Nagy Z, Sandoz J, Weiss A, Egly JM, Le May N, Coin F. Transcription without XPB Establishes a Unified Helicase-Independent Mechanism of Promoter Opening in Eukaryotic Gene Expression. Mol Cell 2017; 65:504-514.e4. [DOI: 10.1016/j.molcel.2017.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/07/2016] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
|
9
|
Zurita M, Cruz-Becerra G. TFIIH: New Discoveries Regarding its Mechanisms and Impact on Cancer Treatment. J Cancer 2016; 7:2258-2265. [PMID: 27994662 PMCID: PMC5166535 DOI: 10.7150/jca.16966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/30/2016] [Indexed: 12/16/2022] Open
Abstract
The deregulation of gene expression is a characteristic of cancer cells, and malignant cells require very high levels of transcription to maintain their cancerous phenotype and survive. Therefore, components of the basal transcription machinery may be considered as targets to preferentially kill cancerous cells. TFIIH is a multisubunit basal transcription factor that also functions in nucleotide excision repair. The recent discoveries of some small molecules that interfere with TFIIH and that preferentially kill cancer cells have increased researchers' interest to elucidate the complex mechanisms by which TFIIH operates. In this review, we summarize the knowledge generated during the 25 years of TFIIH research, highlighting the recent advances in TFIIH structural and mechanistic analyses that suggest the potential of TFIIH as a target for cancer treatment.
Collapse
Affiliation(s)
- Mario Zurita
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca, Morelos 62250, México
| | - Grisel Cruz-Becerra
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca, Morelos 62250, México
| |
Collapse
|
10
|
Cruz-Becerra G, Juárez M, Valadez-Graham V, Zurita M. Analysis of Drosophila p8 and p52 mutants reveals distinct roles for the maintenance of TFIIH stability and male germ cell differentiation. Open Biol 2016; 6:rsob.160222. [PMID: 27805905 PMCID: PMC5090060 DOI: 10.1098/rsob.160222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/18/2016] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic gene expression is activated by factors that interact within complex machinery to initiate transcription. An important component of this machinery is the DNA repair/transcription factor TFIIH. Mutations in TFIIH result in three human syndromes: xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Transcription and DNA repair defects have been linked to some clinical features of these syndromes. However, how mutations in TFIIH affect specific developmental programmes, allowing organisms to develop with particular phenotypes, is not well understood. Here, we show that mutations in the p52 and p8 subunits of TFIIH have a moderate effect on the gene expression programme in the Drosophila testis, causing germ cell differentiation arrest in meiosis, but no Polycomb enrichment at the promoter of the affected differentiation genes, supporting recent data that disagree with the current Polycomb-mediated repression model for regulating gene expression in the testis. Moreover, we found that TFIIH stability is not compromised in p8 subunit-depleted testes that show transcriptional defects, highlighting the role of p8 in transcription. Therefore, this study reveals how defects in TFIIH affect a specific cell differentiation programme and contributes to understanding the specific syndrome manifestations in TFIIH-afflicted patients.
Collapse
Affiliation(s)
- Grisel Cruz-Becerra
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, Mexico
| | - Mandy Juárez
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, Mexico
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, Mexico
| | - Mario Zurita
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, Mexico
| |
Collapse
|
11
|
Caldwell RB, Braselmann H, Schoetz U, Heuer S, Scherthan H, Zitzelsberger H. Positive Cofactor 4 (PC4) is critical for DNA repair pathway re-routing in DT40 cells. Sci Rep 2016; 6:28890. [PMID: 27374870 PMCID: PMC4931448 DOI: 10.1038/srep28890] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/09/2016] [Indexed: 01/06/2023] Open
Abstract
PC4 is an abundant single-strand DNA binding protein that has been implicated in transcription and DNA repair. Here, we show that PC4 is involved in the cellular DNA damage response. To elucidate the role, we used the DT40 chicken B cell model, which produces clustered DNA lesions at Ig loci via the action of activation-induced deaminase. Our results help resolve key aspects of immunoglobulin diversification and suggest an essential role of PC4 in repair pathway choice. We show that PC4 ablation in gene conversion (GC)-active cells significantly disrupts GC but has little to no effect on targeted homologous recombination. In agreement, the global double-strand break repair response, as measured by γH2AX foci analysis, is unperturbed 16 hours post irradiation. In cells with the pseudo-genes removed (GC inactive), PC4 ablation reduced the overall mutation rate while simultaneously increasing the transversion mutation ratio. By tagging the N-terminus of PC4, gene conversion and somatic hypermutation are all but abolished even when native non-tagged PC4 is present, indicating a dominant negative effect. Our data point to a very early and deterministic role for PC4 in DNA repair pathway re-routing.
Collapse
Affiliation(s)
- Randolph B Caldwell
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH). Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Herbert Braselmann
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH). Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Ulrike Schoetz
- Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, Ingolstaedter Landstr 1, 85764, Neuherberg, Germany.,Department of Radiotherapy and Radiation Oncology, Ludwig-Maximilians-University Munich, Marchioninistr 15, 81377, Munich, Germany
| | - Steffen Heuer
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH). Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Harry Scherthan
- Bundeswehr Institute of Radiobiology affiliated to the University of Ulm. Neuherbergstr. 11, 80937 Muenchen, Germany
| | - Horst Zitzelsberger
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH). Department of Radiation Sciences - Research Unit Radiation Cytogenetics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, Ingolstaedter Landstr 1, 85764, Neuherberg, Germany
| |
Collapse
|
12
|
Constantinescu-Aruxandei D, Petrovic-Stojanovska B, Penedo JC, White MF, Naismith JH. Mechanism of DNA loading by the DNA repair helicase XPD. Nucleic Acids Res 2016; 44:2806-15. [PMID: 26896802 PMCID: PMC4824113 DOI: 10.1093/nar/gkw102] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/09/2016] [Indexed: 01/14/2023] Open
Abstract
The xeroderma pigmentosum group D (XPD) helicase is a component of the transcription factor IIH complex in eukaryotes and plays an essential role in DNA repair in the nucleotide excision repair pathway. XPD is a 5′ to 3′ helicase with an essential iron–sulfur cluster. Structural and biochemical studies of the monomeric archaeal XPD homologues have aided a mechanistic understanding of this important class of helicase, but several important questions remain open. In particular, the mechanism for DNA loading, which is assumed to require large protein conformational change, is not fully understood. Here, DNA binding by the archaeal XPD helicase from Thermoplasma acidophilum has been investigated using a combination of crystallography, cross-linking, modified substrates and biochemical assays. The data are consistent with an initial tight binding of ssDNA to helicase domain 2, followed by transient opening of the interface between the Arch and 4FeS domains, allowing access to a second binding site on helicase domain 1 that directs DNA through the pore. A crystal structure of XPD from Sulfolobus acidocaldiarius that lacks helicase domain 2 has an otherwise unperturbed structure, emphasizing the stability of the interface between the Arch and 4FeS domains in XPD.
Collapse
Affiliation(s)
| | | | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| |
Collapse
|
13
|
Wei H, Wang Q, DU J, Li X, Zhang N, Cao Y, Ma W. Unique subcellular distribution of RPB1 with a phosphorylated C-terminal domain (CTD) in mouse oocytes during meiotic division and its relationship with chromosome separation. J Reprod Dev 2015; 61:541-8. [PMID: 26346254 PMCID: PMC4685220 DOI: 10.1262/jrd.2015-051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Polymerase (RNA) II (DNA directed) polypeptide A (RPB1) is the largest subunit of RNA polymerase II
(RNAPII), and phosphorylation of its C-terminal domain (CTD) is required for transcription initiation,
elongation and RNA processing. Little is known about the CTD phosphorylation pattern and potential function
during cell division when transcription is silenced. In this study, we assessed the protein expression and
subcellular distribution of RPB1 during mouse oocyte meiotic division. Western blot analysis revealed that the
RPB1 CTD was highly phosphorylated on Ser2 (pRPB1Ser2), Ser5 (pRPB1Ser5) and Ser7
(pRPB1Ser7). High and stable expression of pRPB1Ser2 and pRPB1Ser5 was
detected from germinal vesicle (GV) to Metaphase II (MII) stage. In contrast, pRPB1Ser7 only
emerged after germinal vesicle breakdown (GVBD) and gradually increased to its peak level at metaphase I (MI)
and MII. Immunofluorescence demonstrated that pRPB1Ser2, pRPB1Ser5 and
pRPB1Ser7 were pronouncedly aggregated within the nucleus of GV oocytes with a non-surrounded
nucleolus (NSN) but very faintly labeled in oocytes with a surrounded nucleolus (SN). After meiotic
resumption, pRPB1Ser2 was again detected at spindle poles and co-localized with key microtubule
organizing center (MTOC) components, pericentrin and γ-tubulin. pRPB1Ser5 and pRPB1Ser7
were assembled as filamentous aggregates and co-localized with microtubules throughout the spindle structure,
responding to spindle-disturbing drugs, nocodazole or taxol, in pattern strongly similar to microtubules.
pRPB1Ser2 and pRPB1Ser5 were constantly localized on chromosomes, with a relatively
high concentration in centromere areas. Taken together, our data suggest that the CTD is highly phosphorylated
and may be required for accurate chromosome segregation in mouse oocytes during meiosis.
Collapse
Affiliation(s)
- HaoJie Wei
- Department of Histology and Embryology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | | | | | | | | | | | | |
Collapse
|
14
|
Regulation of Transcription Elongation by the XPG-TFIIH Complex Is Implicated in Cockayne Syndrome. Mol Cell Biol 2015; 35:3178-88. [PMID: 26149386 DOI: 10.1128/mcb.01401-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/23/2015] [Indexed: 11/20/2022] Open
Abstract
XPG is a causative gene underlying the photosensitive disorder xeroderma pigmentosum group G (XP-G) and is involved in nucleotide excision repair. Here, we show that XPG knockdown represses epidermal growth factor (EGF)-induced FOS transcription at the level of transcription elongation with little effect on EGF signal transduction. XPG interacted with transcription elongation factors in concert with TFIIH, suggesting that the XPG-TFIIH complex serves as a transcription elongation factor. The XPG-TFIIH complex was recruited to promoter and coding regions of both EGF-induced (FOS) and housekeeping (EEF1A1) genes. Further, EGF-induced recruitment of RNA polymerase II and TFIIH to FOS was reduced by XPG knockdown. Importantly, EGF-induced FOS transcription was markedly lower in XP-G/Cockayne syndrome (CS) cells expressing truncated XPG than in control cells expressing wild-type (WT) XPG, with less significant decreases in XP-G cells with XPG nuclease domain mutations. In corroboration of this finding, both WT XPG and a missense XPG mutant from an XP-G patient were recruited to FOS upon EGF stimulation, but an XPG mutant mimicking a C-terminal truncation from an XP-G/CS patient was not. These results suggest that the XPG-TFIIH complex is involved in transcription elongation and that defects in this association may partly account for Cockayne syndrome in XP-G/CS patients.
Collapse
|
15
|
Liu J, Fang H, Chi Z, Wu Z, Wei D, Mo D, Niu K, Balajee AS, Hei TK, Nie L, Zhao Y. XPD localizes in mitochondria and protects the mitochondrial genome from oxidative DNA damage. Nucleic Acids Res 2015; 43:5476-88. [PMID: 25969448 PMCID: PMC4477675 DOI: 10.1093/nar/gkv472] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 04/28/2015] [Indexed: 01/12/2023] Open
Abstract
Xeroderma pigmentosum group D (XPD/ERCC2) encodes an ATP-dependent helicase that plays essential roles in both transcription and nucleotide excision repair of nuclear DNA, however, whether or not XPD exerts similar functions in mitochondria remains elusive. In this study, we provide the first evidence that XPD is localized in the inner membrane of mitochondria, and cells under oxidative stress showed an enhanced recruitment of XPD into mitochondrial compartment. Furthermore, mitochondrial reactive oxygen species production and levels of oxidative stress-induced mitochondrial DNA (mtDNA) common deletion were significantly elevated, whereas capacity for oxidative damage repair of mtDNA was markedly reduced in both XPD-suppressed human osteosarcoma (U2OS) cells and XPD-deficient human fibroblasts. Immunoprecipitation-mass spectrometry analysis was used to identify interacting factor(s) with XPD and TUFM, a mitochondrial Tu translation elongation factor was detected to be physically interacted with XPD. Similar to the findings in XPD-deficient cells, mitochondrial common deletion and oxidative damage repair capacity in U2OS cells were found to be significantly altered after TUFM knock-down. Our findings clearly demonstrate that XPD plays crucial role(s) in protecting mitochondrial genome stability by facilitating an efficient repair of oxidative DNA damage in mitochondria.
Collapse
Affiliation(s)
- Jing Liu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Fang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenfen Chi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zan Wu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Wei
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Hebei North University, Zhangjiakou 075000, China
| | - Dongliang Mo
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaifeng Niu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Adayabalam S Balajee
- REAC/TS, Oak Ridge Associated Universities, Oak Ridge Institute of Science and Engineering, Oak Ridge, TN 37830, USA
| | - Tom K Hei
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Linghu Nie
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongliang Zhao
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
16
|
Singh A, Compe E, Le May N, Egly JM. TFIIH subunit alterations causing xeroderma pigmentosum and trichothiodystrophy specifically disturb several steps during transcription. Am J Hum Genet 2015; 96:194-207. [PMID: 25620205 DOI: 10.1016/j.ajhg.2014.12.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/10/2014] [Indexed: 01/28/2023] Open
Abstract
Mutations in genes encoding the ERCC3 (XPB), ERCC2 (XPD), and GTF2H5 (p8 or TTD-A) subunits of the transcription and DNA-repair factor TFIIH lead to three autosomal-recessive disorders: xeroderma pigmentosum (XP), XP associated with Cockayne syndrome (XP/CS), and trichothiodystrophy (TTD). Although these diseases were originally associated with defects in DNA repair, transcription deficiencies might be also implicated. By using retinoic acid receptor beta isoform 2 (RARB2) as a model in several cells bearing mutations in genes encoding TFIIH subunits, we observed that (1) the recruitment of the TFIIH complex was altered at the activated RARB2 promoter, (2) TFIIH participated in the recruitment of nucleotide excision repair (NER) factors during transcription in a manner different from that observed during NER, and (3) the different TFIIH variants disturbed transcription by having distinct consequences on post-translational modifications of histones, DNA-break induction, DNA demethylation, and gene-loop formation. The transition from heterochromatin to euchromatin was disrupted depending on the variant, illustrating the fact that TFIIH, by contributing to NER factor recruitment, orchestrates chromatin remodeling. The subtle transcriptional differences found between various TFIIH variants thus participate in the phenotypic variability observed among XP, XP/CS, and TTD individuals.
Collapse
Affiliation(s)
- Amita Singh
- Genome Expression and Repair Team, Labellisée Ligue contre le Cancer 2014, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, INSERM, Université de Strasbourg, BP 163, 67404 Illkirch Cedex, CU Strasbourg, France
| | - Emanuel Compe
- Genome Expression and Repair Team, Labellisée Ligue contre le Cancer 2014, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, INSERM, Université de Strasbourg, BP 163, 67404 Illkirch Cedex, CU Strasbourg, France
| | - Nicolas Le May
- Genome Expression and Repair Team, Labellisée Ligue contre le Cancer 2014, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, INSERM, Université de Strasbourg, BP 163, 67404 Illkirch Cedex, CU Strasbourg, France.
| | - Jean-Marc Egly
- Genome Expression and Repair Team, Labellisée Ligue contre le Cancer 2014, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, INSERM, Université de Strasbourg, BP 163, 67404 Illkirch Cedex, CU Strasbourg, France.
| |
Collapse
|
17
|
Umate P, Tuteja N, Tuteja R. Genome-wide comprehensive analysis of human helicases. Commun Integr Biol 2014. [DOI: 10.4161/cib.13844] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
18
|
|
19
|
Yeom E, Hong ST, Choi KW. Crumbs interacts with Xpd for nuclear division control in Drosophila. Oncogene 2014; 34:2777-89. [PMID: 25065591 DOI: 10.1038/onc.2014.202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 05/09/2014] [Accepted: 05/23/2014] [Indexed: 01/03/2023]
Abstract
Crumbs (Crb) family proteins are crucial for cell polarity. Recent studies indicate that they are also involved in growth regulation and cancer. However, it is not well-understood how Crb participates in mitotic processes. Here, we report that Drosophila Crb is critically involved in nuclear division by interacting with Xeroderma pigmentosum D (XPD). A novel gene named galla-1 was identified from a genetic screen for crb modifiers. Galla-1 protein shows homology to MIP18, a subunit of the mitotic spindle-associated MMS19-XPD complex. Loss-of-function galla-1 mutants show abnormal chromosome segregation, defective centrosome positions and branched spindles during nuclear division in early embryos. Embryos with loss-of-function or overexpression of crb show similar mitotic defects and genetic interaction with galla-1. Both Galla-1 and Crb proteins show overlapping localization with spindle microtubules during nuclear division. Galla-1 physically interacts with the intracellular domain of Crb. Interestingly, Galla-1 shows little binding to the Drosophila homolog of XPD, but a related protein Galla-2 binds both Crb and Xpd. Loss-of-function galla-2 mutants show similar mitotic defects as galla-1 and strong genetic interaction with crb. Xpd can form a physical complex with Crb. In imaginal disc, Crb overexpression causes tissue overgrowth as well as DNA damages marked by H2Av phosphorylation. These phenotypes are suppressed by reduction of Xpd. Taken together, this study identifies a novel Crb-Galla-Xpd complex and its function for proper chromosome segregation during nuclear division, implicating a potential link between Crb and Xpd-related genome instability.
Collapse
Affiliation(s)
- E Yeom
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - S-T Hong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - K-W Choi
- 1] Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea [2] Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| |
Collapse
|
20
|
Moslehi R, Ambroggio X, Nagarajan V, Kumar A, Dzutsev A. Nucleotide excision repair/transcription gene defects in the fetus and impaired TFIIH-mediated function in transcription in placenta leading to preeclampsia. BMC Genomics 2014; 15:373. [PMID: 24885447 PMCID: PMC4229886 DOI: 10.1186/1471-2164-15-373] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Preeclampsia is a significant cause of maternal and fetal mortality and morbidity worldwide. We previously reported associations between trichothiodystrophy (TTD) nucleotide excision repair (NER) and transcription gene mutations in the fetus and the risk of gestational complications including preeclampsia. TTD NER/transcription genes, XPD, XPB and TTD-A, code for subunits of Transcription Factor (TF)IIH. Interpreting XPD mutations in the context of available biochemical data led us to propose adverse effects on CDK-activating kinase (CAK) subunit of TFIIH and TFIIH-mediated functions as a relevant mechanism in preeclampsia. In order to gain deeper insight into the underlying biologic mechanisms involving TFIIH-mediated functions in placenta, we analyzed NER/transcription and global gene expression profiles of normal and preeclamptic placentas and studied gene regulatory networks. RESULTS We found high expression of TTD NER/transcription genes in normal human placenta, above the mean of their expression in all organs. XPD and XPB were consistently expressed from 14 to 40 weeks gestation while expression of TTD-A was strongly negatively correlated (r=-0.7, P<0.0001) with gestational age. Analysis of gene expression patterns of placentas from a case-control study of preeclampsia using Algorithm for Reconstruction of Accurate Cellular Networks (ARACNE) revealed GTF2E1, a component of TFIIE which modulates TFIIH, among major regulators of differentially-expressed genes in preeclampsia. The basal transcription pathway was among the largest dysregulated protein-protein interaction networks in this preeclampsia dataset. Within the basal transcription pathway, significantly down-regulated genes besides GTF2E1 included those coding for the CAK complex of TFIIH, namely CDK7, CCNH, and MNAT1. Analysis of other relevant gene expression and gene regulatory network data also underscored the involvement of transcription pathways and identified JUNB and JUND (components of transcription factor AP-1) as transcription regulators of the network involving the TTD genes, GTF2E1, and selected gene regulators implicated in preeclampsia. CONCLUSIONS Our results indicate that TTD NER/transcription genes are expressed in placenta during gestational periods critical to preeclampsia development. Our overall findings suggest that impairment of TFIIH-mediated function in transcription in placenta is a likely mechanism leading to preeclampsia and provide etiologic clues which may be translated into therapeutic and preventive measures.
Collapse
Affiliation(s)
- Roxana Moslehi
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, State University of New York (SUNY), Rensselaer, NY 12144, USA.
| | | | | | | | | |
Collapse
|
21
|
Silva IAL, Cox CJ, Leite RB, Cancela ML, Conceição N. Evolutionary conservation of TFIIH subunits: implications for the use of zebrafish as a model to study TFIIH function and regulation. Comp Biochem Physiol B Biochem Mol Biol 2014; 172-173:9-20. [PMID: 24731924 DOI: 10.1016/j.cbpb.2014.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 11/28/2022]
Abstract
Transcriptional factor IIH (TFIIH) is involved in cell cycle regulation, nucleotide excision repair, and gene transcription. Mutations in three of its subunits, XPB, XPD, and TTDA, lead to human recessive genetic disorders such as trichothiodystrophy and xeroderma pigmentosum, the latter of which is sometimes associated with Cockayne's syndrome. In the present study, we investigate the sequence conservation of TFIIH subunits among several teleost fish species and compare their characteristics and putative regulation by transcription factors to those of human and zebrafish. We report the following findings: (i) comparisons among protein sequences revealed a high sequence identity for each TFIIH subunit analysed; (ii) among transcription factors identified as putative regulators, OCT1 and AP1 have the highest binding-site frequencies in the promoters of TFIIH genes, and (iii) TFIIH genes have alternatively spliced isoforms. Finally, we compared the protein primary structure in human and zebrafish of XPD and XPB - two important ATP-dependent helicases that catalyse the unwinding of the DNA duplex at promoters during transcription - highlighting the conservation of domain regions such as the helicase domains. Our study suggests that zebrafish, a widely used model for many human diseases, could also act as an important model to study the function of TFIIH complex in repair and transcription regulation in humans.
Collapse
Affiliation(s)
- I A L Silva
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - C J Cox
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - R B Leite
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - M L Cancela
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - N Conceição
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal.
| |
Collapse
|
22
|
Integrative transcriptome analysis reveals dysregulation of canonical cancer molecular pathways in placenta leading to preeclampsia. Sci Rep 2014; 3:2407. [PMID: 23989136 PMCID: PMC3757356 DOI: 10.1038/srep02407] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 07/22/2013] [Indexed: 12/18/2022] Open
Abstract
We previously suggested links between specific XPD mutations in the fetal genome and the risk of placental maldevelopment and preeclampsia, possibly due to impairment of Transcription Factor (TF)IIH-mediated functions in placenta. To identify the underlying mechanisms, we conducted the current integrative analysis of several relevant transcriptome data sources. Our meta-analysis revealed downregulation of TFIIH subunits in preeclamptic placentas. Our overall integrative analysis suggested that, in the presence of hypoxia and oxidative stress, EGFR signaling deficiency, which can be caused by TFIIH impairment as well as by other mechanisms, results in ATF3 upregulation, inducing mediators of clinical symptoms of preeclampsia such as FLT1 and ENG. EGFR- and ATF3-dependent pathways play prominent roles in cancer development. We propose that dysregulation of these canonical cancer molecular pathways occurs in preeclampsia and delineate the relevance of TFIIH, providing etiologic clues which could eventually translate into a therapeutic approach.
Collapse
|
23
|
Kim TH, Kim MY, Jo SH, Park JM, Ahn YH. Modulation of the transcriptional activity of peroxisome proliferator-activated receptor gamma by protein-protein interactions and post-translational modifications. Yonsei Med J 2013; 54:545-59. [PMID: 23549795 PMCID: PMC3635639 DOI: 10.3349/ymj.2013.54.3.545] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) belongs to a nuclear receptor superfamily; members of which play key roles in the control of body metabolism principally by acting on adipose tissue. Ligands of PPARγ, such as thiazolidinediones, are widely used in the treatment of metabolic syndromes and type 2 diabetes mellitus (T2DM). Although these drugs have potential benefits in the treatment of T2DM, they also cause unwanted side effects. Thus, understanding the molecular mechanisms governing the transcriptional activity of PPARγ is of prime importance in the development of new selective drugs or drugs with fewer side effects. Recent advancements in molecular biology have made it possible to obtain a deeper understanding of the role of PPARγ in body homeostasis. The transcriptional activity of PPARγ is subject to regulation either by interacting proteins or by modification of the protein itself. New interacting partners of PPARγ with new functions are being unveiled. In addition, post-translational modification by various cellular signals contributes to fine-tuning of the transcriptional activities of PPARγ. In this review, we will summarize recent advancements in our understanding of the post-translational modifications of, and proteins interacting with, PPARγ, both of which affect its transcriptional activities in relation to adipogenesis.
Collapse
Affiliation(s)
- Tae-Hyun Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
- Integrative Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| | - Mi-Young Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
- Integrative Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| | - Seong-Ho Jo
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
- Integrative Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| | - Joo-Man Park
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
- Integrative Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| | - Yong-Ho Ahn
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
- Integrative Genomic Research Center for Metabolic Regulation, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
24
|
Theil AF, Nonnekens J, Steurer B, Mari PO, de Wit J, Lemaitre C, Marteijn JA, Raams A, Maas A, Vermeij M, Essers J, Hoeijmakers JHJ, Giglia-Mari G, Vermeulen W. Disruption of TTDA results in complete nucleotide excision repair deficiency and embryonic lethality. PLoS Genet 2013; 9:e1003431. [PMID: 23637614 PMCID: PMC3630102 DOI: 10.1371/journal.pgen.1003431] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/19/2013] [Indexed: 12/01/2022] Open
Abstract
The ten-subunit transcription factor IIH (TFIIH) plays a crucial role in transcription and nucleotide excision repair (NER). Inactivating mutations in the smallest 8-kDa TFB5/TTDA subunit cause the neurodevelopmental progeroid repair syndrome trichothiodystrophy A (TTD-A). Previous studies have shown that TTDA is the only TFIIH subunit that appears not to be essential for NER, transcription, or viability. We studied the consequences of TTDA inactivation by generating a Ttda knock-out (Ttda−/−) mouse-model resembling TTD-A patients. Unexpectedly, Ttda−/− mice were embryonic lethal. However, in contrast to full disruption of all other TFIIH subunits, viability of Ttda−/− cells was not affected. Surprisingly, Ttda−/− cells were completely NER deficient, contrary to the incomplete NER deficiency of TTD-A patient-derived cells. We further showed that TTD-A patient mutations only partially inactivate TTDA function, explaining the relatively mild repair phenotype of TTD-A cells. Moreover, Ttda−/− cells were also highly sensitive to oxidizing agents. These findings reveal an essential role of TTDA for life, nucleotide excision repair, and oxidative DNA damage repair and identify Ttda−/− cells as a unique class of TFIIH mutants. DNA is under constant attack of various environmental and cellular produced DNA damaging agents. DNA damage hampers normal cell function; however, different DNA repair mechanisms protect our genetic information. Nucleotide Excision Repair is one of the most versatile repair processes, as it removes a large variety of DNA helix-distorting lesions induced by UV light and various chemicals. To remove these lesions, the DNA helix needs to be opened by the transcription/repair factor II H (TFIIH). TFIIH is a multifunctional complex that consists of 10 subunits and plays a fundamental role in opening the DNA helix in both NER and transcription. TTDA, the smallest subunit of TFIIH, was thought to be dispensable for both NER and transcription. However, in this paper, we show for the first time that TTDA is in fact a crucial component of TFIIH for NER. We demonstrate that Ttda−/− mice are embryonic lethal. We also show that Ttda−/− mouse cells are the first known viable TFIIH subunit knock-out cells, which are completely NER deficient and sensitive to oxidative agents (showing a new role for TFIIH outside NER and transcription).
Collapse
Affiliation(s)
- Arjan F. Theil
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Julie Nonnekens
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
| | - Barbara Steurer
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Pierre-Olivier Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
| | - Jan de Wit
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Anja Raams
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Marcel Vermeij
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Giuseppina Giglia-Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
- * E-mail: (WV); (GG-M)
| | - Wim Vermeulen
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- * E-mail: (WV); (GG-M)
| |
Collapse
|
25
|
Nonnekens J, Perez-Fernandez J, Theil AF, Gadal O, Bonnart C, Giglia-Mari G. Mutations in TFIIH causing trichothiodystrophy are responsible for defects in ribosomal RNA production and processing. Hum Mol Genet 2013; 22:2881-93. [DOI: 10.1093/hmg/ddt143] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
26
|
Villicaña C, Cruz G, Zurita M. The genetic depletion or the triptolide inhibition of TFIIH in p53 deficient cells induce a JNK-dependent cell death in Drosophila. J Cell Sci 2013; 126:2502-15. [DOI: 10.1242/jcs.122721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
TFIIH participates in transcription, nucleotide excision repair and the control of the cell cycle. In this work, we demonstrate that the Dmp52 subunit of TFIIH in Drosophila physically interacts with the fly p53 homologue, Dp53. The depletion of Dmp52 in the wing disc generates chromosome fragility, increases apoptosis and produces wings with a reduced number of cells; cellular proliferation, however, is not affected. Interestingly, instead of suppressing the apoptotic phenotype, the depletion of Dp53 in Dmp52-depleted wing disc cells increases apoptosis and the number of cells that suffer from chromosome fragility. The apoptosis induced by the depletion of Dmp52 alone is partially dependent on the JNK pathway. In contrast, the enhanced apoptosis caused by the simultaneous depletion of Dp53 and Dmp52 is absolutely JNK-dependent. In this study, we also show that the anti-proliferative drug triptolide, which inhibits the ATPase activity of the XPB subunit of TFIIH, phenocopies the JNK-dependent massive apoptotic phenotype of Dp53-depleted wing disc cells; this observation suggests that the mechanism by which triptolide induces apoptosis in p53-deficient cancer cells involves the activation of the JNK death pathway.
Collapse
|
27
|
Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O. Functional insights into the core-TFIIH from a comparative survey. Genomics 2012; 101:178-86. [PMID: 23147676 DOI: 10.1016/j.ygeno.2012.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
Abstract
TFIIH is a eukaryotic complex composed of two subcomplexes, the CAK (Cdk activating kinase) and the core-TFIIH. The core-TFIIH, composed of seven subunits (XPB, XPD, P62, P52, P44, P34, and P8), plays a crucial role in transcription and repair. Here, we performed an extended sequence analysis to establish the accurate phylogenetic distribution of the core-TFIIH in 63 eukaryotic organisms. In spite of the high conservation of the seven subunits at the sequence and genomic levels, the non-enzymatic P8, P34, P52 and P62 are absent from one or a few unicellular species. To gain insight into their respective roles, we undertook a comparative genomic analysis of the whole proteome to identify the gene sets sharing similar presence/absence patterns. While little information was inferred for P8 and P62, our studies confirm the known role of P52 in repair and suggest for the first time the implication of the core TFIIH in mRNA splicing via P34.
Collapse
Affiliation(s)
- Florence Bedez
- Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, UDS), BP163, 67404 Illkirch Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Herrera-Cruz M, Cruz G, Valadez-Graham V, Fregoso-Lomas M, Villicaña C, Vázquez M, Reynaud E, Zurita M. Physical and functional interactions between Drosophila homologue of Swc6/p18Hamlet subunit of the SWR1/SRCAP chromatin-remodeling complex with the DNA repair/transcription factor TFIIH. J Biol Chem 2012; 287:33567-80. [PMID: 22865882 DOI: 10.1074/jbc.m112.383505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The multisubunit DNA repair and transcription factor TFIIH maintains an intricate cross-talk with different factors to achieve its functions. The p8 subunit of TFIIH maintains the basal levels of the complex by interacting with the p52 subunit. Here, we report that in Drosophila, the homolog of the p8 subunit (Dmp8) is encoded in a bicistronic transcript with the homolog of the Swc6/p18(Hamlet) subunit (Dmp18) of the SWR1/SRCAP chromatin remodeling complex. The SWR1 and SRCAP complexes catalyze the exchange of the canonical histone H2A with the H2AZ histone variant. In eukaryotic cells, bicistronic transcripts are not common, and in some cases, the two encoded proteins are functionally related. We found that Dmp18 physically interacts with the Dmp52 subunit of TFIIH and co-localizes with TFIIH in the chromatin. We also demonstrated that Dmp18 genetically interacts with Dmp8, suggesting that a cross-talk might exist between TFIIH and a component of a chromatin remodeler complex involved in histone exchange. Interestingly, our results also show that when the level of one of the two proteins is decreased and the other maintained, a specific defect in the fly is observed, suggesting that the organization of these two genes in a bicistronic locus has been selected during evolution to allow co-regulation of both genes.
Collapse
Affiliation(s)
- Mariana Herrera-Cruz
- Department of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, México
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Nucleotide Excision Repair Gene Subunit XPD is Highly Expressed in Cervical Squamous Cell Carcinoma. Pathol Oncol Res 2012; 18:969-75. [DOI: 10.1007/s12253-012-9527-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 03/27/2012] [Indexed: 01/03/2023]
|
30
|
Abstract
Structures of complete 10-subunit yeast TFIIH and of a nested set of subcomplexes, containing 5, 6, and 7 subunits, have been determined by electron microscopy (EM) and 3D reconstruction. Consistency among all the structures establishes the location of the "minimal core" subunits (Ssl1, Tfb1, Tfb2, Tfb4, and Tfb5), and additional densities can be specifically attributed to Rad3, Ssl2, and the TFIIK trimer. These results can be further interpreted by placement of previous X-ray structures into the additional densities to give a preliminary picture of the RNA polymerase II preinitiation complex. In this picture, the key catalytic components of TFIIH, the Ssl2 ATPase/helicase and the Kin28 protein kinase are in proximity to their targets, downstream promoter DNA and the RNA polymerase C-terminal domain.
Collapse
|
31
|
Moslehi R, Kumar A, Mills JL, Ambroggio X, Signore C, Dzutsev A. Phenotype-specific adverse effects of XPD mutations on human prenatal development implicate impairment of TFIIH-mediated functions in placenta. Eur J Hum Genet 2012; 20:626-31. [PMID: 22234153 DOI: 10.1038/ejhg.2011.249] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mutations in XPD (ERCC2), XPB (ERCC3), and TTD-A (GTF2H5), genes involved in nucleotide excision repair and transcription, can cause several disorders including trichothiodystrophy (TTD) and xeroderma pigmentosum (XP). In this study, we tested the hypothesis that mutations in the XPD gene affect placental development in a phenotype-specific manner. To test our hypothesis and decipher potential biologic mechanisms, we compared all XPD-associated TTD (n=43) and XP (n=37) cases reported in the literature with respect to frequencies of gestational complications. Our genetic epidemiologic investigations of TTD and XP revealed that the exact genetic abnormality was relevant to the mechanism leading to gestational complications such as preeclampsia. Through structural mapping, we localized the preeclampsia-associated mutations to a C-terminal motif and the helicase surfaces of XPD, most likely affecting XPD's binding to cdk-activating kinase (CAK) and p44 subunits of transcription factor (TF) IIH. Our results suggested a link between TTD- but not XP-associated XPD mutations, placental maldevelopment and risk of pregnancy complications, possibly due to impairment of TFIIH-mediated functions in placenta. Our findings highlight the importance of the fetal genotype in development of gestational complications, such as preeclampsia. Therefore, future studies of genetic associations of preeclampsia and other placental vascular complications may benefit from focusing on genetic variants within the fetal DNA.
Collapse
Affiliation(s)
- Roxana Moslehi
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Albany, NY 12144, USA.
| | | | | | | | | | | |
Collapse
|
32
|
Baer A, Austin D, Narayanan A, Popova T, Kainulainen M, Bailey C, Kashanchi F, Weber F, Kehn-Hall K. Induction of DNA damage signaling upon Rift Valley fever virus infection results in cell cycle arrest and increased viral replication. J Biol Chem 2012; 287:7399-410. [PMID: 22223653 DOI: 10.1074/jbc.m111.296608] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rift Valley fever virus (RVFV) is a highly pathogenic arthropod-borne virus infecting a wide range of vertebrate hosts. Of particular interest is the nonstructural NSs protein, which forms large filamentous fibril bundles in the nucleus. Past studies have shown NSs to be a multifaceted protein important for virulence through modulation of the interferon response as well acting as a general inhibitor of transcription. Here we investigated the regulation of the DNA damage signaling cascades by RVFV infection and found virally inducted phosphorylation of the classical DNA damage signaling proteins, ataxia-telangiectasia mutated (ATM) (Ser-1981), Chk.2 (Thr-68), H2A.X (Ser-139), and p53 (Ser-15). In contrast, ataxia-telangiectasia mutated and Rad3-related kinase (ATR) (Ser-428) phosphorylation was decreased following RVFV infection. Importantly, both the attenuated vaccine strain MP12 and the fully virulent strain ZH548 showed strong parallels in their up-regulation of the ATM arm of the DNA damage response and in the down-regulation of the ATR pathway. The increase in DNA damage signaling proteins did not result from gross DNA damage as no increase in DNA damage was observed following infection. Rather the DNA damage signaling was found to be dependent on the viral protein NSs, as an NSs mutant virus was not found to induce the equivalent signaling pathways. RVFV MP12-infected cells also displayed an S phase arrest that was found to be dependent on NSs expression. Use of ATM and Chk.2 inhibitors resulted in a marked decrease in S phase arrest as well as viral production. These results indicate that RVFV NSs induces DNA damage signaling pathways that are beneficial for viral replication.
Collapse
Affiliation(s)
- Alan Baer
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Lüscher B, Vervoorts J. Regulation of gene transcription by the oncoprotein MYC. Gene 2011; 494:145-60. [PMID: 22227497 DOI: 10.1016/j.gene.2011.12.027] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/27/2011] [Accepted: 12/15/2011] [Indexed: 02/07/2023]
Abstract
The proteins of the MYC/MAX/MAD network are central regulators of many key processes associated with basic cell physiology. These include the regulation of protein biosynthesis, energy metabolism, proliferation, and apoptosis. Molecularly the MYC/MAX/MAD network achieves these broad activities by controlling the expression of many target genes, which are primarily responsible for the diverse physiological consequences elicited by the network. The MYC proteins of the network possess oncogenic activity and their functional deregulation is associated with the majority of human tumors. Over the last years we have witnessed the accumulation of a considerable number of molecular observations that suggest many different biochemical means and tools by which MYC controls gene expression. We will summarize the more recent findings and discuss how these different building blocks might come together to explain how MYC regulates gene transcription. We note that despite the many molecular details known, we do not have an integrated view of how MYC uses the different tools, neither in a spatial nor in a temporal order.
Collapse
Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany.
| | | |
Collapse
|
34
|
Kuper J, Wolski SC, Michels G, Kisker C. Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation. EMBO J 2011; 31:494-502. [PMID: 22081108 DOI: 10.1038/emboj.2011.374] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/20/2011] [Indexed: 01/16/2023] Open
Abstract
The XPD protein is a vital subunit of the general transcription factor TFIIH which is not only involved in transcription but is also an essential component of the eukaryotic nucleotide excision DNA repair (NER) pathway. XPD is a superfamily-2 5'-3' helicase containing an iron-sulphur cluster. Its helicase activity is indispensable for NER and it plays a role in the damage verification process. Here, we report the first structure of XPD from Thermoplasma acidophilum (taXPD) in complex with a short DNA fragment, thus revealing the polarity of the translocated strand and providing insights into how the enzyme achieves its 5'-3' directionality. Accompanied by a detailed mutational and biochemical analysis of taXPD, we define the path of the translocated DNA strand through the protein and identify amino acids that are critical for protein function.
Collapse
Affiliation(s)
- Jochen Kuper
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
| | | | | | | |
Collapse
|
35
|
Mannuss A, Trapp O, Puchta H. Gene regulation in response to DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:154-65. [PMID: 21867786 DOI: 10.1016/j.bbagrm.2011.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 08/04/2011] [Indexed: 11/17/2022]
Abstract
To deal with different kinds of DNA damages, there are a number of repair pathways that must be carefully orchestrated to guarantee genomic stability. Many proteins that play a role in DNA repair are involved in multiple pathways and need to be tightly regulated to conduct the functions required for efficient repair of different DNA damage types, such as double strand breaks or DNA crosslinks caused by radiation or genotoxins. While most of the factors involved in DNA repair are conserved throughout the different kingdoms, recent results have shown that the regulation of their expression is variable between different organisms. In the following paper, we give an overview of what is currently known about regulating factors and gene expression in response to DNA damage and put this knowledge in context with the different DNA repair pathways in plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
Collapse
Affiliation(s)
- Anja Mannuss
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | | |
Collapse
|
36
|
Slowly progressing nucleotide excision repair in trichothiodystrophy group A patient fibroblasts. Mol Cell Biol 2011; 31:3630-8. [PMID: 21730288 DOI: 10.1128/mcb.01462-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trichothiodystrophy (TTD) is a rare autosomal premature-ageing and neuroectodermal disease. The photohypersensitive form of TTD is caused by inherited mutations in three of the 10 subunits of the basal transcription factor TFIIH. TFIIH is an essential transcription initiation factor that is also pivotal for nucleotide excision repair (NER). Photosensitive TTD is explained by deficient NER, dedicated to removing UV-induced DNA lesions. TTD group A (TTD-A) patients carry mutations in the smallest TFIIH subunit, TTDA, which is an 8-kDa protein that dynamically interacts with TFIIH. TTD-A patients display a relatively mild TTD phenotype, and TTD-A primary fibroblasts exhibit moderate UV sensitivity despite a rather low level of UV-induced unscheduled DNA synthesis (UDS). To investigate the rationale of this seeming discrepancy, we studied the repair kinetics and the binding kinetics of TFIIH downstream NER factors to damaged sites in TTD-A cells. Our results show that TTD-A cells do repair UV lesions, although with reduced efficiency, and that the binding of downstream NER factors on damaged DNA is not completely abolished but only retarded. We conclude that in TTD-A cells repair is not fully compromised but only delayed, and we present a model that explains the relatively mild photosensitive phenotype observed in TTD-A patients.
Collapse
|
37
|
Fuss JO, Tainer JA. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst) 2011; 10:697-713. [PMID: 21571596 DOI: 10.1016/j.dnarep.2011.04.028] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Helicases must unwind DNA at the right place and time to maintain genomic integrity or gene expression. Biologically critical XPB and XPD helicases are key members of the human TFIIH complex; they anchor CAK kinase (cyclinH, MAT1, CDK7) to TFIIH and open DNA for transcription and for repair of duplex distorting damage by nucleotide excision repair (NER). NER is initiated by arrested RNA polymerase or damage recognition by XPC-RAD23B with or without DDB1/DDB2. XP helicases, named for their role in the extreme sun-mediated skin cancer predisposition xeroderma pigmentosum (XP), are then recruited to asymmetrically unwind dsDNA flanking the damage. XPB and XPD genetic defects can also cause premature aging with profound neurological defects without increased cancers: Cockayne syndrome (CS) and trichothiodystrophy (TTD). XP helicase patient phenotypes cannot be predicted from the mutation position along the linear gene sequence and adjacent mutations can cause different diseases. Here we consider the structural biology of DNA damage recognition by XPC-RAD23B, DDB1/DDB2, RNAPII, and ATL, and of helix unwinding by the XPB and XPD helicases plus the bacterial repair helicases UvrB and UvrD in complex with DNA. We then propose unified models for TFIIH assembly and roles in NER. Collective crystal structures with NMR and electron microscopy results reveal functional motifs, domains, and architectural elements that contribute to biological activities: damaged DNA binding, translocation, unwinding, and ATP driven changes plus TFIIH assembly and signaling. Coupled with mapping of patient mutations, these combined structural analyses provide a framework for integrating and unifying the rich biochemical and cellular information that has accumulated over forty years of study. This integration resolves puzzles regarding XP helicase functions and suggests that XP helicase positions and activities within TFIIH detect and verify damage, select the damaged strand for incision, and coordinate repair with transcription and cell cycle through CAK signaling.
Collapse
Affiliation(s)
- Jill O Fuss
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | |
Collapse
|
38
|
MicroRNA-27a regulates basal transcription by targeting the p44 subunit of general transcription factor IIH. Proc Natl Acad Sci U S A 2011; 108:8686-91. [PMID: 21558443 DOI: 10.1073/pnas.1014018108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
General transcription factor IIH (TFIIH) is a complex RNA polymerase II basal transcription factor comprising 10 different polypeptides that display activities involved in transcription and DNA repair processes. Although biochemical studies have uncovered TFIIH importance, little is known about how the mRNAs that code for TFIIH subunits are regulated. Here it is shown that mRNAs encoding seven of the TFIIH subunits (p34, p44, p52, p62, XPB, CDK7, and p8) are regulated at the posttranscriptional level in a Dicer-dependent manner. Indeed, abolition of the miRNA pathway induces abnormal accumulation, stabilization, and translational activation of these seven mRNAs. Herein, miR-27a was identified as a key regulator of p44 mRNA. Moreover, miR-27a was shown to destabilize the p44 subunit of the TFIIH complex during the G2-M phase, thereby modulating the transcriptional shutdown observed during this transition. This work is unique in providing a demonstration of global transcriptional regulation through the action of a single miRNA.
Collapse
|
39
|
NSs protein of rift valley fever virus promotes posttranslational downregulation of the TFIIH subunit p62. J Virol 2011; 85:6234-43. [PMID: 21543505 DOI: 10.1128/jvi.02255-10] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rift Valley fever virus (RVFV; family Bunyaviridae, genus Phlebovirus) is an important emerging pathogen of humans and ruminants. Its NSs protein has previously been identified as a major virulence factor that suppresses host defense through three distinct mechanisms: it directly inhibits beta interferon (IFN-β) promoter activity, it promotes the degradation of double-stranded RNA-dependent protein kinase (PKR), and it suppresses host transcription by disrupting the assembly of the basal transcription factor TFIIH through sequestration of its p44 subunit. Here, we report that in addition to PKR, NSs also promotes the degradation of the TFIIH subunit p62. Infection of cells with the RVFV MP-12 vaccine strain reduced p62 protein levels to below the detection limit early in the course of infection. This NSs-mediated downregulation of p62 was posttranslational, as it was unaffected by pharmacological inhibition of transcription or translation and MP-12 infection had no effect on p62 mRNA levels. Treatment of cells with proteasome inhibitors but not inhibition of lysosomal acidification or nuclear export resulted in a stabilization of p62 in the presence of NSs. Furthermore, p62 could be coprecipitated with NSs from lysates of infected cells. These data suggest that the RVFV NSs protein is able to interact with the TFIIH subunit p62 inside infected cells and promotes its degradation, which can occur directly in the nucleus.
Collapse
|
40
|
Umate P, Tuteja N, Tuteja R. Genome-wide comprehensive analysis of human helicases. Commun Integr Biol 2011; 4:118-37. [PMID: 21509200 PMCID: PMC3073292 DOI: 10.4161/cib.4.1.13844] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 10/03/2010] [Indexed: 12/20/2022] Open
Abstract
Helicases are motor proteins that catalyze the unwinding of duplex nucleic acids in an ATP-dependent manner. They are involved in almost all the nucleic acid transactions. In the present study, we report a comprehensive analysis of helicase gene family in human and its comparison with homologs in model organisms. The human genome encodes for 95 non-redundant helicase proteins, of which 64 are RNA helicases and 31 are DNA helicases. 57 RNA helicases are validated based on annotations and occurrence of conserved helicase signature motifs. These include 14 DExH and 37 DExD subfamily members, six other members such as U5.snRNP, ATR-X, Suv3, FANCJ, and two of superkiller viralicidic activity 2-like helicases. 31 DNA helicases are also identified, which include RecQ, MCM and RuvB-like helicases. Finding a set of helicases in human and almost similar sequences in model organisms suggests that the "core" members of helicase gene family are highly conserved throughout evolution. The present study gives an overview of members of RNA and DNA helicases encoded by the human genome along with their conserved motifs, phylogeny and homologs in model organisms. The study on comparing these homologs will spread light on the organization and complexity of helicase gene family in model organisms. The comprehensive analysis of human helicases presented in this study will further provide an invaluable resource for elaborate biological research on these helicases.
Collapse
Affiliation(s)
- Pavan Umate
- International Center for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
| | | | | |
Collapse
|
41
|
A TFIIH-associated mediator head is a basal factor of small nuclear spliced leader RNA gene transcription in early-diverged trypanosomes. Mol Cell Biol 2010; 30:5502-13. [PMID: 20876299 DOI: 10.1128/mcb.00966-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genome annotation suggested that early-diverged kinetoplastids possess a reduced set of basal transcription factors. More recent work, however, on the lethal parasite Trypanosoma brucei identified extremely divergent orthologs of TBP, TFIIA, TFIIB, and TFIIH which, together with the small nuclear RNA-activating protein complex, form a transcription preinitiation complex (PIC) at the spliced leader (SL) RNA gene (SLRNA) promoter. The SL RNA is a small nuclear RNA and a trans splicing substrate for the maturation of all pre-mRNAs which is metabolized continuously to sustain gene expression. Here, we identified and biochemically characterized a novel TFIIH-associated protein complex in T. brucei (Med-T) consisting of nine subunits whose amino acid sequences are conserved only among kinetoplastid organisms. Functional analyses in vivo and in vitro demonstrated that the complex is essential for cell viability, SLRNA transcription, and PIC integrity. Molecular structure analysis of purified Med-T and Med-T/TFIIH complexes by electron microscopy revealed that Med-T corresponds to the mediator head module of higher eukaryotes. These data therefore show that mediator is a basal factor for small nuclear SL RNA gene transcription in trypanosomes and that the basal transcription function of mediator head is a characteristic feature of eukaryotes which developed early in their evolution.
Collapse
|
42
|
Ito S, Tan LJ, Andoh D, Narita T, Seki M, Hirano Y, Narita K, Kuraoka I, Hiraoka Y, Tanaka K. MMXD, a TFIIH-independent XPD-MMS19 protein complex involved in chromosome segregation. Mol Cell 2010; 39:632-40. [PMID: 20797633 DOI: 10.1016/j.molcel.2010.07.029] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 02/18/2010] [Accepted: 07/16/2010] [Indexed: 12/11/2022]
Abstract
Xeroderma pigmentosum group D (XPD) protein is one of the subunits of TFIIH that is required for nucleotide excision repair and transcription. We found a XPD protein complex containing MMS19 that was assumed to be a regulator of TFIIH. However, the MMS19-XPD complex did not contain any other subunits of TFIIH. Instead, it included FAM96B (now designated MIP18), Ciao1, and ANT2. MMS19, MIP18, and XPD localized to the mitotic spindle during mitosis. The siRNA-mediated knockdown of MMS19, MIP18, or XPD led to improper chromosome segregation and the accumulation of nuclei with abnormal shapes. In addition, the frequency of abnormal mitosis and nuclei was increased in XP-D and XP-D/CS patients' cells. These results indicate that the MMS19-XPD protein complex, now designated MMXD (MMS19-MIP18-XPD), is required for proper chromosome segregation, an abnormality of which could contribute to the pathogenesis in some cases of XP-D and XP-D/CS.
Collapse
Affiliation(s)
- Shinsuke Ito
- Human Cell Biology Group, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Fouillen L, Abdulrahman W, Moras D, Dorsselaer AV, Poterszman A, Sanglier-Cianférani S. Analysis of recombinant phosphoprotein complexes with complementary mass spectrometry approaches. Anal Biochem 2010; 407:34-43. [PMID: 20624369 DOI: 10.1016/j.ab.2010.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 06/11/2010] [Accepted: 07/06/2010] [Indexed: 12/11/2022]
Abstract
The baculovirus expression vector system is recognized as a powerful and versatile tool for producing large quantities of recombinant proteins that cannot be obtained in Escherichia coli. Here we report (i) the purification of the recombinant cyclin-dependent kinase (CDK)-activating kinase (CAK) complex, which includes CDK7, cyclin H, and MAT1 proteins, and (ii) the functional characterization of CAK together with a detailed analysis and mapping of the phosphorylation states and sites using mass spectrometry (MS). In vitro kinase assay showed that recombinant CAK is able to phosphorylate the cyclin-dependent kinase CDK2 implicated in cell cycle progression and the carboxy-terminal domain (CTD) of the eukaryotic RNA polymerase II. An original combination of MS techniques was used for the determination of the phosphorylation sites of each constitutive subunit at both protein and peptide levels. Liquid chromatography (LC)-MS analysis of intact proteins demonstrated that none of the CAK subunits was fully modified and that the phosphorylation pattern of recombinant CAK is extremely heterogeneous. Finally, matrix-assisted laser desorption/ionization (MALDI)-MS and nanoLC-tandem mass spectrometry (MS/MS) techniques were used for the analysis of the major phosphorylation sites of each subunit, showing that all correspond to Ser/Thr phosphorylation sites. Phosphorylations occurred on Ser164 and Thr170 residues of CDK7, Thr315 residue of cyclin H, and Ser279 residue of MAT1.
Collapse
Affiliation(s)
- Laetitia Fouillen
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, IPHC, 67087 Strasbourg, France
| | | | | | | | | | | |
Collapse
|
44
|
Le May N, Egly JM, Coin F. True lies: the double life of the nucleotide excision repair factors in transcription and DNA repair. J Nucleic Acids 2010; 2010. [PMID: 20725631 PMCID: PMC2915888 DOI: 10.4061/2010/616342] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 05/21/2010] [Indexed: 01/09/2023] Open
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway in eukaryotic cells. NER removes structurally diverse lesions such as pyrimidine dimers, arising upon UV irradiation or bulky chemical adducts, arising upon exposure to carcinogens and some chemotherapeutic drugs. NER defects lead to three genetic disorders that result in predisposition to cancers, accelerated aging, neurological and developmental defects. During NER, more than 30 polypeptides cooperate to recognize, incise, and excise a damaged oligonucleotide from the genomic DNA. Recent papers reveal an additional and unexpected role for the NER factors. In the absence of a genotoxic attack, the promoters of RNA polymerases I- and II-dependent genes recruit XPA, XPC, XPG, and XPF to initiate gene expression. A model that includes the growth arrest and DNA damage 45α protein (Gadd45α) and the NER factors, in order to maintain the promoter of active genes under a hypomethylated state, has been proposed but remains controversial. This paper focuses on the double life of the NER factors in DNA repair and transcription and describes the possible roles of these factors in the RNA synthesis process.
Collapse
Affiliation(s)
- Nicolas Le May
- Department of Functional Genomics, IGBMC, CNRS/INSERM/Université de Strasbourg, BP 163, 67404 Illkirch Cedex, Strasbourg, France
| | | | | |
Collapse
|
45
|
Stefanini M, Botta E, Lanzafame M, Orioli D. Trichothiodystrophy: from basic mechanisms to clinical implications. DNA Repair (Amst) 2010; 9:2-10. [PMID: 19931493 DOI: 10.1016/j.dnarep.2009.10.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2009] [Indexed: 10/20/2022]
Abstract
Trichothiodystrophy (TTD) is an autosomal recessive disorder with symptoms affecting several tissues and organs. The most relevant features are hair abnormalities, physical and mental retardation, ichthyosis, signs of premature aging and cutaneous photosensitivity. The clinical spectrum of TTD varies widely from patients with only brittle, fragile hair to patients with the most severe neuroectodermal symptoms. To date, four genes have been identified as responsible for TTD: XPD, XPB, p8/TTDA, and TTDN1. Whereas the function of TTDN1 is still unknown, the former three genes encode subunits of TFIIH, the multiprotein complex involved in basal and activated transcription and in nucleotide excision repair (NER). Ongoing investigations on TTD are elucidating not only the pathogenesis of the disease, which appears to be mainly related to transcriptional impairment, but also the modalities of NER and transcription in human cells and how TFIIH operates in these two fundamental cellular processes.
Collapse
Affiliation(s)
- M Stefanini
- Istituto di Genetica Molecolare CNR, via Abbiategrasso 207, Pavia, Italy.
| | | | | | | |
Collapse
|
46
|
Akhtar MS, Heidemann M, Tietjen JR, Zhang DW, Chapman RD, Eick D, Ansari AZ. TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol Cell 2009; 34:387-93. [PMID: 19450536 DOI: 10.1016/j.molcel.2009.04.016] [Citation(s) in RCA: 227] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Revised: 03/09/2009] [Accepted: 04/13/2009] [Indexed: 11/24/2022]
Abstract
Posttranslational modifications of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) specify a molecular recognition code that is deciphered by proteins involved in RNA biogenesis. The CTD is comprised of a repeating heptapeptide (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)). Recently, phosphorylation of serine 7 was shown to be important for cotranscriptional processing of two snRNAs in mammalian cells. Here we report that Kin28/Cdk7, a subunit of the evolutionarily conserved TFIIH complex, is a Ser7 kinase. The ability of Kin28/Cdk7 to phosphorylate Ser7 is particularly surprising because this kinase functions at promoters of protein-coding genes, rather than being restricted to promoter-distal regions of snRNA genes. Kin28/Cdk7 is also known to phosphorylate Ser5 residues of the CTD at gene promoters. Taken together, our results implicate the TFIIH kinase in placing bivalent Ser5 and Ser7 marks early in gene transcription. These bivalent CTD marks, in concert with cues within nascent transcripts, specify the cotranscriptional engagement of the relevant RNA processing machinery.
Collapse
Affiliation(s)
- Md Sohail Akhtar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Lee JH, Jung HS, Günzl A. Transcriptionally active TFIIH of the early-diverged eukaryote Trypanosoma brucei harbors two novel core subunits but not a cyclin-activating kinase complex. Nucleic Acids Res 2009; 37:3811-20. [PMID: 19386623 PMCID: PMC2699521 DOI: 10.1093/nar/gkp236] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Trypanosoma brucei is a member of the early-diverged, protistan family Trypanosomatidae and a lethal parasite causing African Sleeping Sickness in humans. Recent studies revealed that T. brucei harbors extremely divergent orthologues of the general transcription factors TBP, TFIIA, TFIIB and TFIIH and showed that these factors are essential for initiating RNA polymerase II-mediated synthesis of spliced leader (SL) RNA, a trans splicing substrate and key molecule in trypanosome mRNA maturation. In yeast and metazoans, TFIIH is composed of a core of seven conserved subunits and the ternary cyclin-activating kinase (CAK) complex. Conversely, only four TFIIH subunits have been identified in T. brucei. Here, we characterize the first protistan TFIIH which was purified in its transcriptionally active form from T. brucei extracts. The complex consisted of all seven core subunits but lacked the CAK sub-complex; instead it contained two trypanosomatid-specific subunits, which were indispensable for parasite viability and SL RNA gene transcription. These findings were corroborated by comparing the molecular structures of trypanosome and human TFIIH. While the ring-shaped core domain was surprisingly congruent between the two structures, trypanosome TFIIH lacked the knob-like CAK moiety and exhibited extra densities on either side of the ring, presumably due to the specific subunits.
Collapse
Affiliation(s)
- Ju Huck Lee
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3301, USA
| | | | | |
Collapse
|
48
|
Abstract
The genome of all organisms is constantly attacked by a variety of environmental and endogenous mutagens that cause cell death, apoptosis, senescence, genetic diseases and cancer. To mitigate these deleterious endpoints of genotoxic reactions, living organisms have evolved one or more mechanisms for repairing every type of naturally occurring DNA lesion. For example, double-strand breaks are rapidly religated by non-homologous end-joining. Homologous recombination is used for the high-fidelity repair of interstrand cross-links, double-strand breaks and other DNA injuries that disrupt the replication fork. Some genotoxic lesions inflicted by alkylating agents can be repaired by direct reversal of DNA damage. The base excision repair pathway takes advantage of multiple DNA glycosylases to remove modified or incorrect bases. Finally, the nucleotide excision repair machinery provides a versatile strategy to monitor DNA quality and eliminate all forms of helix-distorting DNA lesions, including a wide diversity of carcinogen adducts. The efficiency of DNA repair responses is enhanced by their coupling to transcription and coordination with the cell cycle circuit.
Collapse
|
49
|
Genotoxic stress in plants: Shedding light on DNA damage, repair and DNA repair helicases. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2009; 681:134-149. [DOI: 10.1016/j.mrrev.2008.06.004] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 06/24/2008] [Accepted: 06/24/2008] [Indexed: 01/03/2023]
|
50
|
Shiraishi S, Tamamura N, Jogo M, Tanaka Y, Tamura TA. Rapid proteasomal degradation of transcription factor IIB in accordance with F9 cell differentiation. Gene 2009; 436:115-20. [PMID: 19393171 DOI: 10.1016/j.gene.2009.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 12/15/2008] [Accepted: 01/25/2009] [Indexed: 11/28/2022]
Abstract
We found that the levels of all general transcription factors (GTFs) for RNA polymerase II decreased in F9 cells when the cells were subjected to a differentiation procedure. Different from other GTFs, decrease of TFIIB during the differentiation was suppressed by addition of a proteasome inhibitor, MG132. The half-life of TFIIB in the differentiated cells was remarkably reduced compared with that in the undifferentiated cells. Moreover, it was demonstrated that TFIIB is a poly-ubiquitinated protein. Results of this study suggest that components of the transcription machinery decreased in accordance with cell differentiation and that TFIIB is specifically and rapidly degraded by the ubiquitin-proteasome pathway.
Collapse
Affiliation(s)
- Seiji Shiraishi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | | | | | | | | |
Collapse
|