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Abstract
XPD, as part of the TFIIH complex, has classically been linked to the damage verification step of nucleotide excision repair (NER). However, recent data indicate that XPD, due to its iron-sulfur center interacts with the iron sulfur cluster assembly proteins, and may interact with other proteins in the cell to mediate a diverse set of biological functions including cell cycle regulation, mitosis, and mitochondrial function. In this perspective, after first reviewing the function and some of the key disease causing variants that affect XPD's interaction with TFIIH and the CDK-activating kinase complex (CAK), we investigate these intriguing cellular roles of XPD and highlight important unanswered questions that provide a fertile ground for further scientific exploration.
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Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States.
| | - Jochen Kuper
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, Wuerzburg, Germany.
| | - Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, Wuerzburg, Germany.
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Andersen SL, Zhang A, Dominska M, Moriel-Carretero M, Herrera-Moyano E, Aguilera A, Petes TD. High-Resolution Mapping of Homologous Recombination Events in rad3 Hyper-Recombination Mutants in Yeast. PLoS Genet 2016; 12:e1005938. [PMID: 26968037 PMCID: PMC4788294 DOI: 10.1371/journal.pgen.1005938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/24/2016] [Indexed: 11/18/2022] Open
Abstract
The Saccharomyces cerevisae RAD3 gene is the homolog of human XPD, an essential gene encoding a DNA helicase of the TFIIH complex involved in both nucleotide excision repair (NER) and transcription. Some mutant alleles of RAD3 (rad3-101 and rad3-102) have partial defects in DNA repair and a strong hyper-recombination (hyper-Rec) phenotype. Previous studies showed that the hyper-Rec phenotype associated with rad3-101 and rad3-102 can be explained as a consequence of persistent single-stranded DNA gaps that are converted to recombinogenic double-strand breaks (DSBs) by replication. The systems previously used to characterize the hyper-Rec phenotype of rad3 strains do not detect the reciprocal products of mitotic recombination. We have further characterized these events using a system in which the reciprocal products of mitotic recombination are recovered. Both rad3-101 and rad3-102 elevate the frequency of reciprocal crossovers about 100-fold. Mapping of these events shows that three-quarters of these crossovers reflect DSBs formed at the same positions in both sister chromatids (double sister-chromatid breaks, DSCBs). The remainder reflects DSBs formed in single chromatids (single chromatid breaks, SCBs). The ratio of DSCBs to SCBs is similar to that observed for spontaneous recombination events in wild-type cells. We mapped 216 unselected genomic alterations throughout the genome including crossovers, gene conversions, deletions, and duplications. We found a significant association between the location of these recombination events and regions with elevated gamma-H2AX. In addition, there was a hotspot for deletions and duplications at the IMA2 and HXT11 genes near the left end of chromosome XV. A comparison of these data with our previous analysis of spontaneous mitotic recombination events suggests that a sub-set of spontaneous events in wild-type cells may be initiated by incomplete NER reactions, and that DSCBs, which cannot be repaired by sister-chromatid recombination, are a major source of mitotic recombination between homologous chromosomes.
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Affiliation(s)
- Sabrina L. Andersen
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Aimee Zhang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - María Moriel-Carretero
- Department of Molecular Biology, Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER-Universidad de Sevilla, Seville, Spain
| | - Emilia Herrera-Moyano
- Department of Molecular Biology, Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER-Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Department of Molecular Biology, Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER-Universidad de Sevilla, Seville, Spain
| | - Thomas D. Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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53
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Jullien L, Kannengiesser C, Kermasson L, Cormier-Daire V, Leblanc T, Soulier J, Londono-Vallejo A, de Villartay JP, Callebaut I, Revy P. Mutations of the RTEL1 Helicase in a Hoyeraal-Hreidarsson Syndrome Patient Highlight the Importance of the ARCH Domain. Hum Mutat 2016; 37:469-72. [PMID: 26847928 DOI: 10.1002/humu.22966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/22/2016] [Indexed: 01/29/2023]
Abstract
The DNA helicase RTEL1 participates in telomere maintenance and genome stability. Biallelic mutations in the RTEL1 gene account for the severe telomere biology disorder characteristic of the Hoyeraal-Hreidarsson syndrome (HH). Here, we report a HH patient (P4) carrying two novel compound heterozygous mutations in RTEL1: a premature stop codon (c.949A>T, p.Lys317*) and an intronic deletion leading to an exon skipping and an in-frame deletion of 25 amino-acids (p.Ile398_Lys422). P4's cells exhibit short and dysfunctional telomeres similarly to other RTEL1-deficient patients. 3D structure predictions indicated that the p.Ile398_Lys422 deletion affects a part of the helicase ARCH domain, which lines the pore formed with the core HD and the iron-sulfur cluster domains and is highly specific of sequences from the eukaryotic XPD family members.
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Affiliation(s)
- Laurent Jullien
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Caroline Kannengiesser
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris, France
| | - Laetitia Kermasson
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Valérie Cormier-Daire
- Department of Genetics, INSERM UMR 1163, Paris Descartes University-Sorbonne Paris Cité, Imagine Institute, Necker enfants malades Hospital, Paris, France
| | - Thierry Leblanc
- Assistance Publique - Hôpitaux de Paris, Hôpital Robert-Debré, Service d'Hématologie Pédiatrique, Paris, France
| | - Jean Soulier
- Institute of Hematology (IUH), INSERM UMR944/CNRS UMR7212, Saint-Louis Hospital and University Paris Diderot, Sorbonne Paris Cité, av Claude, Vellefaux, Paris, France
| | - Arturo Londono-Vallejo
- Telomeres and Cancer Laboratory, Labellisé Ligue, Department UMR3244, Institut Curie, Paris, France
| | - Jean-Pierre de Villartay
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités, UMR CNRS 7590, UPMC Univ Paris06, Muséum National d'Histoire Naturelle, IRD UMR 206, Paris, France
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
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54
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Abstract
Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process. The eighth gene, XPV, codes for the DNA polymerase ɳ, which replicates through DNA lesions in a process called translesion synthesis (TLS). Over the past decade, detailed structural information of these DNA repair proteins involved in eukaryotic NER and TLS have emerged. These structures allow us now to understand the molecular mechanism of the NER and TLS processes in quite some detail and we have begun to understand the broad substrate specificity of NER. In this review, we aim to highlight recent advances in the process of damage recognition and repair as well as damage tolerance by the XP proteins.
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55
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Tripartite DNA Lesion Recognition and Verification by XPC, TFIIH, and XPA in Nucleotide Excision Repair. Mol Cell 2015; 59:1025-34. [PMID: 26384665 DOI: 10.1016/j.molcel.2015.08.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 07/09/2015] [Accepted: 08/17/2015] [Indexed: 11/23/2022]
Abstract
Transcription factor IIH (TFIIH) is essential for both transcription and nucleotide excision repair (NER). DNA lesions are initially detected by NER factors XPC and XPE or stalled RNA polymerases, but only bulky lesions are preferentially repaired by NER. To elucidate substrate specificity in NER, we have prepared homogeneous human ten-subunit TFIIH and its seven-subunit core (Core7) without the CAK module and show that bulky lesions in DNA inhibit the ATPase and helicase activities of both XPB and XPD in Core7 to promote NER, whereas non-genuine NER substrates have no such effect. Moreover, the NER factor XPA activates unwinding of normal DNA by Core7, but inhibits the Core7 helicase activity in the presence of bulky lesions. Finally, the CAK module inhibits DNA binding by TFIIH and thereby enhances XPC-dependent specific recruitment of TFIIH. Our results support a tripartite lesion verification mechanism involving XPC, TFIIH, and XPA for efficient NER.
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56
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Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell 2015; 59:794-806. [PMID: 26340423 DOI: 10.1016/j.molcel.2015.07.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/10/2015] [Accepted: 07/17/2015] [Indexed: 10/23/2022]
Abstract
TFIIH is essential for both RNA polymerase II transcription and DNA repair, and mutations in TFIIH can result in human disease. Here, we determine the molecular architecture of human and yeast TFIIH by an integrative approach using chemical crosslinking/mass spectrometry (CXMS) data, biochemical analyses, and previously published electron microscopy maps. We identified four new conserved "topological regions" that function as hubs for TFIIH assembly and more than 35 conserved topological features within TFIIH, illuminating a network of interactions involved in TFIIH assembly and regulation of its activities. We show that one of these conserved regions, the p62/Tfb1 Anchor region, directly interacts with the DNA helicase subunit XPD/Rad3 in native TFIIH and is required for the integrity and function of TFIIH. We also reveal the structural basis for defects in patients with xeroderma pigmentosum and trichothiodystrophy, with mutations found at the interface between the p62 Anchor region and the XPD subunit.
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Affiliation(s)
- Jie Luo
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Peter Cimermancic
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shruthi Viswanath
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Bong Kim
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Marine Dehecq
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, PO Box 19024, Mailstop A1-162, Seattle, WA 98109, USA; Génétique des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3525, 25-28 rue du docteur Roux, 75015 Paris, France
| | - Vishnu Raman
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Steven Hahn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, PO Box 19024, Mailstop A1-162, Seattle, WA 98109, USA
| | - Jeff Ranish
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.
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57
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Tajedin L, Tarique M, Tuteja R. Plasmodium falciparum XPD translocates in 5' to 3' direction, is expressed throughout the blood stages, and interacts with p44. PROTOPLASMA 2015; 252:1487-1504. [PMID: 25708921 DOI: 10.1007/s00709-015-0779-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
XPD helicase, a TFIIH subunit, is essential for several processes including transcription, NER, cell cycle regulation, and apoptosis in eukaryotes. Another component of TFIIH, namely p44, is among the well-known interacting partners of XPD and is vital in regulating the helicase activities of latter. However, none of the above mentioned proteins have been functionally characterized in Plasmodium falciparum. Consequently, in this study, we performed detailed studies on XPD and its interacting partner, p44, from P. falciparum 3D7 strain. Accordingly, we expressed and purified recombinant PfXPD and its fragments and Pfp44 proteins and characterized the enzymatic activities of PfXPD and its fragments. The in vivo stage-specific expression and subcellular localizations of PfXPD and Pfp44 proteins were studied using the specific antibodies in the intraerythrocytic developmental stages of P. falciparum 3D7 strain. Our results suggest that PfXPD displays the characteristic ssDNA-dependent ATPase and 5'-3' DNA helicase activities. We also report the existence of two high molecular weight forms of p44 in P. falciparum 3D7 strain. Both PfXPD and Pfp44 colocalize in the nucleus and interact with each other, which suggest that they are most likely components of the same complex apparently, TFIIH. Furthermore, during trophozoite and schizont stages, both proteins exhibit a distinct cytoplasmic distribution pattern which implies that PfXPD and Pfp44 might also be involved in other functions. These studies will aid in understanding the basic biology of malaria parasite.
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Affiliation(s)
- Leila Tajedin
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Mohammed Tarique
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Road, New Delhi, 110067, India.
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58
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Abstract
The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.
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59
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Increased Oxidative Damage and Reduced DNA Repair Enzyme XPD Involvement in High Glucose-Mediated Enhancement of Levobupivacaine-Induced Neurotoxicity. Neurochem Res 2015; 40:1919-28. [DOI: 10.1007/s11064-015-1685-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 06/28/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
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60
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Lye MS, Visuvanathan S, Chong PP, Yap YY, Lim CC, Ban EZ. Homozygous Wildtype of XPD K751Q Polymorphism Is Associated with Increased Risk of Nasopharyngeal Carcinoma in Malaysian Population. PLoS One 2015; 10:e0130530. [PMID: 26086338 PMCID: PMC4472930 DOI: 10.1371/journal.pone.0130530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/21/2015] [Indexed: 01/26/2023] Open
Abstract
The xeroderma pigmentosum group D (XPD) gene encodes a DNA helicase, an important component in transcription factor IIH (TFIIH) complex. XPD helicase plays a pivotal role in unwinding DNA at the damaged region during nucleotide excision repair (NER) mechanism. Dysfunctional XPD helicase protein from polymorphic diversity may contribute to increased risk of developing cancers. This study aims to determine the association between XPD K751Q polymorphism (rs13181) and risk of nasopharyngeal carcinoma (NPC) in the Malaysian population. In this hospital-based matched case-control study, 356 controls were matched by age, gender and ethnicity to 356 cases. RFLP-PCR was used to genotype the XPD K751Q polymorphism. A significant association was observed between XPD K751Q polymorphism and the risk of NPC using conditional logistic regression. Subjects with homozygous Lys/Lys (wildtype) genotype have 1.58 times higher odds of developing NPC compared to subjects with recessive combination of heterozygous Lys/Gln and homozygous Gln/Gln genotypes (OR = 1.58, 95% CI = 1.05–2.38 p = 0.028) adjusted for cigarette smoking, alcohol and salted fish consumption. Our data suggests that Lys/Lys (wildtype) of XPD K751Q contributes to increased risk of NPC in the Malaysian population.
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Affiliation(s)
- Munn-Sann Lye
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- * E-mail:
| | - Shaneeta Visuvanathan
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Pei-Pei Chong
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yoke-Yeow Yap
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chin-Chye Lim
- National Cancer Institute, Ministry of Health Malaysia, Putrajaya, Malaysia
| | - Eng-Zhuan Ban
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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61
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Ghoneim M, Spies M. Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. NANO LETTERS 2014; 14:5920-31. [PMID: 25204359 PMCID: PMC4189620 DOI: 10.1021/nl502890g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report a dual illumination, single-molecule imaging strategy to dissect directly and in real-time the correlation between nanometer-scale domain motion of a DNA repair protein and its interaction with individual DNA substrates. The strategy was applied to XPD, an FeS cluster-containing DNA repair helicase. Conformational dynamics was assessed via FeS-mediated quenching of a fluorophore site-specifically incorporated into XPD. Simultaneously, binding of DNA molecules labeled with a spectrally distinct fluorophore was detected by colocalization of the DNA- and protein-derived signals. We show that XPD undergoes thermally driven conformational transitions that manifest in spatial separation of its two auxiliary domains. DNA binding does not strictly enforce a specific conformation. Interaction with a cognate DNA damage, however, stabilizes the compact conformation of XPD by increasing the weighted average lifetime of this state by 140% relative to an undamaged DNA. Our imaging strategy will be a valuable tool to study other FeS-containing nucleic acid processing enzymes.
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Affiliation(s)
- Mohamed Ghoneim
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Maria Spies
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
- E-mail: . Phone +1-319-335-3221
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In TFIIH, XPD helicase is exclusively devoted to DNA repair. PLoS Biol 2014; 12:e1001954. [PMID: 25268380 PMCID: PMC4182028 DOI: 10.1371/journal.pbio.1001954] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/14/2014] [Indexed: 01/13/2023] Open
Abstract
The eukaryotic XPD helicase is an essential subunit of TFIIH involved in both transcription and nucleotide excision repair (NER). Mutations in human XPD are associated with several inherited diseases such as xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. We performed a comparative analysis of XPD from Homo sapiens and Chaetomium thermophilum (a closely related thermostable fungal orthologue) to decipher the different molecular prerequisites necessary for either transcription or DNA repair. In vitro and in vivo assays demonstrate that mutations in the 4Fe4S cluster domain of XPD abrogate the NER function of TFIIH and do not affect its transcriptional activity. We show that the p44-dependent activation of XPD is promoted by the stimulation of its ATPase activity. Furthermore, we clearly demonstrate that XPD requires DNA binding, ATPase, and helicase activity to function in NER. In contrast, these enzymatic properties are dispensable for transcription initiation. XPD helicase is thus exclusively devoted to NER and merely acts as a structural scaffold to maintain TFIIH integrity during transcription.
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63
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Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:206735. [PMID: 24701133 PMCID: PMC3950489 DOI: 10.1155/2014/206735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 11/29/2013] [Indexed: 12/28/2022]
Abstract
As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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