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Wettasinghe AP, Seifi MO, Bravo M, Adams AC, Patel A, Lou M, Kahanda D, Peng H, Stelling AL, Fan L, Slinker JD. Molecular wrench activity of DNA helicases: Keys to modulation of rapid kinetics in DNA repair. Protein Sci 2023; 32:e4815. [PMID: 37874269 PMCID: PMC10659936 DOI: 10.1002/pro.4815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
DNA helicase activity is essential for the vital DNA metabolic processes of recombination, replication, transcription, translation, and repair. Recently, an unexpected, rapid exponential ATP-stimulated DNA unwinding rate was observed from an Archaeoglobus fulgidus helicase (AfXPB) as compared to the slower conventional helicases from Sulfolobus tokodaii, StXPB1 and StXPB2. This unusual rapid activity suggests a "molecular wrench" mechanism arising from the torque applied by AfXPB on the duplex structure in transitioning from open to closed conformations. However, much remains to be understood. Here, we investigate the concentration dependence of DNA helicase binding and ATP-stimulated kinetics of StXPB2 and AfXPB, as well as their binding and activity in Bax1 complexes, via an electrochemical assay with redox-active DNA monolayers. StXPB2 ATP-stimulated activity is concentration-independent from 8 to 200 nM. Unexpectedly, AfXPB activity is concentration-dependent in this range, with exponential rate constants varying from seconds at concentrations greater than 20 nM to thousands of seconds at lower concentrations. At 20 nM, rapid exponential signal decay ensues, linearly reverses, and resumes with a slower exponential decay. This change in AfXPB activity as a function of its concentration is rationalized as the crossover between the fast molecular wrench and slower conventional helicase modes. AfXPB-Bax1 inhibits rapid activity, whereas the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations. This activity is rationalized with the crystal structures of these complexes. These findings illuminate the different physical models governing molecular wrench activity for improved biological insight into a key factor in DNA repair.
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Affiliation(s)
| | - Melodee O. Seifi
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Marco Bravo
- Department of BiochemistryUniversity of CaliforniaRiversideCaliforniaUSA
| | - Austen C. Adams
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Aman Patel
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Monica Lou
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Dimithree Kahanda
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
| | - Hao‐Che Peng
- Department of ChemistryThe University of Texas at DallasRichardsonTexasUSA
| | | | - Li Fan
- Department of ChemistryThe University of Texas at DallasRichardsonTexasUSA
| | - Jason D. Slinker
- Department of PhysicsThe University of Texas at DallasRichardsonTexasUSA
- Department of ChemistryThe University of Texas at DallasRichardsonTexasUSA
- Department of Materials Science and EngineeringThe University of Texas at DallasRichardsonTexasUSA
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2
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He F, Bravo M, Fan L. Helicases required for nucleotide excision repair: structure, function and mechanism. Enzymes 2023; 54:273-304. [PMID: 37945175 DOI: 10.1016/bs.enz.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway conserved from bacteria to humans. Various DNA helicases, a group of enzymes capable of separating DNA duplex into two strands through ATP binding and hydrolysis, are required by NER to unwind the DNA duplex around the lesion to create a repair bubble and for damage verification and removal. In prokaryotes, UvrB helicase is required for repair bubble formation and damage verification, while UvrD helicase is responsible for the removal of the excised damage containing single-strand (ss) DNA fragment. In addition, UvrD facilitates transcription-coupled repair (TCR) by backtracking RNA polymerase stalled at the lesion. In eukaryotes, two helicases XPB and XPD from the transcription factor TFIIH complex fulfill the helicase requirements of NER. Interestingly, homologs of all these four helicases UvrB, UvrD, XPB, and XPD have been identified in archaea. This review summarizes our current understanding about the structure, function, and mechanism of these four helicases.
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Affiliation(s)
- Feng He
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Marco Bravo
- Department of Biochemistry, University of California, Riverside, CA, United States
| | - Li Fan
- Department of Biochemistry, University of California, Riverside, CA, United States.
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3
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Yu J, Yan C, Dodd T, Tsai CL, Tainer JA, Tsutakawa SE, Ivanov I. Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases. Nat Commun 2023; 14:2758. [PMID: 37179334 PMCID: PMC10183003 DOI: 10.1038/s41467-023-38416-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH's global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.
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Affiliation(s)
- Jina Yu
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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Bao X, Chen Y, Lou X, Du J, Li H, Liu N, Tang Z, Hua J, Guo W, Liu SB. Comprehensive analysis of ERCC3 prognosis value and ceRNA network in AML. Clin Transl Oncol 2023; 25:1053-1066. [PMID: 36472749 DOI: 10.1007/s12094-022-03012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a hematological malignancy with high molecular and clinical heterogeneity, and is the most common type of acute leukemia in adults. Due to limited treatment options, AML is prone to relapse and has a poor prognosis. Excision repair cross-complementing 3 (ERCC3) is an important member of nucleotide excision repair (NER) that is overexpressed in types of solid cancers and potentially regarded as a prognostic factor. However, its role in AML remains unclear. The purpose of this study was to explore ERCC3 expression and functions in AML. METHODS The Cancer Genome Atlas (TCGA) and GEO (Gene Expression Omnibus) were used to test the accuracy of ERCC3 expression levels for AML diagnosis. Using online databases and R packages, we also explored the signaling pathway, epigenetic regulation, infiltration of immune cells, clinical prognostic value, and ceRNA network in AML. RESULTS Our results revealed that ERCC3 expression was increased in AML and that high ERCC3 expression had good value for disease-free survival and overall survival in AML patients who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT). We found that ERCC3 and co-expressed genes were mainly involved in chemical carcinogenesis/reactive oxygen species, ubiquitin-mediated protein degradation and oxidative phosphorylation. In addition, almost all the m6A-related coding genes (except GF2BP1) were positively associated with ERCC3 expression. We also constructed a ceRNA regulatory network containing ERCC3 in AML and identified 6 pairs of ceRNA networks, indicating that ERCC3 expression is regulated by a noncoding RNA system. CONCLUSION This study demonstrated that ERCC3 was overexpressed in AML and that high ERCC3 expression can be considered a biomarker conducive to allo-HSCT in AML patients.
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Affiliation(s)
- Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yao Chen
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, 28 Kehua Road, Suzhou, 215009, China
| | - Xiao Lou
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China
| | - Jiahui Du
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, 28 Kehua Road, Suzhou, 215009, China
| | - Huijun Li
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Nian Liu
- School of Chemistry and Life Science, Biology and Materials Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Jingsheng Hua
- Department of Hematology, Taizhou Municipal Hospital Affiliated to Taizhou University, Taizhou, 318000, China.
| | - Weiqiang Guo
- School of Chemistry and Life Science, Biology and Materials Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, 28 Kehua Road, Suzhou, 215009, China.
- School of Chemistry and Life Science, Biology and Materials Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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5
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Yang C, Li X, Zhang Y, Jin H. Transcriptome analysis of Populus × canadensis 'Zhongliao1' in response to low temperature stress. BMC Genomics 2023; 24:77. [PMID: 36803355 PMCID: PMC9936654 DOI: 10.1186/s12864-023-09187-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Low temperatures are known to limit the growth and geographical distribution of poplars. Although some transcriptomic studies have been conducted to explore the response of poplar leaves to cold stress, only a few have comprehensively analyzed the effects of low temperature on the transcriptome of poplars and identified genes related to cold stress response and repair of freeze-thaw injury. RESULTS We exposed the Euramerican poplar Zhongliao1 to low temperatures; after stems were exposed to - 40℃, 4℃, and 20℃, the mixture of phloem and cambium was collected for transcriptome sequencing and bioinformatics analysis. A total of 29,060 genes were detected, including 28,739 known genes and 321 novel genes. Several differentially expressed genes (n = 36) were found to be involved in the Ca2+ signaling pathway, starch-sucrose metabolism pathway, abscisic acid signaling pathway, and DNA repair. They were functionally annotated; glucan endo-1,3-beta-glucosidase and UDP-glucuronosyltransferase genes, for instance, showed a close relationship with cold resistance. The expression of 11 differentially expressed genes was verified by qRT-PCR; RNA-Seq and qRT-PCR data were found to be consistent, which validated the robustness of our RNA-Seq findings. Finally, multiple sequence alignment and evolutionary analysis were performed, the results of which suggested a close association between several novel genes and cold resistance in Zhongliao1. CONCLUSION We believe that the cold resistance and freeze-thaw injury repair genes identified in this study are of great significance for cold tolerance breeding.
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Affiliation(s)
- Chengchao Yang
- Liaoning Provincial Institute of Poplar, 115213, Gaizhou, China.
| | - Xiaoyu Li
- Liaoning Provincial Institute of Poplar, 115213 Gaizhou, China
| | - Yan Zhang
- Liaoning Provincial Institute of Poplar, 115213 Gaizhou, China
| | - Hua Jin
- grid.440687.90000 0000 9927 2735College of Environment and Bioresources, Dalian Minzu University, 116600 Dalian, China
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Wang S, Liu W, Ni Y, Wang L, Zhu Y, Shi Q, Yi Z, Wang W, Liu L, Yang L, Kuang Y, Zhu Y, Zhang Q, Yang Z. Overexpression of ERCC3 is associated with poor prognosis in patients with pancreatic cancer. J Cancer 2021; 12:2550-2559. [PMID: 33854616 PMCID: PMC8040713 DOI: 10.7150/jca.54576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Pancreatic cancer is associated with poor prognosis due to limited therapeutic options. Excision repair cross-complementing 3 (ERCC3) is an important member of nucleotide excision repair (NER) that is overexpressed in some cancers and may be regarded as a poor prognostic factor. Yet, its role in pancreatic cancer remains unclear. This study aimed to investigate the expression and functions of ERCC3 in pancreatic cancer patients and its relation with clinicopathological features. Our data suggested that the protein expression level of ERCC3 was higher in tumor tissues than in adjacent tissues. In addition, the expression of ERCC3 has shown to be associated with the tumor extent (p=0.035). Besides, analysis of the dataset in The Cancer Genome Atlas (TCGA) revealed that high expression of ERCC3 was associated with poor overall survival in pancreatic cancer patients (p=0.0136). In Cox regression analysis, ERCC3 was an independent prognostic factor for overall survival in pancreatic cancer (p<0.001). Furthermore, our in vitro data further suggested that the overexpression of ERCC3 significantly promoted pancreatic cancer (BxPC-3, CFPAC-1, and PANC-1 cells) proliferation, invasion, and migration. Taken together, this study suggested that high expression of ERCC3 might be a poor prognostic factor in human pancreatic cancer and might be used as a promising therapeutic target for pancreatic cancer treatment.
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Affiliation(s)
- Shujie Wang
- Department of pathology, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Wenjing Liu
- Department of pathology, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Yueli Ni
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Lifeng Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Yuzhi Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Qiong Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Yunnan, China
| | - Zihan Yi
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Yunnan, China
| | - Wenjie Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Lili Liu
- Department of pathology, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Lijuan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Yingmin Kuang
- Department of Organ Transplantation, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Yuechun Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Qiao Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Zhe Yang
- Department of pathology, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
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Kappenberger J, Koelmel W, Schoenwetter E, Scheuer T, Woerner J, Kuper J, Kisker C. How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH. Nucleic Acids Res 2020; 48:12282-12296. [PMID: 33196848 PMCID: PMC7708078 DOI: 10.1093/nar/gkaa911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 09/28/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
The superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. The ATPase activity of XPB is required in both processes. We investigated the interaction network that regulates XPB via the p52 and p8 subunits with functional mutagenesis based on our crystal structure of the p52/p8 complex and current cryo-EM structures. Importantly, we show that XPB’s ATPase can be activated either by DNA or by the interaction with the p52/p8 proteins. Intriguingly, we observe that the ATPase activation by p52/p8 is significantly weaker than the activation by DNA and when both p52/p8 and DNA are present, p52/p8 dominates the maximum activation. We therefore define p52/p8 as the master regulator of XPB acting as an activator and speed limiter at the same time. A correlative analysis of the ATPase and translocase activities of XPB shows that XPB only acts as a translocase within the context of complete core TFIIH and that XPA increases the processivity of the translocase complex without altering XPB’s ATPase activity. Our data define an intricate network that tightly controls the activity of XPB during transcription and nucleotide excision repair.
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Affiliation(s)
- Jeannette Kappenberger
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Wolfgang Koelmel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Elisabeth Schoenwetter
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Tobias Scheuer
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Julia Woerner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
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8
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He F, DuPrez K, Hilario E, Chen Z, Fan L. Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA. Nucleic Acids Res 2020; 48:11695-11705. [PMID: 32986831 PMCID: PMC7672443 DOI: 10.1093/nar/gkaa801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide excision repair (NER) removes various DNA lesions caused by UV light and chemical carcinogens. The DNA helicase XPB plays a key role in DNA opening and coordinating damage incision by nucleases during NER, but the underlying mechanisms remain unclear. Here, we report crystal structures of XPB from Sulfurisphaera tokodaii (St) bound to the nuclease Bax1 and their complex with a bubble DNA having one arm unwound in the crystal. StXPB and Bax1 together spirally encircle 10 base pairs of duplex DNA at the double-/single-stranded (ds–ss) junction. Furthermore, StXPB has its ThM motif intruding between the two DNA strands and gripping the 3′-overhang while Bax1 interacts with the 5′-overhang. This ternary complex likely reflects the state of repair bubble extension by the XPB and nuclease machine. ATP binding and hydrolysis by StXPB could lead to a spiral translocation along dsDNA and DNA strand separation by the ThM motif, revealing an unconventional DNA unwinding mechanism. Interestingly, the DNA is kept away from the nuclease domain of Bax1, potentially preventing DNA incision by Bax1 during repair bubble extension.
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Affiliation(s)
- Feng He
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Kevin DuPrez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Eduardo Hilario
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Zhenhang Chen
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Li Fan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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9
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DuPrez K, He F, Chen Z, Hilario E, Fan L. Structural basis of the XPB-Bax1 complex as a dynamic helicase-nuclease machinery for DNA repair. Nucleic Acids Res 2020; 48:6326-6339. [PMID: 32374860 PMCID: PMC7293015 DOI: 10.1093/nar/gkaa324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures of XPB in complex with Bax1 from Archaeoglobus fulgidus (Af) and Sulfolobus tokodaii (St). These structures reveal for the first time four domains in Bax1, which interacts with XPB mainly through its N-terminal domain. A Cas2-like domain likely helps to position Bax1 at the forked DNA allowing the nuclease domain to incise one arm of the fork. Bax1 exists in monomer or homodimer but forms a heterodimer exclusively with XPB. StBax1 keeps StXPB in a closed conformation and stimulates ATP hydrolysis by XPB while AfBax1 maintains AfXPB in the open conformation and reduces its ATPase activity. Bax1 contains two distinguished nuclease active sites to presumably incise DNA damage. Our results demonstrate that protein-protein interactions regulate the activities of XPB ATPase and Bax1 nuclease. These structures provide a platform to understand the XPB-nuclease interactions important for the coordination of DNA unwinding and damage incision in eukaryotic NER.
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Affiliation(s)
- Kevin DuPrez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Feng He
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Zhenhang Chen
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Eduardo Hilario
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Li Fan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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10
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Masuda HP, Nakabashi M, Morgante PG, Kajihara D, de Setta N, Menck CFM, Van Sluys MA. Evidence for sub-functionalization of tandemly duplicated XPB nucleotide excision repair genes in Arabidopsis thaliana. Gene 2020; 754:144818. [PMID: 32485308 DOI: 10.1016/j.gene.2020.144818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022]
Abstract
Plants are continuously exposed to agents that can generate DNA lesions. Nucleotide Excision Repair (NER) is one of the repair pathways employed by plants to protect their genome, including from sunlight. The Xeroderma Pigmentosum type B (XPB) protein is a DNA helicase shown to be involved in NER and is also an essential subunitof the Transcription Factor IIH (TFIIH) complex. XPB was found to be a single copy gene in eukaryotes, but found as a tandem duplication in the plant Arabidopsis thaliana, AtXPB1 and AtXPB2. We aimed to investigate whether the XPB in tandem duplication was common within members of the Brassicaceae. We analyzed genomic DNA of species from different tribes of the family and the results indicate that the tandem duplication occurred in Camelineae tribe ancestor, of which A. thaliana belongs, at approximately 8 million years ago. Further experiments were devised to study possible functional roles for the A. thaliana AtXPB paralogs. A non-coincident expression profile of the paralogs was observed in various plant organs, developmental and cell cycle stages. AtXPB2 expression was observed in proliferating cells and clustered with the transcription of other components of the TFIIH such as p44, p52 and XPD/UVH6 along the cell cycle. AtXPB1 gene transcription, on the other hand, was enhanced specifically after UV-B irradiation in leaf trichomes. Altogether, our results reported herein suggest a functional specialization for the AtXPB paralogs: while the AtXPB2 paralog may have a role in cell proliferation and repair as XPB of other eukaryotes, the AtXPB1 paralog is most likely implicated in repair functions in highly specialized A. thaliana cells.
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Affiliation(s)
- Hana Paula Masuda
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Myna Nakabashi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Patricia G Morgante
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Universidade Estadual Paulista (UNESP), Campus de Registro São Paulo, SP, Brazil
| | - Daniela Kajihara
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Laboratório de Biologia Vascular, Instituto do Coração (InCor) da Faculdade de Medicina, Universidade de São Paulo, SP, Brazil
| | - Nathalia de Setta
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil; Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | | | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil.
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Hu Z, Ghosh A, Stolze SC, Horváth M, Bai B, Schaefer S, Zündorf S, Liu S, Harzen A, Hajheidari M, Sarnowski TJ, Nakagami H, Koncz Z, Koncz C. Gene modification by fast-track recombineering for cellular localization and isolation of components of plant protein complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:411-429. [PMID: 31276249 PMCID: PMC6852550 DOI: 10.1111/tpj.14450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/14/2019] [Accepted: 06/26/2019] [Indexed: 05/04/2023]
Abstract
To accelerate the isolation of plant protein complexes and study cellular localization and interaction of their components, an improved recombineering protocol is described for simple and fast site-directed modification of plant genes in bacterial artificial chromosomes (BACs). Coding sequences of fluorescent and affinity tags were inserted into genes and transferred together with flanking genomic sequences of desired size by recombination into Agrobacterium plant transformation vectors using three steps of E. coli transformation with PCR-amplified DNA fragments. Application of fast-track recombineering is illustrated by the simultaneous labelling of CYCLIN-DEPENDENT KINASE D (CDKD) and CYCLIN H (CYCH) subunits of kinase module of TFIIH general transcription factor and the CDKD-activating CDKF;1 kinase with green fluorescent protein (GFP) and mCherry (green and red fluorescent protein) tags, and a PIPL (His18 -StrepII-HA) epitope. Functionality of modified CDKF;1 gene constructs is verified by complementation of corresponding T-DNA insertion mutation. Interaction of CYCH with all three known CDKD homologues is confirmed by their co-localization and co-immunoprecipitation. Affinity purification and mass spectrometry analyses of CDKD;2, CYCH, and DNA-replication-coupled HISTONE H3.1 validate their association with conserved TFIIH subunits and components of CHROMATIN ASSEMBLY FACTOR 1, respectively. The results document that simple modification of plant gene products with suitable tags by fast-track recombineering is well suited to promote a wide range of protein interaction and proteomics studies.
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Affiliation(s)
- Zhoubo Hu
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Ajit Ghosh
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Department of Biochemistry and Molecular BiologyShahjalal University of Science and TechnologySylhet3114, Bangladesh
| | - Sara C. Stolze
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Mihály Horváth
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Bing Bai
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Sabine Schaefer
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Simone Zündorf
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Shanda Liu
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Anne Harzen
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Mohsen Hajheidari
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Botanical InstituteCologne Biocenter, Cluster of Excellence on Plant Sciences, University of CologneD‐50674CologneGermany
| | - Tomasz J. Sarnowski
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5A02‐106WarsawPoland
| | - Hirofumi Nakagami
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Zsuzsa Koncz
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Csaba Koncz
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Institute of Plant BiologyBiological Research Center of Hungarian Academy of SciencesTemesvári krt. 62H‐6726SzegedHungary
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12
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Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nat Struct Mol Biol 2019; 26:397-406. [PMID: 31110295 PMCID: PMC6642811 DOI: 10.1038/s41594-019-0220-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/29/2019] [Indexed: 12/11/2022]
Abstract
Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly's global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE-p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.
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Affiliation(s)
- Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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13
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Krishnan A, Burroughs AM, Iyer LM, Aravind L. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements. iScience 2018; 9:192-208. [PMID: 30396152 PMCID: PMC6222260 DOI: 10.1016/j.isci.2018.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/29/2022] Open
Abstract
The provenance of several components of major uniquely eukaryotic molecular machines are increasingly being traced back to prokaryotic biological conflict systems. Here, we demonstrate that the N-terminal single-stranded DNA-binding domain from the anti-restriction protein ArdC, deployed by bacterial mobile elements against their host, was independently acquired twice by eukaryotes, giving rise to the DNA-binding domains of XPC/Rad4 and the Tc-38-like proteins in the stem kinetoplastid. In both instances, the ArdC-N domain tandemly duplicated forming an extensive DNA-binding interface. In XPC/Rad4, the ArdC-N domains (BHDs) also fused to the inactive transglutaminase domain of a peptide-N-glycanase ultimately derived from an archaeal conflict system. Alongside, we delineate several parallel acquisitions from conjugative elements/bacteriophages that gave rise to key components of the kinetoplast DNA (kDNA) replication apparatus. These findings resolve two outstanding questions in eukaryote biology: (1) the origin of the unique DNA lesion-recognition component of NER and (2) origin of the unusual, plasmid-like features of kDNA.
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Affiliation(s)
- Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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14
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Mu H, Geacintov NE, Broyde S, Yeo JE, Schärer OD. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. DNA Repair (Amst) 2018; 71:33-42. [PMID: 30174301 DOI: 10.1016/j.dnarep.2018.08.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) is the main pathway for the removal of bulky lesions from DNA and is characterized by an extraordinarily wide substrate specificity. Remarkably, the efficiency of lesion removal varies dramatically and certain lesions escape repair altogether and are therefore associated with high levels of mutagenicity. Central to the multistep mechanism of damage recognition in NER is the sensing of lesion-induced thermodynamic and structural alterations of DNA by the XPC-RAD23B protein and the verification of the damage by the transcription/repair factor TFIIH. Additional factors contribute to the process: UV-DDB, for the recognition of certain UV-induced lesions in particular in the context of chromatin, while the XPA protein is believed to have a role in damage verification and NER complex assembly. Here we consider the molecular mechanisms that determine repair efficiency in GG-NER based on recent structural, computational, biochemical, cellular and single molecule studies of XPC-RAD23B and its yeast ortholog Rad4. We discuss how the actions of XPC-RAD23B are integrated with those of other NER proteins and, based on recent high-resolution structures of TFIIH, present a structural model of how XPC-RAD23B and TFIIH cooperate in damage recognition and verification.
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Affiliation(s)
- Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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15
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Bonaventura R, Zito F, Chiaramonte M, Costa C, Russo R. Nickel toxicity in P. lividus embryos: Dose dependent effects and gene expression analysis. MARINE ENVIRONMENTAL RESEARCH 2018; 139:113-121. [PMID: 29773318 DOI: 10.1016/j.marenvres.2018.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/29/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Many industrial activities release Nickel (Ni) in the environment with harmful effects for terrestrial and marine organisms. Despite many studies on the mechanisms of Ni toxicity are available, the understanding about its toxic effects on marine organisms is more limited. We used Paracentrotus lividus as a model to analyze the effects on the stress pathways in embryos continuously exposed to different Ni doses, ranging from 0.03 to 0.5 mM. We deeply examined the altered embryonic morphologies at 24 and 48 h after Ni exposure. Some different phenotypes have been classified, showing alterations at the expenses of the dorso-ventral axis as well as the skeleton and/or the pigment cells. At the lowest dose used, Ni mainly induced a multi-spicule phenotype observed at 24 h after treatment. On the contrary, at the highest dose of Ni (0.5 mM), 90% of embryos showed no skeleton and no pigment cells. Therefore, we focused on this dose to study protein and gene expression patterns at 24 and 48 h after exposure. Among the proteins analyzed, i.e. p38MAPK, Grp78 and Mn-SOD, only p38MAPK was induced by Ni treatment. Moreover, we analyzed the mRNA profiles of a pool of genes that are involved in stress response and in development mechanisms, i.e. the transcription factors Pl-NFkB and Pl-FOXO; a marker of DNA repair, Pl-XPB/ERCC3; a mitogen-activated protein kinase (MAPK), Pl-p38; an ER stress gene, Pl-grp78; an adapter protein, Pl-14-3-3ε; two markers of pigment cells, Pl-PKS1 and Pl-gcm. The spatial expression of mesenchymal marker genes has been evaluated in Ni-treated embryos at both 24 and 48 h after exposure. Our results indicated that Ni acts at several levels in P. lividus sea urchin, by affecting embryo development, influencing the embryonic immune response and activating stress response pathways to counteract the suffered injury and to promote embryos surviving.
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Affiliation(s)
- Rosa Bonaventura
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy.
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Marco Chiaramonte
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Caterina Costa
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
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16
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Analysis of the conserved NER helicases (XPB and XPD) and UV-induced DNA damage in Hydra. Biochim Biophys Acta Gen Subj 2018; 1862:2031-2042. [PMID: 29959982 DOI: 10.1016/j.bbagen.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/04/2018] [Accepted: 06/26/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleotide excision repair (NER) pathway is an evolutionarily conserved mechanism of genome maintenance. It detects and repairs distortions in DNA double helix. Xeroderma Pigmentosum group B (XPB) and group D (XPD) are important helicases in NER and are also critical subunits of TFIIH complex. We have studied XPB and XPD for the first time from the basal metazoan Hydra which exhibits lack of organismal senescence. METHODS In silico analysis of proteins was performed using MEGA 6.0, Clustal Omega, Swiss Model, etc. Gene expression was studied by in situ hybridization and qRT-PCR. Repair of CPDs was studied by DNA blot assay. Interactions between proteins were determined by co- immunoprecipitation. HyXPB and HyXPD were cloned in pET28b, overexpressed and helicase activity of purified proteins was checked. RESULTS In silico analysis revealed presence of seven classical helicase motifs in HyXPB and HyXPD. Both proteins revealed polarity-dependent helicase activity. Hydra repairs most of the thymine dimers induced by UVC (500 J/m2) by 72 h post-UV exposure. HyXPB and HyXPD transcripts, localized all over the body column, remained unaltered post-UV exposure indicating their constitutive expression. In spite of high levels of sequence conservation, XPB and XPD failed to rescue defects in human XPB- and XPD-deficient cell lines. This was due to their inability to get incorporated into the TFIIH multiprotein complex. CONCLUSIONS Present results along with our earlier work on DNA repair proteins in Hydra bring out the utility of Hydra as model system to study evolution of DNA repair mechanisms in metazoans.
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17
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Kahanda D, DuPrez KT, Hilario E, McWilliams MA, Wohlgamuth CH, Fan L, Slinker JD. Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA. Anal Chem 2018; 90:2178-2185. [PMID: 29285929 PMCID: PMC5957534 DOI: 10.1021/acs.analchem.7b04515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Much remains to be understood about the kinetics and thermodynamics of DNA helicase binding and activity. Here, we utilize probe-modified DNA monolayers on multiplexed gold electrodes as a sensitive recognition element and morphologically responsive transducer of helicase-DNA interactions. The electrochemical signals from these devices are highly sensitive to structural distortion of the DNA produced by the helicases. We used this DNA electrochemistry to distinguish the details of the DNA interactions of three distinct XPB helicases, which belong to the superfamily-2 of helicases. Clear changes in DNA melting temperature and duplex stability were observed upon helicase binding, shifts that could not be observed with conventional UV-visible absorption measurements. Binding dissociation constants were estimated in the range from 10 to 50 nM and correlated with observations of activity. ATP-stimulated DNA unwinding activity was also followed, revealing exponential time scales and distinct time constants associated with conventional and molecular wrench modes of operation further confirmed by crystal structures. These devices thus provide a sensitive measure of the structural thermodynamics and kinetics of helicase-DNA interactions.
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Affiliation(s)
- Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
| | - Kevin T. DuPrez
- Department of Biochemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department of Biochemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Marc A. McWilliams
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
| | - Chris H. Wohlgamuth
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
| | - Li Fan
- Department of Biochemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Jason D. Slinker
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, PHY 36, Richardson, Texas 75080, United States
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18
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Bukowska B, Karwowski BT. Actual state of knowledge in the field of diseases related with defective nucleotide excision repair. Life Sci 2018; 195:6-18. [DOI: 10.1016/j.lfs.2017.12.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
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19
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Third EU-US workshop on “Nucleotide excision repair and crosslink repair—From molecules to mankind”, Smolenice Castle, Slovak Republic, May 7th–11th 2017. DNA Repair (Amst) 2017. [DOI: 10.1016/j.dnarep.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Tuteja R. Unraveling the importance of the malaria parasite helicases. FEBS J 2017; 284:2592-2603. [DOI: 10.1111/febs.14109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/04/2017] [Accepted: 05/10/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Renu Tuteja
- Parasite Biology Group; International Centre for Genetic Engineering and Biotechnology; New Delhi India
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21
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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]
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22
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Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants. Oncotarget 2016; 7:7497-533. [PMID: 26848775 PMCID: PMC4884935 DOI: 10.18632/oncotarget.7120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/23/2016] [Indexed: 12/25/2022] Open
Abstract
Trisomy 21-driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and miRNA-target analyses. We used whole thymic tissue--obtained at heart surgery from Down syndrome (DS) and karyotipically normal subjects (CT)--and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires (communities) and the interactions between all the system's constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS networks corresponded to community changes. Distinct communities of highly interconnected genes were topologically identified in these networks. The role of miRNAs in modulating the expression of highly connected genes in CT and DS was revealed through miRNA-target analysis. Trisomy 21 gene dysregulation in thymus may be depicted as the breakdown and altered reorganization of transcriptional modules. Leading networks acting in normal or disease states were identified. CT networks would depict the "canonical" way of thymus functioning. Conversely, DS networks represent a "non-canonical" way, i.e., thymic tissue adaptation under trisomy 21 genomic dysregulation. This adaptation is probably driven by epigenetic mechanisms acting at chromatin level and through the miRNA control of transcriptional programs involving the networks' high-hierarchy genes.
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Hindman R, Gollnick P. Nucleoside Triphosphate Phosphohydrolase I (NPH I) Functions as a 5' to 3' Translocase in Transcription Termination of Vaccinia Early Genes. J Biol Chem 2016; 291:14826-38. [PMID: 27189950 DOI: 10.1074/jbc.m116.730135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 12/21/2022] Open
Abstract
Vaccinia virus early genes are transcribed immediately upon infection. Nucleoside triphosphate phosphohydrolase I (NPH I) is an essential component of the early gene transcription complex. NPH I hydrolyzes ATP to release transcripts during transcription termination. The ATPase activity of NPH I requires single-stranded (ss) DNA as a cofactor; however, the source of this cofactor within the transcription complex is not known. Based on available structures of transcription complexes it has been hypothesized that the ssDNA cofactor is obtained from the unpaired non-template strand within the transcription bubble. In vitro transcription on templates that lack portions of the non-template strand within the transcription bubble showed that the upstream portion of the transcription bubble is required for efficient NPH I-mediated transcript release. Complementarity between the template and non-template strands in this region is also required for NPH I-mediated transcript release. This observation complicates locating the source of the ssDNA cofactor within the transcription complex because removal of the non-template strand also disrupts transcription bubble reannealing. Prior studies have shown that ssRNA binds to NPH I, but it does not activate ATPase activity. Chimeric transcription templates with RNA in the non-template strand confirm that the source of the ssDNA cofactor for NPH I is the upstream portion of the non-template strand in the transcription bubble. Consistent with this conclusion we also show that isolated NPH I acts as a 5' to 3' translocase on single-stranded DNA.
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Affiliation(s)
- Ryan Hindman
- From the Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260-4610
| | - Paul Gollnick
- From the Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260-4610
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Hisama FM, Oshima J, Martin GM. How Research on Human Progeroid and Antigeroid Syndromes Can Contribute to the Longevity Dividend Initiative. Cold Spring Harb Perspect Med 2016; 6:a025882. [PMID: 26931459 DOI: 10.1101/cshperspect.a025882] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Although translational applications derived from research on basic mechanisms of aging are likely to enhance health spans and life spans for most of us (the longevity dividend), there will remain subsets of individuals with special vulnerabilities. Medical genetics is a discipline that describes such "private" patterns of aging and can reveal underlying mechanisms, many of which support genomic instability as a major mechanism of aging. We review examples of three classes of informative disorders: "segmental progeroid syndromes" (those that appear to accelerate multiple features of aging), "unimodal progeroid syndromes" (those that impact on a single disorder of aging), and "unimodal antigeroid syndromes," variants that provide enhanced protection against specific disorders of aging; we urge our colleagues to expand our meager research efforts on the latter, including ancillary somatic cell genetic approaches.
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Affiliation(s)
- Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195
| | - Junko Oshima
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195 Department of Medicine, Chiba University, Chiba 260-8670, Japan
| | - George M Martin
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195
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25
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Dynamic structures in DNA damage responses & cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 117:129-133. [PMID: 25934179 DOI: 10.1016/j.pbiomolbio.2015.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Khan I, Sommers JA, Brosh RM. Close encounters for the first time: Helicase interactions with DNA damage. DNA Repair (Amst) 2015; 33:43-59. [PMID: 26160335 DOI: 10.1016/j.dnarep.2015.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 01/17/2023]
Abstract
DNA helicases are molecular motors that harness the energy of nucleoside triphosphate hydrolysis to unwinding structured DNA molecules that must be resolved during cellular replication, DNA repair, recombination, and transcription. In vivo, DNA helicases are expected to encounter a wide spectrum of covalent DNA modifications to the sugar phosphate backbone or the nitrogenous bases; these modifications can be induced by endogenous biochemical processes or exposure to environmental agents. The frequency of lesion abundance can vary depending on the lesion type. Certain adducts such as oxidative base modifications can be quite numerous, and their effects can be helix-distorting or subtle perturbations to DNA structure. Helicase encounters with specific DNA lesions and more novel forms of DNA damage will be discussed. We will also review the battery of assays that have been used to characterize helicase-catalyzed unwinding of damaged DNA substrates. Characterization of the effects of specific DNA adducts on unwinding by various DNA repair and replication helicases has proven to be insightful for understanding mechanistic and biological aspects of helicase function in cellular DNA metabolism.
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Affiliation(s)
- Irfan Khan
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA.
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