1
|
Padayachy L, Ntallis SG, Halazonetis TD. RECQL4 is not critical for firing of human DNA replication origins. Sci Rep 2024; 14:7708. [PMID: 38565932 PMCID: PMC10987555 DOI: 10.1038/s41598-024-58404-0] [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: 12/25/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Human RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, the Xenopus laevis homolog of RECQL4 has been implicated in initiating DNA replication in egg extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (knock-out; KO) or expression of a full-length, mutant protein lacking helicase activity (helicase-dead; HD). Interestingly, both the RECQL4 KO and HD cells were viable and exhibited essentially identical origin firing profiles as the parental cells. Analysis of the rate of fork progression revealed increased rates in the RECQL4 KO cells, which might be indicative of decreased origin firing efficiency. Our results are consistent with human RECQL4 having a less critical role in firing of DNA replication origins, than its budding yeast homolog Sld2.
Collapse
Affiliation(s)
- Laura Padayachy
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Sotirios G Ntallis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland.
| |
Collapse
|
2
|
Sekelsky J. DNA Repair in Drosophila: Mutagens, Models, and Missing Genes. Genetics 2017; 205:471-490. [PMID: 28154196 PMCID: PMC5289830 DOI: 10.1534/genetics.116.186759] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/18/2016] [Indexed: 12/22/2022] Open
Abstract
The numerous processes that damage DNA are counterbalanced by a complex network of repair pathways that, collectively, can mend diverse types of damage. Insights into these pathways have come from studies in many different organisms, including Drosophila melanogaster Indeed, the first ideas about chromosome and gene repair grew out of Drosophila research on the properties of mutations produced by ionizing radiation and mustard gas. Numerous methods have been developed to take advantage of Drosophila genetic tools to elucidate repair processes in whole animals, organs, tissues, and cells. These studies have led to the discovery of key DNA repair pathways, including synthesis-dependent strand annealing, and DNA polymerase theta-mediated end joining. Drosophila appear to utilize other major repair pathways as well, such as base excision repair, nucleotide excision repair, mismatch repair, and interstrand crosslink repair. In a surprising number of cases, however, DNA repair genes whose products play important roles in these pathways in other organisms are missing from the Drosophila genome, raising interesting questions for continued investigations.
Collapse
Affiliation(s)
- Jeff Sekelsky
- Department of Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, North Carolina 27599
| |
Collapse
|
3
|
Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells. Oncotarget 2016; 6:40464-79. [PMID: 26588054 PMCID: PMC4747346 DOI: 10.18632/oncotarget.6342] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 12/17/2022] Open
Abstract
DNA replication is a highly coordinated process that is initiated at multiple replication origins in eukaryotes. These origins are bound by the origin recognition complex (ORC), which subsequently recruits the Mcm2-7 replicative helicase in a Cdt1/Cdc6-dependent manner. In budding yeast, two essential replication factors, Sld2 and Mcm10, are then important for the activation of replication origins. In humans, the putative Sld2 homolog, RECQ4, interacts with MCM10. Here, we have identified two mutants of human RECQ4 that are deficient in binding to MCM10. We show that these RECQ4 variants are able to complement the lethality of an avian cell RECQ4 deletion mutant, indicating that the essential function of RECQ4 in vertebrates is unlikely to require binding to MCM10. Nevertheless, we show that the RECQ4-MCM10 interaction is important for efficient replication origin firing.
Collapse
|
4
|
RECQ4 selectively recognizes Holliday junctions. DNA Repair (Amst) 2015; 30:80-9. [PMID: 25769792 DOI: 10.1016/j.dnarep.2015.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 12/23/2022]
Abstract
The RECQ4 protein belongs to the RecQ helicase family, which plays crucial roles in genome maintenance. Mutations in the RECQ4 gene are associated with three insidious hereditary disorders: Rothmund-Thomson, Baller-Gerold, and RAPADILINO syndromes. These syndromes are characterized by growth deficiency, radial ray defects, red rashes, and higher predisposition to malignancy, especially osteosarcomas. Within the RecQ family, RECQ4 is the least characterized, and its role in DNA replication and repair remains unknown. We have identified several DNA binding sites within RECQ4. Two are located at the N-terminus and one is located within the conserved helicase domain. N-terminal domains probably cooperate with one another and promote the strong annealing activity of RECQ4. Surprisingly, the region spanning 322-400aa shows a very high affinity for branched DNA substrates, especially Holliday junctions. This study demonstrates biochemical activities of RECQ4 that could be involved in genome maintenance and suggest its possible role in processing replication and recombination intermediates.
Collapse
|
5
|
Zegerman P. Evolutionary conservation of the CDK targets in eukaryotic DNA replication initiation. Chromosoma 2015; 124:309-21. [PMID: 25575982 DOI: 10.1007/s00412-014-0500-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
Abstract
A fundamental requirement for all organisms is the faithful duplication and transmission of the genetic material. Failure to accurately copy and segregate the genome during cell division leads to loss of genetic information and chromosomal abnormalities. Such genome instability is the hallmark of the earliest stages of tumour formation. Cyclin-dependent kinase (CDK) plays a vital role in regulating the duplication of the genome within the eukaryotic cell cycle. Importantly, this kinase is deregulated in many cancer types and is an emerging target of chemotherapeutics. In this review, I will consider recent advances concerning the role of CDK in replication initiation across eukaryotes. The implications for strict CDK-dependent regulation of genome duplication in the context of the cell cycle will be discussed.
Collapse
Affiliation(s)
- Philip Zegerman
- Department of Biochemistry, Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, The Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK,
| |
Collapse
|
6
|
Keijzers G, Maynard S, Shamanna RA, Rasmussen LJ, Croteau DL, Bohr VA. The role of RecQ helicases in non-homologous end-joining. Crit Rev Biochem Mol Biol 2014; 49:463-72. [PMID: 25048400 DOI: 10.3109/10409238.2014.942450] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
DNA double-strand breaks are highly toxic DNA lesions that cause genomic instability, if not efficiently repaired. RecQ helicases are a family of highly conserved proteins that maintain genomic stability through their important roles in several DNA repair pathways, including DNA double-strand break repair. Double-strand breaks can be repaired by homologous recombination (HR) using sister chromatids as templates to facilitate precise DNA repair, or by an HR-independent mechanism known as non-homologous end-joining (NHEJ) (error-prone). NHEJ is a non-templated DNA repair process, in which DNA termini are directly ligated. Canonical NHEJ requires DNA-PKcs and Ku70/80, while alternative NHEJ pathways are DNA-PKcs and Ku70/80 independent. This review discusses the role of RecQ helicases in NHEJ, alternative (or back-up) NHEJ (B-NHEJ) and microhomology-mediated end-joining (MMEJ) in V(D)J recombination, class switch recombination and telomere maintenance.
Collapse
Affiliation(s)
- Guido Keijzers
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark and
| | | | | | | | | | | |
Collapse
|
7
|
Gaggioli V, Zeiser E, Rivers D, Bradshaw CR, Ahringer J, Zegerman P. CDK phosphorylation of SLD-2 is required for replication initiation and germline development in C. elegans. ACTA ACUST UNITED AC 2014; 204:507-22. [PMID: 24535824 PMCID: PMC3926958 DOI: 10.1083/jcb.201310083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Timely phosphorylation of SLD-2 by CDK is essential for proper replication initiation and cell proliferation in the germline of C. elegans. Cyclin-dependent kinase (CDK) plays a vital role in proliferation control across eukaryotes. Despite this, how CDK mediates cell cycle and developmental transitions in metazoa is poorly understood. In this paper, we identify orthologues of Sld2, a CDK target that is important for DNA replication in yeast, and characterize SLD-2 in the nematode worm Caenorhabditis elegans. We demonstrate that SLD-2 is required for replication initiation and the nuclear retention of a critical component of the replicative helicase CDC-45 in embryos. SLD-2 is a CDK target in vivo, and phosphorylation regulates the interaction with another replication factor, MUS-101. By mutation of the CDK sites in sld-2, we show that CDK phosphorylation of SLD-2 is essential in C. elegans. Finally, using a phosphomimicking sld-2 mutant, we demonstrate that timely CDK phosphorylation of SLD-2 is an important control mechanism to allow normal proliferation in the germline. These results determine an essential function of CDK in metazoa and identify a developmental role for regulated SLD-2 phosphorylation.
Collapse
Affiliation(s)
- Vincent Gaggioli
- Wellcome Trust/Cancer Research UK Gurdon Institute, 2 Department of Genetics, and 3 Department of Zoology, University of Cambridge, Cambridge CB2 1QN, England, UK
| | | | | | | | | | | |
Collapse
|
8
|
Croteau DL, Popuri V, Opresko PL, Bohr VA. Human RecQ helicases in DNA repair, recombination, and replication. Annu Rev Biochem 2014; 83:519-52. [PMID: 24606147 DOI: 10.1146/annurev-biochem-060713-035428] [Citation(s) in RCA: 425] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RecQ helicases are an important family of genome surveillance proteins conserved from bacteria to humans. Each of the five human RecQ helicases plays critical roles in genome maintenance and stability, and the RecQ protein family members are often referred to as guardians of the genome. The importance of these proteins in cellular homeostasis is underscored by the fact that defects in BLM, WRN, and RECQL4 are linked to distinct heritable human disease syndromes. Each human RecQ helicase has a unique set of protein-interacting partners, and these interactions dictate its specialized functions in genome maintenance, including DNA repair, recombination, replication, and transcription. Human RecQ helicases also interact with each other, and these interactions have significant impact on enzyme function. Future research goals in this field include a better understanding of the division of labor among the human RecQ helicases and learning how human RecQ helicases collaborate and cooperate to enhance genome stability.
Collapse
Affiliation(s)
- Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, Maryland 21224;
| | | | | | | |
Collapse
|
9
|
Abstract
The RECQ family of DNA helicases is a conserved group of enzymes that are important for maintaining genomic integrity. In humans, there are five RECQ helicase genes, and mutations in three of them-BLM, WRN, and RECQL4-are associated with the genetic disorders Bloom syndrome, Werner syndrome, and Rothmund-Thomson syndrome (RTS), respectively. Importantly all three diseases are cancer predisposition syndromes. Patients with RTS are highly and uniquely susceptible to developing osteosarcoma; thus, RTS provides a good model to study the pathogenesis of osteosarcoma. The "tumor suppressor" role of RECQL4 and the other RECQ helicases is an area of active investigation. This chapter reviews what is currently known about the cellular functions of RECQL4 and how these may relate to tumorigenesis, as well as ongoing efforts to understand RECQL4's functions in vivo using animal models. Understanding the RECQ pathways may provide insight into avenues for novel cancer therapies in the future.
Collapse
|
10
|
Yu Z, Wu H, Chen H, Wang R, Liang X, Liu J, Li C, Deng WM, Jiao R. CAF-1 promotes Notch signaling through epigenetic control of target gene expression during Drosophila development. Development 2013; 140:3635-44. [PMID: 23942516 DOI: 10.1242/dev.094599] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The histone chaperone CAF-1 is known for its role in DNA replication-coupled histone deposition. However, loss of function causes lethality only in higher multicellular organisms such as mice and flies, but not in unicellular organisms such as yeasts, suggesting that CAF-1 has other important functions than histone deposition during animal development. Emerging evidence indicates that CAF-1 also has a role in higher order chromatin organization and heterochromatin-mediated gene expression; it remains unclear whether CAF-1 has a role in specific signaling cascades to promote gene expression during development. Here, we report that knockdown of one of the subunits of Drosophila CAF-1, dCAF-1-p105 (Caf1-105), results in phenotypes that resemble those of, and are augmented synergistically by, mutations of Notch positive regulatory pathway components. Depletion of dCAF-1-p105 leads to abrogation of cut expression and to downregulation of other Notch target genes in wing imaginal discs. dCAF-1-p105 is associated with Suppressor of Hairless [Su(H)] and regulates its binding to the enhancer region of E(spl)mβ. The association of dCAF-1-p105 with Su(H) on chromatin establishes an active local chromatin status for transcription by maintaining a high level of histone H4 acetylation. In response to induced Notch activation, dCAF-1 associates with the Notch intracellular domain to activate the expression of Notch target genes in cultured S2 cells, manifesting the role of dCAF-1 in Notch signaling. Together, our results reveal a novel epigenetic function of dCAF-1 in promoting Notch pathway activity that regulates normal Drosophila development.
Collapse
Affiliation(s)
- Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, China
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Jensen MB, Dunn CA, Keijzers G, Kulikowicz T, Rasmussen LJ, Croteau DL, Bohr VA. The helicase and ATPase activities of RECQL4 are compromised by mutations reported in three human patients. Aging (Albany NY) 2013; 4:790-802. [PMID: 23238538 PMCID: PMC3560432 DOI: 10.18632/aging.100506] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
RECQL4 is one of five members of the human RecQ helicase family, and is implicated in three syndromes displaying accelerating aging, developmental abnormalities and a predisposition to cancer. In this study, we purified three variants of RECQL4 carrying previously reported patient mutations. These three mutant proteins were analyzed for the known biochemical activities of RECQL4: DNA binding, unwinding of duplex DNA, ATP hydrolysis and annealing of simplex DNA. Further, the mutant proteins were evaluated for stability and recruitment to sites of laser-induced DNA damage. One mutant was helicase-dead, had marginal ATPase activity and may be structurally compromised, while the other two showed greatly reduced helicase and ATPase activities. The remaining biochemical activities and ability to recruit to damage sites were not significantly impaired for any of the mutants. Our findings demonstrate a consistent pattern of functional deficiency and provide further support for a helicase-dependent cellular function of RECQL4 in addition to its Nterminus-dependent role in initiation of replication, a function that may underlie the phenotype of RECQL4-linked disease.
Collapse
Affiliation(s)
- Martin Borch Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | | | | | | | | | | |
Collapse
|
12
|
Wei C, Liu J, Yu Z, Zhang B, Gao G, Jiao R. TALEN or Cas9 - rapid, efficient and specific choices for genome modifications. J Genet Genomics 2013; 40:281-9. [PMID: 23790627 DOI: 10.1016/j.jgg.2013.03.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 03/18/2013] [Accepted: 03/24/2013] [Indexed: 12/16/2022]
Abstract
Precise modifications of complex genomes at the single nucleotide level have been one of the big goals for scientists working in basic and applied genetics, including biotechnology, drug development, gene therapy and synthetic biology. However, the relevant techniques for making these manipulations in model organisms and human cells have been lagging behind the rapid high throughput studies in the post-genomic era with a bottleneck of low efficiency, time consuming and laborious manipulation, and off-targeting problems. Recent discoveries of TALEs (transcription activator-like effectors) coding system and CRISPR (clusters of regularly interspaced short palindromic repeats) immune system in bacteria have enabled the development of customized TALENs (transcription activator-like effector nucleases) and CRISPR/Cas9 to rapidly edit genomic DNA in a variety of cell types, including human cells, and different model organisms at a very high efficiency and specificity. In this review, we first briefly summarize the development and applications of TALENs and CRISPR/Cas9-mediated genome editing technologies; compare the advantages and constraints of each method; particularly, discuss the expected applications of both techniques in the field of site-specific genome modification and stem cell based gene therapy; finally, propose the future directions and perspectives for readers to make the choices.
Collapse
Affiliation(s)
- Chuanxian Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Datun Road 15, Beijing 100101, China
| | | | | | | | | | | |
Collapse
|
13
|
Dui W, Wei B, He F, Lu W, Li C, Liang X, Ma J, Jiao R. The Drosophila F-box protein dSkp2 regulates cell proliferation by targeting Dacapo for degradation. Mol Biol Cell 2013; 24:1676-87, S1-7. [PMID: 23552694 PMCID: PMC3667721 DOI: 10.1091/mbc.e12-10-0772] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
dSkp2 regulates cell cycle progression by antagonizing Dap in Drosophila, which resolves the question of whether dSkp2 has a role in regulating Dap stability and suggests the possibility of using Drosophila as a model system in which to study Skp2-mediated tumorigenesis. Cell cycle progression is controlled by a complex regulatory network consisting of interacting positive and negative factors. In humans, the positive regulator Skp2, an F-box protein, has been a subject of intense investigation in part because of its oncogenic activity. By contrast, the molecular and developmental functions of its Drosophila homologue, dSkp2, are poorly understood. Here we investigate the role of dSkp2 by focusing on its functional relationship with Dacapo (Dap), the Drosophila homologue of the cyclin-dependent kinase inhibitors p21cip1/p27kip1/p57kip2. We show that dSkp2 interacts physically with Dap and has a role in targeting Dap for ubiquitination and proteasome-mediated degradation. We present evidence that dSkp2 regulates cell cycle progression by antagonizing Dap in vivo. dSkp2 knockdown reduces cell density in the wing by prolonging the cell doubling time. In addition, the wing phenotype caused by dSkp2 knockdown resembles that caused by dap overexpression and can be partially suppressed by reducing the gene dose of dap. Our study thus documents a conserved functional relationship between dSkp2 and Dap in their control of cell cycle progression, suggesting the possibility of using Drosophila as a model system to study Skp2-mediated tumorigenesis.
Collapse
Affiliation(s)
- Wen Dui
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Marino F, Vindigni A, Onesti S. Bioinformatic analysis of RecQ4 helicases reveals the presence of a RQC domain and a Zn knuckle. Biophys Chem 2013; 177-178:34-9. [PMID: 23624328 DOI: 10.1016/j.bpc.2013.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 02/25/2013] [Accepted: 02/25/2013] [Indexed: 01/10/2023]
Abstract
RecQ helicases play essential roles in the maintenance of genome stability and contain a highly conserved helicase region generally followed by a characteristic RecQ-C-terminal (RQC) domain, plus a number of variable associated domains. Notable exceptions are the RecQ4 helicases, where none of these additional regions have been described. Particularly striking was the fact that no RQC domain had been reported, considering that the RQC domain had been shown to play an essential role in the catalytic mechanism of most RecQ family members. Here we present the results of detailed bioinformatic analyses of RecQ4 proteins that identify, for the first time, the presence of a putative RQC domain, including some of the key residues involved in DNA binding and unwinding. We also describe the presence of a novel "Zn knuckle" domain, as well as an additional Sld2-homology region, providing new insights into the architecture, function and evolution of these enzymes.
Collapse
Affiliation(s)
- Francesca Marino
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste SCpA, Area Science Park, Basovizza, Trieste, Italy.
| | | | | |
Collapse
|
15
|
dCAF-1-p55 is Essential for Drosophila Development and Involved in The Maintenance of Chromosomal Stability*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2012.00084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Crevel G, Vo N, Crevel I, Hamid S, Hoa L, Miyata S, Cotterill S. Drosophila RecQ4 is directly involved in both DNA replication and the response to UV damage in S2 cells. PLoS One 2012; 7:e49505. [PMID: 23166690 PMCID: PMC3500301 DOI: 10.1371/journal.pone.0049505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/10/2012] [Indexed: 11/18/2022] Open
Abstract
The RecQ4 protein shows homology to both the S.cerevisiae DNA replication protein Sld2 and the DNA repair related RecQ helicases. Experimental data also suggest replication and repair functions for RecQ4, but the precise details of its involvement remain to be clarified. Here we show that depletion of DmRecQ4 by dsRNA interference in S2 cells causes defects consistent with a replication function for the protein. The cells show reduced proliferation associated with an S phase block, reduced BrdU incorporation, and an increase in cells with a subG1 DNA content. At the molecular level we observe reduced chromatin association of DNA polymerase-alpha and PCNA. We also observe increased chromatin association of phosphorylated H2AvD - consistent with the presence of DNA damage and increased apoptosis. Analysis of DmRecQ4 repair function suggests a direct role in NER, as the protein shows rapid but transient nuclear localisation after UV treatment. Re-localisation is not observed after etoposide or H2O2 treatment, indicating that the involvement of DmRecQ4 in repair is likely to be pathway specific. Deletion analysis of DmRecQ4 suggests that the SLD2 domain was essential, but not sufficient, for replication function. In addition a DmRecQ4 N-terminal deletion could efficiently re-localise on UV treatment, suggesting that the determinants for this response are contained in the C terminus of the protein. Finally several deletions show differential rescue of dsRNA generated replication and proliferation phenotypes. These will be useful for a molecular analysis of the specific role of DmRecQ4 in different cellular pathways.
Collapse
Affiliation(s)
- Gilles Crevel
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
| | - Nicole Vo
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
| | - Isabelle Crevel
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
| | - Sana Hamid
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
| | - Lily Hoa
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
| | - Seiji Miyata
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Sue Cotterill
- Department Basic Medical Sciences, St. Georges University London, Cranmer Terrace, London, United Kingdom
- * E-mail:
| |
Collapse
|
17
|
Liu J, Li C, Yu Z, Huang P, Wu H, Wei C, Zhu N, Shen Y, Chen Y, Zhang B, Deng WM, Jiao R. Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. J Genet Genomics 2012; 39:209-15. [PMID: 22624882 DOI: 10.1016/j.jgg.2012.04.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 01/19/2023]
Abstract
Technology development has always been one of the forces driving breakthroughs in biomedical research. Since the time of Thomas Morgan, Drosophilists have, step by step, developed powerful genetic tools for manipulating and functionally dissecting the Drosophila genome, but room for improving these technologies and developing new techniques is still large, especially today as biologists start to study systematically the functional genomics of different model organisms, including humans, in a high-throughput manner. Here, we report, for the first time in Drosophila, a rapid, easy, and highly specific method for modifying the Drosophila genome at a very high efficiency by means of an improved transcription activator-like effector nuclease (TALEN) strategy. We took advantage of the very recently developed "unit assembly" strategy to assemble two pairs of specific TALENs designed to modify the yellow gene (on the sex chromosome) and a novel autosomal gene. The mRNAs of TALENs were subsequently injected into Drosophila embryos. From 31.2% of the injected F(0) fertile flies, we detected inheritable modification involving the yellow gene. The entire process from construction of specific TALENs to detection of inheritable modifications can be accomplished within one month. The potential applications of this TALEN-mediated genome modification method in Drosophila are discussed.
Collapse
Affiliation(s)
- Jiyong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing 100101, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Xie G, Zhang H, Du G, Huang Q, Liang X, Ma J, Jiao R. Uif, a large transmembrane protein with EGF-like repeats, can antagonize Notch signaling in Drosophila. PLoS One 2012; 7:e36362. [PMID: 22558447 PMCID: PMC3340373 DOI: 10.1371/journal.pone.0036362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 04/05/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Notch signaling is a highly conserved pathway in multi-cellular organisms ranging from flies to humans. It controls a variety of developmental processes by stimulating the expression of its target genes in a highly specific manner both spatially and temporally. The diversity, specificity and sensitivity of the Notch signaling output are regulated at distinct levels, particularly at the level of ligand-receptor interactions. METHODOLOGY/PRINCIPAL FINDINGS Here, we report that the Drosophila gene uninflatable (uif), which encodes a large transmembrane protein with eighteen EGF-like repeats in its extracellular domain, can antagonize the canonical Notch signaling pathway. Overexpression of Uif or ectopic expression of a neomorphic form of Uif, Uif*, causes Notch signaling defects in both the wing and the sensory organ precursors. Further experiments suggest that ectopic expression of Uif* inhibits Notch signaling in cis and acts at a step that is dependent on the extracellular domain of Notch. Our results suggest that Uif can alter the accessibility of the Notch extracellular domain to its ligands during Notch activation. CONCLUSIONS/SIGNIFICANCE Our study shows that Uif can modulate Notch activity, illustrating the importance of a delicate regulation of this signaling pathway for normal patterning.
Collapse
Affiliation(s)
- Gengqiang Xie
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
| | - Hongtao Zhang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Guiping Du
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Qinglei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
| | - Xuehong Liang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
| | - Jun Ma
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
- * E-mail: (RJ); (JM)
| | - Renjie Jiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- * E-mail: (RJ); (JM)
| |
Collapse
|
19
|
Kohzaki M, Chiourea M, Versini G, Adachi N, Takeda S, Gagos S, Halazonetis TD. The helicase domain and C-terminus of human RecQL4 facilitate replication elongation on DNA templates damaged by ionizing radiation. Carcinogenesis 2012; 33:1203-10. [PMID: 22508716 DOI: 10.1093/carcin/bgs149] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vertebrate RECQL4 (RECQ4) gene is thought to be the ortholog of budding yeast SLD2. However, RecQL4 contains within its C-terminus a RecQ-like helicase domain, which is absent in Sld2. We established human pre-B lymphocyte Nalm-6 cells, in which the endogenous RECQL4 gene was homozygously targeted such that the entire C-terminus would not be expressed. The RECQL4(ΔC/ΔC) cells behaved like the parental cells during unperturbed DNA replication or after treatment with agents that induce stalling of DNA replication forks, such as hydroxyurea (HU). However, after exposure to ionizing radiation (IR), the RECQL4(ΔC/ΔC) cells exhibited hypersensitivity, inability to complete S phase and prematurely terminated or paused DNA replication forks. Deletion of BLM, a gene that also encodes a RecQ helicase, had the opposite phenotype; an almost wild-type response to IR, but hypersensitivity to HU. Targeting both RECQL4 and BLM resulted in viable cells, which exhibited mostly additive phenotypes compared with those exhibited by the RECQL4(ΔC/ΔC) and the BLM(-/-) cells. We propose that RecQL4 facilitates DNA replication in cells that have been exposed to IR.
Collapse
Affiliation(s)
- Masaoki Kohzaki
- Department of Molecular Biology, University of Geneva, Switzerland
| | | | | | | | | | | | | |
Collapse
|
20
|
Aves SJ, Liu Y, Richards TA. Evolutionary diversification of eukaryotic DNA replication machinery. Subcell Biochem 2012; 62:19-35. [PMID: 22918578 DOI: 10.1007/978-94-007-4572-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA replication research to date has focused on model organisms such as the vertebrate Xenopus laevis and the yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. However, animals and fungi both belong to the Opisthokonta, one of about six eukaryotic phylogenetic 'supergroups', and therefore represent only a fraction of eukaryotic diversity. To explore evolutionary diversification of the eukaryotic DNA replication machinery a bioinformatic approach was used to investigate the presence or absence of yeast/animal replisome components in other eukaryotic taxa. A comparative genomic survey was undertaken of 59 DNA replication proteins in a diverse range of 36 eukaryotes from all six supergroups. Twenty-three proteins including Mcm2-7, Cdc45, RPA1, primase, some DNA polymerase subunits, RFC1-5, PCNA and Fen1 are present in all species examined. A further 20 proteins are present in all six eukaryotic supergroups, although not necessarily in every species: with the exception of RNase H2B and the fork protection complex component Timeless/Tof1, all of these are members of anciently derived paralogous families such as ORC, MCM, GINS or RPA. Together these form a set of 43 proteins that must have been present in the last common eukaryotic ancestor (LCEA). This minimal LCEA replisome is significantly more complex than the related replisome in Archaea, indicating evolutionary events including duplications of DNA replication genes in the LCEA lineage which parallel the early evolution of other complex eukaryotic cellular features.
Collapse
Affiliation(s)
- Stephen J Aves
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK,
| | | | | |
Collapse
|
21
|
Su Y, Meador JA, Calaf GM, DeSantis LP, Zhao Y, Bohr VA, Balajee AS. Human RecQL4 helicase plays critical roles in prostate carcinogenesis. Cancer Res 2010; 70:9207-17. [PMID: 21045146 PMCID: PMC3058916 DOI: 10.1158/0008-5472.can-10-1743] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Prostate cancer is the second leading cause of cancer-associated deaths among men in the western countries. Here, we report that human RecQL4 helicase, which is implicated in the pathogenesis of a subset of cancer-prone Rothmund-Thomson syndrome, is highly elevated in metastatic prostate cancer cell lines. Increased RecQL4 expression was also detected in human prostate tumor tissues as a function of tumor grade with the highest expression level in metastatic tumor samples, suggesting that RecQL4 may be a potential prognostic factor for advanced stage of prostate cancer. Transient and stable suppression of RecQL4 by small interfering RNA and short hairpin RNA vectors drastically reduced the growth and survival of metastatic prostate cancer cells, indicating that RecQL4 is a prosurvival factor for prostate cancer cells. RecQL4 suppression led to increased poly(ADP-ribose) polymerase (PARP) synthesis and RecQL4-suppressed prostate cancer cells underwent an extensive apoptotic death in a PARP-1-dependent manner. Most notably, RecQL4 knockdown in metastatic prostate cancer cells drastically reduced their cell invasiveness in vitro and tumorigenicity in vivo, showing that RecQL4 is essential for prostate cancer promotion. Observation of a direct interaction of retinoblastoma (Rb) and E2F1 proteins with RecQL4 promoter suggests that Rb-E2F1 pathway may regulate RecQL4 expression. Collectively, our study shows that RecQL4 is an essential factor for prostate carcinogenesis.
Collapse
Affiliation(s)
- Yanrong Su
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jarah A. Meador
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Gloria M. Calaf
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Yongliang Zhao
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600, Nathan Shock Drive, Baltimore, MD21224, USA
| | - Adayabalam S. Balajee
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
| |
Collapse
|
22
|
Rossi ML, Ghosh AK, Kulikowicz T, Croteau DL, Bohr VA. Conserved helicase domain of human RecQ4 is required for strand annealing-independent DNA unwinding. DNA Repair (Amst) 2010; 9:796-804. [PMID: 20451470 PMCID: PMC2893255 DOI: 10.1016/j.dnarep.2010.04.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 04/01/2010] [Accepted: 04/01/2010] [Indexed: 12/16/2022]
Abstract
Humans have five members of the well conserved RecQ helicase family: RecQ1, Bloom syndrome protein (BLM), Werner syndrome protein (WRN), RecQ4, and RecQ5, which are all known for their roles in maintaining genome stability. BLM, WRN, and RecQ4 are associated with premature aging and cancer predisposition. Of the three, RecQ4's biological and cellular roles have been least thoroughly characterized. Here we tested the helicase activity of purified human RecQ4 on various substrates. Consistent with recent results, we detected ATP-dependent RecQ4 unwinding of forked duplexes. However, our results provide the first evidence that human RecQ4's unwinding is independent of strand annealing, and that it does not require the presence of excess ssDNA. Moreover, we demonstrate that a point mutation of the conserved lysine in the Walker A motif abolished helicase activity, implying that not the N-terminal portion, but the helicase domain is solely responsible for the enzyme's unwinding activity. In addition, we demonstrate a novel stimulation of RecQ4's helicase activity by replication protein A, similar to that of RecQ1, BLM, WRN, and RecQ5. Together, these data indicate that specific biochemical activities and protein partners of RecQ4 are conserved with those of the other RecQ helicases.
Collapse
Affiliation(s)
- Marie L. Rossi
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224
| | - Avik K. Ghosh
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224
| | - Deborah L. Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224
| |
Collapse
|
23
|
Drosophila RecQ5 is required for efficient SSA repair and suppression of LOH in vivo. Protein Cell 2010; 1:478-90. [PMID: 21203963 DOI: 10.1007/s13238-010-0058-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 04/25/2010] [Indexed: 10/19/2022] Open
Abstract
RecQ5 in mammalian cells has been suggested to suppress inappropriate homologous recombination. However, the specific pathway(s) in which it is involved and the underlining mechanism(s) remain poorly understood. We took advantage of genetic tools in Drosophila to investigate how Drosophila RecQ5 (dRecQ5) functions in vivo in homologous recombination-mediated double strand break (DSB) repair. We generated null alleles of dRecQ5 using the targeted recombination technique. The mutant animals are homozygous viable, but with growth retardation during development. The mutants are sensitive to both exogenous DSB-inducing treatment, such as gamma-irradiation, and endogenously induced double strand breaks (DSBs) by I-Sce I endonuclease. In the absence of dRecQ5, single strand annealing (SSA)-mediated DSB repair is compromised with compensatory increases in either inter-homologous gene conversion, or non-homologous end joining (NHEJ) when inter-chromosomal homologous sequence is unavailable. Loss of function of dRecQ5 also leads to genome instability in loss of heterozygosity (LOH) assays. Together, our data demonstrate that dRecQ5 functions in SSA-mediated DSB repair to achieve its full efficiency and in suppression of LOH in Drosophila.
Collapse
|
24
|
Abstract
Recent work has greatly contributed to the understanding of the biology and biochemistry of RecQ4. It plays an essential non-enzymatic role in the formation of the CMG complex, and thus replication initiation, by means of its Sld2 homologous domain. The helicase domain of RecQ4 has now been demonstrated to possess 3'-5' DNA helicase activity, like the other members of the RecQ family. The biological purpose of this activity is still unclear, but helicase-dead mutants are unable to restore viability in the absence of wildtype RecQ4. This indicates that RecQ4 performs a second role, which requires helicase activity and is implicated in replication and DNA repair. Thus, it is clear that two helicases, RecQ4 and Mcm2-7, are integral to replication. The nature of the simultaneous involvement of these two helicases remains to be determined, and possible models will be proposed.
Collapse
Affiliation(s)
- Christopher Capp
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| | - Jianhong Wu
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| | - Tao-shih Hsieh
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| |
Collapse
|
25
|
Kusser W, Zimmer K, Fiedler F. Characteristics of the binding of aminoglycoside antibiotics to teichoic acids. A potential model system for interaction of aminoglycosides with polyanions. Dev Dyn 1985; 243:117-31. [PMID: 2411558 DOI: 10.1002/dvdy.24060] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/09/2013] [Accepted: 08/30/2013] [Indexed: 12/15/2022] Open
Abstract
The binding of the aminoglycoside antibiotic dihydrostreptomycin to defined cell-wall teichoic acids and to lipoteichoic acid isolated from various gram-positive eubacteria was followed by equilibrium dialysis. Dihydrostreptomycin was used at a wide range of concentration under different conditions of ionic strength, concentration of teichoic acid, presence of cationic molecules like Mg2+, spermidine, other aminoglycoside antibiotics (gentamicin, neomycin, paromomycin). Interaction of dihydrostreptomycin with teichoic acid was found to be a cooperative binding process. The binding characteristics seem to be dependent on structural features of teichoic acid and are influenced by cationic molecules. Mg2+, spermidine and other aminoglycosides antibiotics inhibit the binding of dihydrostreptomycin to teichoic acid competitively. The binding of aminoglycosides to teichoic acids is considered as a model system for the interaction of aminoglycoside antibiotics with cellular polyanions. Conclusions of physiological significance are drawn.
Collapse
|