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Bainbridge LJ, Daigaku Y. Bulk synthesis and beyond: The roles of eukaryotic replicative DNA polymerases. DNA Repair (Amst) 2024; 141:103740. [PMID: 39096696 DOI: 10.1016/j.dnarep.2024.103740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
An organism's genomic DNA must be accurately duplicated during each cell cycle. DNA synthesis is catalysed by DNA polymerase enzymes, which extend nucleotide polymers in a 5' to 3' direction. This inherent directionality necessitates that one strand is synthesised forwards (leading), while the other is synthesised backwards discontinuously (lagging) to couple synthesis to the unwinding of duplex DNA. Eukaryotic cells possess many diverse polymerases that coordinate to replicate DNA, with the three main replicative polymerases being Pol α, Pol δ and Pol ε. Studies conducted in yeasts and human cells utilising mutant polymerases that incorporate molecular signatures into nascent DNA implicate Pol ε in leading strand synthesis and Pol α and Pol δ in lagging strand replication. Recent structural insights have revealed how the spatial organization of these enzymes around the core helicase facilitates their strand-specific roles. However, various challenging situations during replication require flexibility in the usage of these enzymes, such as during replication initiation or encounters with replication-blocking adducts. This review summarises the roles of the replicative polymerases in bulk DNA replication and explores their flexible and dynamic deployment to complete genome replication. We also examine how polymerase usage patterns can inform our understanding of global replication dynamics by revealing replication fork directionality to identify regions of replication initiation and termination.
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Affiliation(s)
- Lewis J Bainbridge
- Cancer Genome Dynamics Project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yasukazu Daigaku
- Cancer Genome Dynamics Project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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2
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Jones RM, Reynolds-Winczura A, Gambus A. A Decade of Discovery-Eukaryotic Replisome Disassembly at Replication Termination. BIOLOGY 2024; 13:233. [PMID: 38666845 PMCID: PMC11048390 DOI: 10.3390/biology13040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
The eukaryotic replicative helicase (CMG complex) is assembled during DNA replication initiation in a highly regulated manner, which is described in depth by other manuscripts in this Issue. During DNA replication, the replicative helicase moves through the chromatin, unwinding DNA and facilitating nascent DNA synthesis by polymerases. Once the duplication of a replicon is complete, the CMG helicase and the remaining components of the replisome need to be removed from the chromatin. Research carried out over the last ten years has produced a breakthrough in our understanding, revealing that replication termination, and more specifically replisome disassembly, is indeed a highly regulated process. This review brings together our current understanding of these processes and highlights elements of the mechanism that are conserved or have undergone divergence throughout evolution. Finally, we discuss events beyond the classic termination of DNA replication in S-phase and go over the known mechanisms of replicative helicase removal from chromatin in these particular situations.
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Affiliation(s)
- Rebecca M. Jones
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
- School of Biosciences, Aston University, Birmingham B4 7ET, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
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3
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Vipat S, Moiseeva TN. The TIMELESS Roles in Genome Stability and Beyond. J Mol Biol 2024; 436:168206. [PMID: 37481157 DOI: 10.1016/j.jmb.2023.168206] [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: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
TIMELESS protein (TIM) protects replication forks from stalling at difficult-to-replicate regions and plays an important role in DNA damage response, including checkpoint signaling, protection of stalled replication forks and DNA repair. Loss of TIM causes severe replication stress, while its overexpression is common in various types of cancer, providing protection from DNA damage and resistance to chemotherapy. Although TIM has mostly been studied for its part in replication stress response, its additional roles in supporting genome stability and a wide variety of other cellular pathways are gradually coming to light. This review discusses the diverse functions of TIM and its orthologs in healthy and cancer cells, open questions, and potential future directions.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia.
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4
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Yang Y, Tang X, Lin Z, Zheng T, Zhang S, Liu T, Yang X. An integrative evaluation of circadian gene TIMELESS as a pan-cancer immunological and predictive biomarker. Eur J Med Res 2023; 28:563. [PMID: 38053143 DOI: 10.1186/s40001-023-01519-3] [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: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND The gene TIMELESS, which is involved in the circadian clock and the cell cycle, has recently been linked to various human cancers. Nevertheless, the association between TIMELESS expression and the prognosis of individuals afflicted with pan-cancer remains largely unknown. OBJECTIVES The present study aims to exhaustively scrutinize the expression patterns, functional attributes, prognostic implications, and immunological contributions of TIMELESS across diverse types of human cancer. METHODS The expression of TIMELESS in normal and malignant tissues was examined, as well as their clinicopathologic and survival data. The characteristics of genetic alteration and molecular subtypes of cancers were also investigated. In addition, the relationship of TIMELESS with immune infiltration, tumor mutation burden (TMB), microsatellite instability (MSI), and drug sensitivity was illustrated. Immunohistochemistry (IHC) was used to validate the expression of TIMELESS in clinical patients with several types of cancer. RESULTS In contrast to the matching normal controls, most tumor types were found to often overexpress TIMELESS. Abnormal expression of TIMELESS was significantly related to more advanced tumor stage and poorer prognosis of breast cancer, as well as infiltrating immune cells such as cancer-associated fibroblast infiltration in various tumors. Multiple cancer types exhibited abnormal expression of TIMELESS, which was also highly correlated with MSI and TMB. More crucially, TIMELESS showed promise in predicting the effectiveness of immunotherapy and medication sensitivity in cancer therapy. Moreover, cell cycle, DNA replication, circadian rhythm, and mismatch repair were involved in the functional mechanisms of TIMELESS on carcinogenesis. Furthermore, immunohistochemical results manifested that the TIMELESS expression was abnormal in some cancers. CONCLUSIONS This study provides new insights into the link between the circadian gene TIMELESS and the development of various malignant tumors. The findings suggest that TIMELESS could be a prospective prognostic and immunological biomarker for pan-cancer.
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Affiliation(s)
- Yaocheng Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou First People's Hospital, Chenzhou, Hunan, China
| | - Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Tao Zheng
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Sheng Zhang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xiaolun Yang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China.
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5
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Pellegrini L. The CMG DNA helicase and the core replisome. Curr Opin Struct Biol 2023; 81:102612. [PMID: 37244171 DOI: 10.1016/j.sbi.2023.102612] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/29/2023]
Abstract
Eukaryotic DNA replication is performed by the replisome, a large and dynamic multi-protein machine endowed with the required enzymatic components for the synthesis of new DNA. Recent cryo-electron microscopy (cryoEM) analyses have revealed the conserved architecture of the core eukaryotic replisome, comprising the CMG (Cdc45-MCM-GINS) DNA helicase, the leading-strand DNA polymerase epsilon, the Timeless-Tipin heterodimer, the hub protein AND-1 and the checkpoint protein Claspin. These results bid well for arriving soon at an integrated understanding of the structural basis of semi-discontinuous DNA replication. They further set the scene for the characterisation of the mechanisms that interface DNA synthesis with concurrent processes such as DNA repair, propagation of chromatin structure and establishment of sister chromatid cohesion.
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6
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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7
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Patel JA, Kim H. The TIMELESS effort for timely DNA replication and protection. Cell Mol Life Sci 2023; 80:84. [PMID: 36892674 PMCID: PMC9998586 DOI: 10.1007/s00018-023-04738-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023]
Abstract
Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.
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Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
- Stony Brook Cancer Center and Renaissance School of Medicine, Stony Brook University, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
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8
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Stoy H, Zwicky K, Kuster D, Lang KS, Krietsch J, Crossley MP, Schmid JA, Cimprich KA, Merrikh H, Lopes M. Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids. Nat Struct Mol Biol 2023; 30:348-359. [PMID: 36864174 PMCID: PMC10023573 DOI: 10.1038/s41594-023-00928-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/23/2023] [Indexed: 03/04/2023]
Abstract
Transcription-replication collisions (TRCs) are crucial determinants of genome instability. R-loops were linked to head-on TRCs and proposed to obstruct replication fork progression. The underlying mechanisms, however, remained elusive due to the lack of direct visualization and of non-ambiguous research tools. Here, we ascertained the stability of estrogen-induced R-loops on the human genome, visualized them directly by electron microscopy (EM), and measured R-loop frequency and size at the single-molecule level. Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. Altogether, our findings suggest that TRC-associated replication interference entails transactions that follow initial R-loop bypass by the replication fork.
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Affiliation(s)
- Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Katharina Zwicky
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Kevin S Lang
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonas A Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Houra Merrikh
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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9
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Koyanagi E, Kakimoto Y, Minamisawa T, Yoshifuji F, Natsume T, Higashitani A, Ogi T, Carr AM, Kanemaki MT, Daigaku Y. Global landscape of replicative DNA polymerase usage in the human genome. Nat Commun 2022; 13:7221. [PMID: 36434012 PMCID: PMC9700718 DOI: 10.1038/s41467-022-34929-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
The division of labour among DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequencing (Pu-seq) in HCT116 cells and mapped Polε and Polα usage genome wide. The polymerase usage profiles show Polε synthesises the leading strand and Polα contributes mainly to lagging strand synthesis. Combining the Polε and Polα profiles, we accurately predict the genome-wide pattern of fork directionality plus zones of replication initiation and termination. We confirm that transcriptional activity contributes to the pattern of initiation and termination and, by separately analysing the effect of transcription on co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands is compromised by transcription in both co-directional and convergent forks. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability. Together, our result demonstrated that Pu-seq in human cells provides a powerful and straightforward methodology to explore DNA polymerase usage and replication fork dynamics.
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Affiliation(s)
- Eri Koyanagi
- grid.69566.3a0000 0001 2248 6943Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Yoko Kakimoto
- grid.69566.3a0000 0001 2248 6943Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Tamiko Minamisawa
- grid.410807.a0000 0001 0037 4131Cancer Genome Dynamics project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Fumiya Yoshifuji
- grid.69566.3a0000 0001 2248 6943Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Toyoaki Natsume
- grid.418987.b0000 0004 1764 2181National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan ,grid.275033.00000 0004 1763 208XDepartment of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan ,grid.272456.00000 0000 9343 3630Present Address: Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Atsushi Higashitani
- grid.69566.3a0000 0001 2248 6943Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomoo Ogi
- grid.27476.300000 0001 0943 978XResearch Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Antony M. Carr
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ UK
| | - Masato T. Kanemaki
- grid.418987.b0000 0004 1764 2181National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan ,grid.275033.00000 0004 1763 208XDepartment of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yasukazu Daigaku
- grid.69566.3a0000 0001 2248 6943Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan ,grid.410807.a0000 0001 0037 4131Cancer Genome Dynamics project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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10
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Solving the MCM paradox by visualizing the scaffold of CMG helicase at active replisomes. Nat Commun 2022; 13:6090. [PMID: 36241664 PMCID: PMC9568601 DOI: 10.1038/s41467-022-33887-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Genome duplication is safeguarded by constantly adjusting the activity of the replicative CMG (CDC45-MCM2-7-GINS) helicase. However, minichromosome maintenance proteins (MCMs)-the structural core of the CMG helicase-have never been visualized at sites of DNA synthesis inside a cell (the so-called MCM paradox). Here, we solve this conundrum by showing that anti-MCM antibodies primarily detect inactive MCMs. Upon conversion of inactive MCMs to CMGs, factors that are required for replisome activity bind to the MCM scaffold and block MCM antibody binding sites. Tagging of endogenous MCMs by CRISPR-Cas9 bypasses this steric hindrance and enables MCM visualization at active replisomes. Thus, by defining conditions for detecting the structural core of the replicative CMG helicase, our results explain the MCM paradox, provide visual proof that MCMs are an integral part of active replisomes in vivo, and enable the investigation of replication dynamics in living cells exposed to a constantly changing environment.
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11
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Mellor C, Perez C, Sale JE. Creation and resolution of non-B-DNA structural impediments during replication. Crit Rev Biochem Mol Biol 2022; 57:412-442. [PMID: 36170051 PMCID: PMC7613824 DOI: 10.1080/10409238.2022.2121803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence that secondary structures are a significant and frequent source of replication stress that must be actively countered. Taking advantage of recent advances in the molecular and structural biology of the yeast and human replisomes, we examine how structures form and how they may be sensed and resolved during replication.
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Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
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12
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Van Ravenstein SX, Mehta KP, Kavlashvili T, Byl JAW, Zhao R, Osheroff N, Cortez D, Dewar JM. Topoisomerase II poisons inhibit vertebrate DNA replication through distinct mechanisms. EMBO J 2022; 41:e110632. [PMID: 35578785 PMCID: PMC9194788 DOI: 10.15252/embj.2022110632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Topoisomerase II (TOP2) unlinks chromosomes during vertebrate DNA replication. TOP2 "poisons" are widely used chemotherapeutics that stabilize TOP2 complexes on DNA, leading to cytotoxic DNA breaks. However, it is unclear how these drugs affect DNA replication, which is a major target of TOP2 poisons. Using Xenopus egg extracts, we show that the TOP2 poisons etoposide and doxorubicin both inhibit DNA replication through different mechanisms. Etoposide induces TOP2-dependent DNA breaks and TOP2-dependent fork stalling by trapping TOP2 behind replication forks. In contrast, doxorubicin does not lead to appreciable break formation and instead intercalates into parental DNA to stall replication forks independently of TOP2. In human cells, etoposide stalls forks in a TOP2-dependent manner, while doxorubicin stalls forks independently of TOP2. However, both drugs exhibit TOP2-dependent cytotoxicity. Thus, etoposide and doxorubicin inhibit DNA replication through distinct mechanisms despite shared genetic requirements for cytotoxicity.
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Affiliation(s)
| | - Kavi P Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Runxiang Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
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13
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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14
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McKie SJ, Desai P, Seol Y, Allen AM, Maxwell A, Neuman KC. Topoisomerase VI is a chirally-selective, preferential DNA decatenase. eLife 2022; 11:67021. [PMID: 35076393 PMCID: PMC8837201 DOI: 10.7554/elife.67021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase; however, robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a significant increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.
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Affiliation(s)
- Shannon J McKie
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Parth Desai
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Adam Mb Allen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Anthony Maxwell
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
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15
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Safaric B, Chacin E, Scherr MJ, Rajappa L, Gebhardt C, Kurat CF, Cordes T, Duderstadt KE. The fork protection complex recruits FACT to reorganize nucleosomes during replication. Nucleic Acids Res 2022; 50:1317-1334. [PMID: 35061899 PMCID: PMC8860610 DOI: 10.1093/nar/gkac005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/21/2021] [Accepted: 01/05/2022] [Indexed: 01/14/2023] Open
Abstract
Chromosome replication depends on efficient removal of nucleosomes by accessory factors to ensure rapid access to genomic information. Here, we show this process requires recruitment of the nucleosome reorganization activity of the histone chaperone FACT. Using single-molecule FRET, we demonstrate that reorganization of nucleosomal DNA by FACT requires coordinated engagement by the middle and C-terminal domains of Spt16 and Pob3 but does not require the N-terminus of Spt16. Using structure-guided pulldowns, we demonstrate instead that the N-terminal region is critical for recruitment by the fork protection complex subunit Tof1. Using in vitro chromatin replication assays, we confirm the importance of these interactions for robust replication. Our findings support a mechanism in which nucleosomes are removed through the coordinated engagement of multiple FACT domains positioned at the replication fork by the fork protection complex.
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Affiliation(s)
- Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Erika Chacin
- Biomedical Center (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Christoph F Kurat
- Biomedical Center (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,Physics Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
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16
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Zhang H, Liu R, Zhang B, Huo H, Song Z. Advances in the Study of Circadian Genes in Non-Small Cell Lung Cancer. Integr Cancer Ther 2022; 21:15347354221096080. [PMID: 35575281 PMCID: PMC9121494 DOI: 10.1177/15347354221096080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Circadian genes regulate several physiological functions such as circadian rhythm
and metabolism and participate in the cytogenesis and progression of various
malignancies. The abnormal expression of these genes in non-small cell lung
cancer (NSCLC) is closely related to the clinicopathological features of NSCLC
and may promote or inhibit NSCLC progression. Circadian rhythm disorders and
clock gene abnormalities may increase the risk of lung cancer in some
populations. We collected 15 circadian genes in NSCLC, namely PER1,
PER2, PER3, TIMELESS, Cry1, Cry2, CLOCK, BMAL1/ARNTL-1, ARNTL2, NPAS2,
NR1D1(REV-ERB), DEC1, DEC2, RORα, and RORγ, and
determined their relationships with the clinicopathological features of patients
and the potential mechanisms promoting or inhibiting NSCLC progression. We also
summarized the studies on circadian rhythm disorders and circadian genes
associated with lung cancer risk. The present study aimed to provide theoretical
support for the future exploration of new therapeutic targets and for the
primary prevention of NSCLC from the perspective of circadian genes.
Interpretation of circadian rhythms in lung cancer could guide further lung
cancer mechanism research and drug development that could lead to more effective
treatments and improve patient outcomes.
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Affiliation(s)
- Hao Zhang
- Tianjin Medical University General Hospital, Tianjin, China
| | - Renwang Liu
- Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Zhang
- Tianjin Medical University General Hospital, Tianjin, China
| | - Huandong Huo
- Tianjin Medical University General Hospital, Tianjin, China
| | - Zuoqing Song
- Tianjin Medical University General Hospital, Tianjin, China
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17
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Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [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: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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18
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Homologous Recombination as a Fundamental Genome Surveillance Mechanism during DNA Replication. Genes (Basel) 2021; 12:genes12121960. [PMID: 34946909 PMCID: PMC8701046 DOI: 10.3390/genes12121960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Accurate and complete genome replication is a fundamental cellular process for the proper transfer of genetic material to cell progenies, normal cell growth, and genome stability. However, a plethora of extrinsic and intrinsic factors challenge individual DNA replication forks and cause replication stress (RS), a hallmark of cancer. When challenged by RS, cells deploy an extensive range of mechanisms to safeguard replicating genomes and limit the burden of DNA damage. Prominent among those is homologous recombination (HR). Although fundamental to cell division, evidence suggests that cancer cells exploit and manipulate these RS responses to fuel their evolution and gain resistance to therapeutic interventions. In this review, we focused on recent insights into HR-mediated protection of stress-induced DNA replication intermediates, particularly the repair and protection of daughter strand gaps (DSGs) that arise from discontinuous replication across a damaged DNA template. Besides mechanistic underpinnings of this process, which markedly differ depending on the extent and duration of RS, we highlight the pathophysiological scenarios where DSG repair is naturally silenced. Finally, we discuss how such pathophysiological events fuel rampant mutagenesis, promoting cancer evolution, but also manifest in adaptative responses that can be targeted for cancer therapy.
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19
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Das SK, Kuzin V, Cameron DP, Sanford S, Jha RK, Nie Z, Rosello MT, Holewinski R, Andresson T, Wisniewski J, Natsume T, Price DH, Lewis BA, Kouzine F, Levens D, Baranello L. MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome". Mol Cell 2021; 82:140-158.e12. [PMID: 34890565 DOI: 10.1016/j.molcel.2021.11.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 08/11/2021] [Accepted: 11/13/2021] [Indexed: 12/25/2022]
Abstract
High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must manage this interfering torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with topoisomerase 1 (TOP1) and TOP2 that was confirmed in vitro and in cells. Beyond recruiting topoisomerases, MYC directly stimulates their activities. We identify a MYC-nucleated "topoisome" complex that unites TOP1 and TOP2 and increases their levels and activities at promoters, gene bodies, and enhancers. Whether TOP2A or TOP2B is included in the topoisome is dictated by the presence of MYC versus MYCN, respectively. Thus, in vitro and in cells, MYC assembles tools that simplify DNA topology and promote genome function under high output conditions.
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Affiliation(s)
- Subhendu K Das
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Donald P Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Suzanne Sanford
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Rajiv Kumar Jha
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Zuqin Nie
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Marta Trullols Rosello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ronald Holewinski
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 21701, USA
| | - Thorkell Andresson
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 21701, USA
| | - Jan Wisniewski
- Confocal Microscopy and Digital Imaging Facility, National Cancer Institute, Bethesda, MD 20892, USA
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Shizuoka 411-8540, Japan; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Brian A Lewis
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Fedor Kouzine
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA.
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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20
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Kemiha S, Poli J, Lin YL, Lengronne A, Pasero P. Toxic R-loops: Cause or consequence of replication stress? DNA Repair (Amst) 2021; 107:103199. [PMID: 34399314 DOI: 10.1016/j.dnarep.2021.103199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 01/08/2023]
Abstract
Transcription-replication conflicts (TRCs) represent a potential source of endogenous replication stress (RS) and genomic instability in eukaryotic cells but the mechanisms that underlie this instability remain poorly understood. Part of the problem could come from non-B DNA structures called R-loops, which are formed of a RNA:DNA hybrid and a displaced ssDNA loop. In this review, we discuss different scenarios in which R-loops directly or indirectly interfere with DNA replication. We also present other types of TRCs that may not depend on R-loops to impede fork progression. Finally, we discuss alternative models in which toxic RNA:DNA hybrids form at stalled forks as a consequence - but not a cause - of replication stress and interfere with replication resumption.
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Affiliation(s)
- Samira Kemiha
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
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21
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Topoisomerase II deficiency leads to a postreplicative structural shift in all Saccharomyces cerevisiae chromosomes. Sci Rep 2021; 11:14940. [PMID: 34294749 PMCID: PMC8298500 DOI: 10.1038/s41598-021-93875-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
The key role of Topoisomerase II (Top2) is the removal of topological intertwines between sister chromatids. In yeast, inactivation of Top2 brings about distinct cell cycle responses. In the case of the conditional top2-5 allele, interphase and mitosis progress on schedule but cells suffer from a chromosome segregation catastrophe. We here show that top2-5 chromosomes fail to enter a Pulsed-Field Gel Electrophoresis (PFGE) in the first cell cycle, a behavior traditionally linked to the presence of replication and recombination intermediates. We distinguished two classes of affected chromosomes: the rDNA-bearing chromosome XII, which fails to enter a PFGE at the beginning of S-phase, and all the other chromosomes, which fail at a postreplicative stage. In synchronously cycling cells, this late PFGE retention is observed in anaphase; however, we demonstrate that this behavior is independent of cytokinesis, stabilization of anaphase bridges, spindle pulling forces and, probably, anaphase onset. Strikingly, once the PFGE retention has occurred it becomes refractory to Top2 re-activation. DNA combing, two-dimensional electrophoresis, genetic analyses, and GFP-tagged DNA damage markers suggest that neither recombination intermediates nor unfinished replication account for the postreplicative PFGE shift, which is further supported by the fact that the shift does not trigger the G2/M checkpoint. We propose that the absence of Top2 activity leads to a general chromosome structural/topological change in mitosis.
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22
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Shyian M, Shore D. Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes. Front Cell Dev Biol 2021; 9:672510. [PMID: 34124054 PMCID: PMC8194067 DOI: 10.3389/fcell.2021.672510] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
During nuclear DNA replication multiprotein replisome machines have to jointly traverse and duplicate the total length of each chromosome during each cell cycle. At certain genomic locations replisomes encounter tight DNA-protein complexes and slow down. This fork pausing is an active process involving recognition of a protein barrier by the approaching replisome via an evolutionarily conserved Fork Pausing/Protection Complex (FPC). Action of the FPC protects forks from collapse at both programmed and accidental protein barriers, thus promoting genome integrity. In addition, FPC stimulates the DNA replication checkpoint and regulates topological transitions near the replication fork. Eukaryotic cells have been proposed to employ physiological programmed fork pausing for various purposes, such as maintaining copy number at repetitive loci, precluding replication-transcription encounters, regulating kinetochore assembly, or controlling gene conversion events during mating-type switching. Here we review the growing number of approaches used to study replication pausing in vivo and in vitro as well as the characterization of additional factors recently reported to modulate fork pausing in different systems. Specifically, we focus on the positive role of topoisomerases in fork pausing. We describe a model where replisome progression is inherently cautious, which ensures general preservation of fork stability and genome integrity but can also carry out specialized functions at certain loci. Furthermore, we highlight classical and novel outstanding questions in the field and propose venues for addressing them. Given how little is known about replisome pausing at protein barriers in human cells more studies are required to address how conserved these mechanisms are.
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Affiliation(s)
- Maksym Shyian
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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23
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Agashe S, Joseph CR, Reyes TAC, Menolfi D, Giannattasio M, Waizenegger A, Szakal B, Branzei D. Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites. Nat Commun 2021; 12:2111. [PMID: 33833229 PMCID: PMC8032827 DOI: 10.1038/s41467-021-22217-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Smc5/6 is essential for genome structural integrity by yet unknown mechanisms. Here we find that Smc5/6 co-localizes with the DNA crossed-strand processing complex Sgs1-Top3-Rmi1 (STR) at genomic regions known as natural pausing sites (NPSs) where it facilitates Top3 retention. Individual depletions of STR subunits and Smc5/6 cause similar accumulation of joint molecules (JMs) composed of reversed forks, double Holliday Junctions and hemicatenanes, indicative of Smc5/6 regulating Sgs1 and Top3 DNA processing activities. We isolate an intra-allelic suppressor of smc6-56 proficient in Top3 retention but affected in pathways that act complementarily with Sgs1 and Top3 to resolve JMs arising at replication termination. Upon replication stress, the smc6-56 suppressor requires STR and Mus81-Mms4 functions for recovery, but not Srs2 and Mph1 helicases that prevent maturation of recombination intermediates. Thus, Smc5/6 functions jointly with Top3 and STR to mediate replication completion and influences the function of other DNA crossed-strand processing enzymes at NPSs.
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Affiliation(s)
- Sumedha Agashe
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Demis Menolfi
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Michele Giannattasio
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | | | - Barnabas Szakal
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy. .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy.
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24
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Bonnell E, Pasquier E, Wellinger RJ. Telomere Replication: Solving Multiple End Replication Problems. Front Cell Dev Biol 2021; 9:668171. [PMID: 33869233 PMCID: PMC8047117 DOI: 10.3389/fcell.2021.668171] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes are highly complex and divided into linear chromosomes that require end protection from unwarranted fusions, recombination, and degradation in order to maintain genomic stability. This is accomplished through the conserved specialized nucleoprotein structure of telomeres. Due to the repetitive nature of telomeric DNA, and the unusual terminal structure, namely a protruding single stranded 3' DNA end, completing telomeric DNA replication in a timely and efficient manner is a challenge. For example, the end replication problem causes a progressive shortening of telomeric DNA at each round of DNA replication, thus telomeres eventually lose their protective capacity. This phenomenon is counteracted by the recruitment and the activation at telomeres of the specialized reverse transcriptase telomerase. Despite the importance of telomerase in providing a mechanism for complete replication of telomeric ends, the majority of telomere replication is in fact carried out by the conventional DNA replication machinery. There is significant evidence demonstrating that progression of replication forks is hampered at chromosomal ends due to telomeric sequences prone to form secondary structures, tightly DNA-bound proteins, and the heterochromatic nature of telomeres. The telomeric loop (t-loop) formed by invasion of the 3'-end into telomeric duplex sequences may also impede the passage of replication fork. Replication fork stalling can lead to fork collapse and DNA breaks, a major cause of genomic instability triggered notably by unwanted repair events. Moreover, at chromosomal ends, unreplicated DNA distal to a stalled fork cannot be rescued by a fork coming from the opposite direction. This highlights the importance of the multiple mechanisms involved in overcoming fork progression obstacles at telomeres. Consequently, numerous factors participate in efficient telomeric DNA duplication by preventing replication fork stalling or promoting the restart of a stalled replication fork at telomeres. In this review, we will discuss difficulties associated with the passage of the replication fork through telomeres in both fission and budding yeasts as well as mammals, highlighting conserved mechanisms implicated in maintaining telomere integrity during replication, thus preserving a stable genome.
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Affiliation(s)
| | | | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, QC, Canada
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25
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Lang KS, Merrikh H. Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts. Cell Rep 2021; 34:108797. [PMID: 33657379 PMCID: PMC7986047 DOI: 10.1016/j.celrep.2021.108797] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 12/18/2022] Open
Abstract
Conflicts between the replication and transcription machineries have profound effects on chromosome duplication, genome organization, and evolution across species. Head-on conflicts (lagging-strand genes) are significantly more detrimental than codirectional conflicts (leading-strand genes). The fundamental reason for this difference is unknown. Here, we report that topological stress significantly contributes to this difference. We find that head-on, but not codirectional, conflict resolution requires the relaxation of positive supercoils by the type II topoisomerases DNA gyrase and Topo IV, at least in the Gram-positive model bacterium Bacillus subtilis. Interestingly, our data suggest that after positive supercoil resolution, gyrase introduces excessive negative supercoils at head-on conflict regions, driving pervasive R-loop formation. Altogether, our results reveal a fundamental mechanistic difference between the two types of encounters, addressing a long-standing question in the field of replication-transcription conflicts. Lang and Merrikh show that resolution of head-on, but not codirectional, conflicts between replication and transcription machineries requires type II topoisomerases, suggesting that a fundamental difference between the two types of conflicts is supercoil buildup in DNA. Furthermore, they show that supercoil resolution at head-on conflict regions drives R-loop formation.
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Affiliation(s)
- Kevin S Lang
- Department of Biochemistry, Light Hall, Vanderbilt University, Nashville, TN, USA
| | - Houra Merrikh
- Department of Biochemistry, Light Hall, Vanderbilt University, Nashville, TN, USA.
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26
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Westhorpe R, Keszthelyi A, Minchell NE, Jones D, Baxter J. Separable functions of Tof1/Timeless in intra-S-checkpoint signalling, replisome stability and DNA topological stress. Nucleic Acids Res 2020; 48:12169-12187. [PMID: 33166393 PMCID: PMC7708041 DOI: 10.1093/nar/gkaa963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
The highly conserved Tof1/Timeless proteins minimise replication stress and promote normal DNA replication. They are required to mediate the DNA replication checkpoint (DRC), the stable pausing of forks at protein fork blocks, the coupling of DNA helicase and polymerase functions during replication stress (RS) and the preferential resolution of DNA topological stress ahead of the fork. Here we demonstrate that the roles of the Saccharomyces cerevisiae Timeless protein Tof1 in DRC signalling and resolution of DNA topological stress require distinct N and C terminal regions of the protein, whereas the other functions of Tof1 are closely linked to the stable interaction between Tof1 and its constitutive binding partner Csm3/Tipin. By separating the role of Tof1 in DRC from fork stabilisation and coupling, we show that Tof1 has distinct activities in checkpoint activation and replisome stability to ensure the viable completion of DNA replication following replication stress.
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Affiliation(s)
- Rose Westhorpe
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Nicola E Minchell
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - David Jones
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
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27
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Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A. Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome. Cell Rep 2020; 28:2673-2688.e8. [PMID: 31484077 PMCID: PMC6737378 DOI: 10.1016/j.celrep.2019.07.104] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 01/12/2023] Open
Abstract
In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding. Vertical DNA movement through the MCM ring requires rotation inside the pore Structural asymmetries in MCM-DNA are captured during ATPase-powered translocation Asymmetric rotation explains selective ATPase site requirements for translocation The fork-stabilization complex strengthens parental-DNA engagement by the MCM
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Affiliation(s)
- Patrik Eickhoff
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Hazal B Kose
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Fabrizio Martino
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Tatjana Petojevic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Nele Tamberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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28
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Grabarczyk DB. Crystal structure and interactions of the Tof1-Csm3 (Timeless-Tipin) fork protection complex. Nucleic Acids Res 2020; 48:6996-7004. [PMID: 32469068 PMCID: PMC7337906 DOI: 10.1093/nar/gkaa456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/13/2022] Open
Abstract
The Tof1-Csm3 fork protection complex has a central role in the replisome-it promotes the progression of DNA replication forks and protects them when they stall, while also enabling cohesion establishment and checkpoint responses. Here, I present the crystal structure of the Tof1-Csm3 complex from Chaetomium thermophilum at 3.1 Å resolution. The structure reveals that both proteins together form an extended alpha helical repeat structure, which suggests a mechanical or scaffolding role for the complex. Expanding on this idea, I characterize a DNA interacting region and a cancer-associated Mrc1 binding site. This study provides the molecular basis for understanding the functions of the Tof1-Csm3 complex, its human orthologue the Timeless-Tipin complex and additionally the Drosophila circadian rhythm protein Timeless.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg, Germany
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29
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Heintzman DR, Campos LV, Byl JAW, Osheroff N, Dewar JM. Topoisomerase II Is Crucial for Fork Convergence during Vertebrate Replication Termination. Cell Rep 2020; 29:422-436.e5. [PMID: 31597101 PMCID: PMC6919565 DOI: 10.1016/j.celrep.2019.08.097] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 11/28/2022] Open
Abstract
Termination of DNA replication occurs when two replication forks converge upon the same stretch of DNA. Resolution of topological stress by topoisomerases is crucial for fork convergence in bacteria and viruses, but it is unclear whether similar mechanisms operate during vertebrate termination. Using Xenopus egg extracts, we show that topoisomerase II (Top2) resolves topological stress to prevent converging forks from stalling during termination. Under these conditions, stalling arises due to an inability to unwind the final stretch of DNA ahead of each fork. By promoting fork convergence, Top2 facilitates all downstream events of termination. Converging forks ultimately overcome stalling independently of Top2, indicating that additional mechanisms support fork convergence. Top2 acts throughout replication to prevent the accumulation of topological stress that would otherwise stall converging forks. Thus, termination poses evolutionarily conserved topological problems that can be mitigated by careful execution of the earlier stages of replication.
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Affiliation(s)
- Darren R Heintzman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lillian V Campos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Medicine (Hematology, Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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30
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Guilliam TA, Yeeles JTP. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit Rev Biochem Mol Biol 2020; 55:469-481. [PMID: 32883112 DOI: 10.1080/10409238.2020.1811630] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.
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Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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31
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Finardi A, Massari LF, Visintin R. Anaphase Bridges: Not All Natural Fibers Are Healthy. Genes (Basel) 2020; 11:genes11080902. [PMID: 32784550 PMCID: PMC7464157 DOI: 10.3390/genes11080902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which are loaded on the sister chromatids as they are generated during S phase. Cohesion between sister chromatids must be fully removed at anaphase to allow chromosome segregation. Other (non-proteinaceous) sources of cohesion between sister chromatids consist of DNA linkages or sister chromatid intertwines. DNA linkages are a natural consequence of DNA replication, but must be timely resolved before chromosome segregation to avoid the arising of DNA lesions and genome instability, a hallmark of cancer development. As complete resolution of sister chromatid intertwines only occurs during chromosome segregation, it is not clear whether DNA linkages that persist in mitosis are simply an unwanted leftover or whether they have a functional role. In this review, we provide an overview of DNA linkages between sister chromatids, from their origin to their resolution, and we discuss the consequences of a failure in their detection and processing and speculate on their potential role.
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Affiliation(s)
- Alice Finardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Lucia F. Massari
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Rosella Visintin
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5748-9859; Fax: +39-02-9437-5991
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32
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Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication. Int J Mol Sci 2020; 21:ijms21124504. [PMID: 32599919 PMCID: PMC7349988 DOI: 10.3390/ijms21124504] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Key DNA transactions, such as genome replication and transcription, rely on the speedy translocation of specialized protein complexes along a double-stranded, right-handed helical template. Physical tethering of these molecular machines during translocation, in conjunction with their internal architectural features, generates DNA topological strain in the form of template supercoiling. It is known that the build-up of transient excessive supercoiling poses severe threats to genome function and stability and that highly specialized enzymes—the topoisomerases (TOP)—have evolved to mitigate these threats. Furthermore, due to their intracellular abundance and fast supercoil relaxation rates, it is generally assumed that these enzymes are sufficient in coping with genome-wide bursts of excessive supercoiling. However, the recent discoveries of chromatin architectural factors that play important accessory functions have cast reasonable doubts on this concept. Here, we reviewed the background of these new findings and described emerging models of how these accessory factors contribute to supercoil homeostasis. We focused on DNA replication and the generation of positive (+) supercoiling in front of replisomes, where two accessory factors—GapR and HMGA2—from pro- and eukaryotic cells, respectively, appear to play important roles as sinks for excessive (+) supercoiling by employing a combination of supercoil constrainment and activation of topoisomerases. Looking forward, we expect that additional factors will be identified in the future as part of an expanding cellular repertoire to cope with bursts of topological strain. Furthermore, identifying antagonists that target these accessory factors and work synergistically with clinically relevant topoisomerase inhibitors could become an interesting novel strategy, leading to improved treatment outcomes.
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33
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A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:1853-1867. [PMID: 32265288 PMCID: PMC7263696 DOI: 10.1534/g3.120.401137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homologous recombination is an important mechanism for genome integrity maintenance, and several homologous recombination genes are mutated in various cancers and cancer-prone syndromes. However, since in some cases homologous recombination can lead to mutagenic outcomes, this pathway must be tightly regulated, and mitotic hyper-recombination is a hallmark of genomic instability. We performed two screens in Saccharomyces cerevisiae for genes that, when deleted, cause hyper-recombination between direct repeats. One was performed with the classical patch and replica-plating method. The other was performed with a high-throughput replica-pinning technique that was designed to detect low-frequency events. This approach allowed us to validate the high-throughput replica-pinning methodology independently of the replicative aging context in which it was developed. Furthermore, by combining the two approaches, we were able to identify and validate 35 genes whose deletion causes elevated spontaneous direct-repeat recombination. Among these are mismatch repair genes, the Sgs1-Top3-Rmi1 complex, the RNase H2 complex, genes involved in the oxidative stress response, and a number of other DNA replication, repair and recombination genes. Since several of our hits are evolutionarily conserved, and repeated elements constitute a significant fraction of mammalian genomes, our work might be relevant for understanding genome integrity maintenance in humans.
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34
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Le TT, Gao X, Park SH, Lee J, Inman JT, Lee JH, Killian JL, Badman RP, Berger JM, Wang MD. Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity. Cell 2020; 179:619-631.e15. [PMID: 31626768 PMCID: PMC6899335 DOI: 10.1016/j.cell.2019.09.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/16/2019] [Accepted: 09/24/2019] [Indexed: 12/23/2022]
Abstract
DNA replication in eukaryotes generates DNA supercoiling, which may intertwine (braid) daughter chromatin fibers to form precatenanes, posing topological challenges during chromosome segregation. The mechanisms that limit precatenane formation remain unclear. By making direct torque measurements, we demonstrate that the intrinsic mechanical properties of chromatin play a fundamental role in dictating precatenane formation and regulating chromatin topology. Whereas a single chromatin fiber is torsionally soft, a braided fiber is torsionally stiff, indicating that supercoiling on chromatin substrates is preferentially directed in front of the fork during replication. We further show that topoisomerase II relaxation displays a strong preference for a single chromatin fiber over a braided fiber. These results suggest a synergistic coordination-the mechanical properties of chromatin inherently suppress precatenane formation during replication elongation by driving DNA supercoiling ahead of the fork, where supercoiling is more efficiently removed by topoisomerase II. VIDEO ABSTRACT.
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Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Xiang Gao
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Seong Ha Park
- Biophysics Program, Cornell University, Ithaca, NY 14853, USA
| | - Jaeyoon Lee
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica L Killian
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Ryan P Badman
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA.
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35
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Minchell NE, Keszthelyi A, Baxter J. Cohesin Causes Replicative DNA Damage by Trapping DNA Topological Stress. Mol Cell 2020; 78:739-751.e8. [PMID: 32259483 PMCID: PMC7242899 DOI: 10.1016/j.molcel.2020.03.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/12/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022]
Abstract
DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae, we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological-stress-linked damage in these regions. At cohesin-enriched centromeres, cohesin activity causes the accumulation of DNA damage, RF rotation, and pre-catenation, confirming that cohesin-dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA, cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that, as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress.
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Affiliation(s)
- Nicola Elizabeth Minchell
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK.
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36
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Zhang T, Wang BF, Wang XY, Xiang L, Zheng P, Li HY, Tao PX, Wang DF, Gu BH, Chen H. Key Genes Associated with Prognosis and Tumor Infiltrating Immune Cells in Gastric Cancer Patients Identified by Cross-Database Analysis. Cancer Biother Radiopharm 2020; 35:696-710. [PMID: 32401038 DOI: 10.1089/cbr.2019.3423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: The molecular mechanisms underlying gastric cancer (GC) progression are unclear. The authors examined key genes associated with the prognosis and tumor-infiltrating immune cells in patients with GC. Materials and Methods: Gene expression omnibus (GEO) was used to filter and obtain GC-related differentially expressed genes (DEGs). The molecular functions, biological processes, and cellular components of the DEGs were subjected to enrichment analysis. Protein-protein interaction networks of proteins encoded by the DEGs were analyzed using STRING. The authors also identified hub genes of GC, as well as their expression levels in GC and their relationship with patient prognosis. The relationship between hub genes and tumor-infiltrating immune cells was analyzed by Tumor IMmune Estimation Resource. Results: Six GEO datasets were included in this study, and 265 DEGs were identified. These DEGs were enriched in different signaling pathways and had different biological functions. Six hub genes were potentially significantly related to the molecular mechanisms of GC (TOP2A, FN1, SPARC, COL3A1, COL1A1, and TIMP1). These genes are potential markers of prognosis. Five hub genes were significantly positively correlated with the number of macrophages, neutrophils, and dendritic cells. Conclusions: The authors provide a theoretical basis for exploring the molecular regulation mechanism underlying GC and identifying therapeutic targets.
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Affiliation(s)
- Tao Zhang
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China.,Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Bo-Fang Wang
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Xue-Yan Wang
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Lin Xiang
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Peng Zheng
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Hai-Yuan Li
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Peng-Xian Tao
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Deng-Feng Wang
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Bao-Hong Gu
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Hao Chen
- The Second Clinical Medical College of Lanzhou University, Lanzhou, China.,Cancer Center, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Digestive System Tumors, Lanzhou University Second Hospital, Lanzhou, China
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37
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Amir M, Mohammad T, Dohare R, Islam A, Ahmad F, Imtaiyaz Hassan M. Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present. Brief Funct Genomics 2020; 19:377-389. [PMID: 32393969 DOI: 10.1093/bfgp/elaa008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.
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38
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Baretić D, Jenkyn-Bedford M, Aria V, Cannone G, Skehel M, Yeeles JTP. Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. Mol Cell 2020; 78:926-940.e13. [PMID: 32369734 PMCID: PMC7276988 DOI: 10.1016/j.molcel.2020.04.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022]
Abstract
The eukaryotic replisome, organized around the Cdc45-MCM-GINS (CMG) helicase, orchestrates chromosome replication. Multiple factors associate directly with CMG, including Ctf4 and the heterotrimeric fork protection complex (Csm3/Tof1 and Mrc1), which has important roles including aiding normal replication rates and stabilizing stalled forks. How these proteins interface with CMG to execute these functions is poorly understood. Here we present 3 to 3.5 Å resolution electron cryomicroscopy (cryo-EM) structures comprising CMG, Ctf4, and the fork protection complex at a replication fork. The structures provide high-resolution views of CMG-DNA interactions, revealing a mechanism for strand separation, and show Csm3/Tof1 “grip” duplex DNA ahead of CMG via a network of interactions important for efficient replication fork pausing. Although Mrc1 was not resolved in our structures, we determine its topology in the replisome by cross-linking mass spectrometry. Collectively, our work reveals how four highly conserved replisome components collaborate with CMG to facilitate replisome progression and maintain genome stability. Cryo-EM structure of Csm3/Tof1 and Ctf4 bound to the eukaryotic CMG helicase Csm3/Tof1 are positioned at the front of the replisome where they grip duplex DNA High-resolution views of CMG-DNA contacts suggest a mechanism for strand separation Mrc1 binds across one side of CMG contacting the front and back of the replisome
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Affiliation(s)
- Domagoj Baretić
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | | | - Valentina Aria
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Giuseppe Cannone
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Mark Skehel
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Joseph T P Yeeles
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK.
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39
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Martínez V, Schaerer C, Hernández P, Krimer DB, Schvartzman JB, Fernández-Nestosa MJ. Distribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules. J Biomol Struct Dyn 2020; 39:2266-2277. [DOI: 10.1080/07391102.2020.1751294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Víctor Martínez
- Polytechnic School, National University of Asunción, San Lorenzo, Paraguay
| | - Christian Schaerer
- Polytechnic School, National University of Asunción, San Lorenzo, Paraguay
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Dora B. Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Jorge B. Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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40
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Abstract
The double-helical structure of genomic DNA is both elegant and functional in that it serves both to protect vulnerable DNA bases and to facilitate DNA replication and compaction. However, these design advantages come at the cost of having to evolve and maintain a cellular machinery that can manipulate a long polymeric molecule that readily becomes topologically entangled whenever it has to be opened for translation, replication, or repair. If such a machinery fails to eliminate detrimental topological entanglements, utilization of the information stored in the DNA double helix is compromised. As a consequence, the use of B-form DNA as the carrier of genetic information must have co-evolved with a means to manipulate its complex topology. This duty is performed by DNA topoisomerases, which therefore are, unsurprisingly, ubiquitous in all kingdoms of life. In this review, we focus on how DNA topoisomerases catalyze their impressive range of DNA-conjuring tricks, with a particular emphasis on DNA topoisomerase III (TOP3). Once thought to be the most unremarkable of topoisomerases, the many lives of these type IA topoisomerases are now being progressively revealed. This research interest is driven by a realization that their substrate versatility and their ability to engage in intimate collaborations with translocases and other DNA-processing enzymes are far more extensive and impressive than was thought hitherto. This, coupled with the recent associations of TOP3s with developmental and neurological pathologies in humans, is clearly making us reconsider their undeserved reputation as being unexceptional enzymes.
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Affiliation(s)
- Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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41
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Abstract
Programmed fork pausing is a complex process allowing cells to arrest replication forks at specific loci in a polar manner. Studies in budding yeast and other model organisms indicate that such replication fork barriers do not act as roadblocks passively impeding fork progression but rather elicit complex interactions between fork and barrier components. In this issue of Genes & Development, Shyian and colleagues (pp. 87-98) show that in budding yeast, the fork protection complex Tof1-Csm3 interacts physically with DNA topoisomerase I (Top1) at replication forks through the C-terminal domain of Tof1. Fork pausing at the ribosomal DNA (rDNA) replication fork barrier (RFB) is impaired in the absence of Top1 or in a tof1 mutant that does not bind Top1, but the function of Top1 can be partially compensated for by Top2. Together, these data indicate that topoisomerases play an unexpected role in the regulation of programmed fork pausing in Saccharomyces cerevisiae.
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Affiliation(s)
- Mélanie V Larcher
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier 34396, France
| | - Philippe Pasero
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier 34396, France
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42
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Schvartzman JB, Hernández P, Krimer DB. Replication Fork Barriers and Topological Barriers: Progression of DNA Replication Relies on DNA Topology Ahead of Forks. Bioessays 2020; 42:e1900204. [PMID: 32115727 DOI: 10.1002/bies.201900204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/05/2020] [Indexed: 11/09/2022]
Abstract
During replication, the topology of DNA changes continuously in response to well-known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow-down and even stall at precise sites. The way these changes in the rate of replisome progression affect DNA topology is not yet well understood. The interplay of DNA topology and replication in several cases where progression of replication forks reacts differently to changes in DNA topology ahead is discussed here. It is proposed, there are at least two types of replication fork barriers: those that behave also as topological barriers and those that do not. Two-Dimensional (2D) agarose gel electrophoresis is the method of choice to distinguish between these two different types of replication fork barriers.
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Affiliation(s)
- Jorge B Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Dora B Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
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43
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Zhou J, Zhang Y, Zou X, Kuai L, Wang L, Wang J, Shen F, Hu J, Zhang X, Huang Y, Chen Y. Aberrantly Expressed Timeless Regulates Cell Proliferation and Cisplatin Efficacy in Cervical Cancer. Hum Gene Ther 2020; 31:385-395. [PMID: 31870179 DOI: 10.1089/hum.2019.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Timeless is a regulator of molecular clockwork in Drosophila and related to cancer development in mammals. This study aimed to investigate the effect of Timeless on cell proliferation and cisplatin sensitivity in cervical cancer. Timeless expression was determined by bioinformatics analysis, immunohistochemistry, and quantitative polymerase chain reaction (qPCR). Chromatin immunoprecipitation assays and reporter gene assays were applied to determine the transcriptional factor contributing to Timeless upregulation. The effects of Timeless depletion on cell proliferation and cisplatin sensitivity were determined through in vitro and in vivo experiments. Cell apoptosis and senescence were assessed by flow cytometry and β-galactosidase staining. DNA damage and DNA repair pathways were determined by comet assay, immunofluorescent staining, and Western blot analysis. Timeless is aberrantly expressed in ∼52.5% of cervical cancer tissues. E2F1 and E2F4 contribute to the transcriptional activation of Timeless. Timeless depletion inhibits cell proliferation and increases cisplatin sensitivity in vitro and in vivo. Knockdown of Timeless induces cell apoptosis and cell senescence. Mechanically, Timeless silencing leads to DNA damage and impairs the activation of the ATR/CHK1 pathway in response to cisplatin in cervical cancer. Timeless is overexpressed in cervical cancer and regulates cell proliferation and cisplatin sensitivity, presenting an attractive target for cisplatin sensitizer in cervical cancer.
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Affiliation(s)
- Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yinghui Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinwei Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lingling Kuai
- Department of Obstetrics and Gynecology, Nanjing Maternity and Child Health Hospital, Nanjing, China
| | - Li Wang
- Department of Gynecology and Obstetrics, Changzhou Maternal and Child Health Care Hospital Affiliated Nanjing Medical University, Changzhou, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jinghui Hu
- Department of Gynecology, The First Affiliated Hospital of Zhejiang University Medical College, Hangzhou, China
| | - Xia Zhang
- Department of Obstetrics and Gynecology, TuHa Petroleum Hospital, Xinjiang, China
| | - Yazhen Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
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44
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Shyian M, Albert B, Zupan AM, Ivanitsa V, Charbonnet G, Dilg D, Shore D. Fork pausing complex engages topoisomerases at the replisome. Genes Dev 2019; 34:87-98. [PMID: 31805522 PMCID: PMC6938670 DOI: 10.1101/gad.331868.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/07/2019] [Indexed: 12/22/2022]
Abstract
In this study, Shyian et al. set out to address mechanistically how the evolutionarily conserved fork pausing complex acts at proteinaceous replication fork barriers (RFBs) to promote fork passage and genome stability. Using several molecular and cell-based assays, the authors propose that forks pause at proteinaceous RFBs through a “sTOP” mechanism (“slowing down with topoisomerases I–II”), which also contributes to protecting cells from topoisomerase-blocking agents. Replication forks temporarily or terminally pause at hundreds of hard-to-replicate regions around the genome. A conserved pair of budding yeast replisome components Tof1–Csm3 (fission yeast Swi1–Swi3 and human TIMELESS–TIPIN) act as a “molecular brake” and promote fork slowdown at proteinaceous replication fork barriers (RFBs), while the accessory helicase Rrm3 assists the replisome in removing protein obstacles. Here we show that the Tof1–Csm3 complex promotes fork pausing independently of Rrm3 helicase by recruiting topoisomerase I (Top1) to the replisome. Topoisomerase II (Top2) partially compensates for the pausing decrease in cells when Top1 is lost from the replisome. The C terminus of Tof1 is specifically required for Top1 recruitment to the replisome and fork pausing but not for DNA replication checkpoint (DRC) activation. We propose that forks pause at proteinaceous RFBs through a “sTOP” mechanism (“slowing down with topoisomerases I–II”), which we show also contributes to protecting cells from topoisomerase-blocking agents.
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Affiliation(s)
- Maksym Shyian
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
| | - Benjamin Albert
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
| | - Andreja Moset Zupan
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
| | - Vitalii Ivanitsa
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
| | - Gabriel Charbonnet
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
| | - Daniel Dilg
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva 4, CH-1211, Switzerland
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45
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Schvartzman JB, Hernández P, Krimer DB, Dorier J, Stasiak A. Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes. Nucleic Acids Res 2019; 47:7182-7198. [PMID: 31276584 PMCID: PMC6698734 DOI: 10.1093/nar/gkz586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/20/2019] [Accepted: 07/02/2019] [Indexed: 01/28/2023] Open
Abstract
Due to helical structure of DNA, massive amounts of positive supercoils are constantly introduced ahead of each replication fork. Positive supercoiling inhibits progression of replication forks but various mechanisms evolved that permit very efficient relaxation of that positive supercoiling. Some of these mechanisms lead to interesting topological situations where DNA supercoiling, catenation and knotting coexist and influence each other in DNA molecules being replicated. Here, we first review fundamental aspects of DNA supercoiling, catenation and knotting when these qualitatively different topological states do not coexist in the same circular DNA but also when they are present at the same time in replicating DNA molecules. We also review differences between eukaryotic and prokaryotic cellular strategies that permit relaxation of positive supercoiling arising ahead of the replication forks. We end our review by discussing very recent studies giving a long-sought answer to the question of how slow DNA topoisomerases capable of relaxing just a few positive supercoils per second can counteract the introduction of hundreds of positive supercoils per second ahead of advancing replication forks.
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Affiliation(s)
- Jorge B Schvartzman
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Hernández
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Dora B Krimer
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Julien Dorier
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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46
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Morafraile EC, Hänni C, Allen G, Zeisner T, Clarke C, Johnson MC, Santos MM, Carroll L, Minchell NE, Baxter J, Banks P, Lydall D, Zegerman P. Checkpoint inhibition of origin firing prevents DNA topological stress. Genes Dev 2019; 33:1539-1554. [PMID: 31624083 PMCID: PMC6824463 DOI: 10.1101/gad.328682.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
A universal feature of DNA damage and replication stress in eukaryotes is the activation of a checkpoint-kinase response. In S-phase, the checkpoint inhibits replication initiation, yet the function of this global block to origin firing remains unknown. To establish the physiological roles of this arm of the checkpoint, we analyzed separation of function mutants in the budding yeast Saccharomyces cerevisiae that allow global origin firing upon replication stress, despite an otherwise normal checkpoint response. Using genetic screens, we show that lack of the checkpoint-block to origin firing results in a dependence on pathways required for the resolution of topological problems. Failure to inhibit replication initiation indeed causes increased DNA catenation, resulting in DNA damage and chromosome loss. We further show that such topological stress is not only a consequence of a failed checkpoint response but also occurs in an unperturbed S-phase when too many origins fire simultaneously. Together we reveal that the role of limiting the number of replication initiation events is to prevent DNA topological problems, which may be relevant for the treatment of cancer with both topoisomerase and checkpoint inhibitors.
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Affiliation(s)
- Esther C Morafraile
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Christine Hänni
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - George Allen
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Theresa Zeisner
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Caroline Clarke
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Mark C Johnson
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Miguel M Santos
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Lauren Carroll
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
| | - Nicola E Minchell
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Jonathan Baxter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Peter Banks
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Dave Lydall
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Philip Zegerman
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge CB2 1QN, United Kingdom
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47
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Stracy M, Wollman AJM, Kaja E, Gapinski J, Lee JE, Leek VA, McKie SJ, Mitchenall LA, Maxwell A, Sherratt DJ, Leake MC, Zawadzki P. Single-molecule imaging of DNA gyrase activity in living Escherichia coli. Nucleic Acids Res 2019; 47:210-220. [PMID: 30445553 PMCID: PMC6326794 DOI: 10.1093/nar/gky1143] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/07/2018] [Indexed: 11/18/2022] Open
Abstract
Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. Removal of these positive supercoils is essential for replication fork progression and for the overall unlinking of the two duplex DNA strands, as well as for ongoing transcription. To address how gyrase copes with these topological challenges, we used high-speed single-molecule fluorescence imaging in live Escherichia coli cells. We demonstrate that at least 300 gyrase molecules are stably bound to the chromosome at any time, with ∼12 enzymes enriched near each replication fork. Trapping of reaction intermediates with ciprofloxacin revealed complexes undergoing catalysis. Dwell times of ∼2 s were observed for the dispersed gyrase molecules, which we propose maintain steady-state levels of negative supercoiling of the chromosome. In contrast, the dwell time of replisome-proximal molecules was ∼8 s, consistent with these catalyzing processive positive supercoil relaxation in front of the progressing replisome.
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Affiliation(s)
- Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Adam J M Wollman
- Biological Physical Sciences Institute (BPSI), Departments of Physics and Biology, University of York, York YO10 5DD, UK
| | - Elzbieta Kaja
- NanoBioMedical Centre, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | - Jacek Gapinski
- Molecular Biophysics Division, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | - Ji-Eun Lee
- Biological Physical Sciences Institute (BPSI), Departments of Physics and Biology, University of York, York YO10 5DD, UK
| | - Victoria A Leek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shannon J McKie
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lesley A Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark C Leake
- Biological Physical Sciences Institute (BPSI), Departments of Physics and Biology, University of York, York YO10 5DD, UK
| | - Pawel Zawadzki
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Molecular Biophysics Division, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
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48
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Abstract
Genome replication involves dealing with obstacles that can result from DNA damage but also from chromatin alterations, topological stress, tightly bound proteins or non-B DNA structures such as R loops. Experimental evidence reveals that an engaged transcription machinery at the DNA can either enhance such obstacles or be an obstacle itself. Thus, transcription can become a potentially hazardous process promoting localized replication fork hindrance and stress, which would ultimately cause genome instability, a hallmark of cancer cells. Understanding the causes behind transcription-replication conflicts as well as how the cell resolves them to sustain genome integrity is the aim of this review.
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49
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Deegan TD, Baxter J, Ortiz Bazán MÁ, Yeeles JTP, Labib KPM. Pif1-Family Helicases Support Fork Convergence during DNA Replication Termination in Eukaryotes. Mol Cell 2019; 74:231-244.e9. [PMID: 30850330 PMCID: PMC6477153 DOI: 10.1016/j.molcel.2019.01.040] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/26/2018] [Accepted: 01/29/2019] [Indexed: 01/21/2023]
Abstract
The convergence of two DNA replication forks creates unique problems during DNA replication termination. In E. coli and SV40, the release of torsional strain by type II topoisomerases is critical for converging replisomes to complete DNA synthesis, but the pathways that mediate fork convergence in eukaryotes are unknown. We studied the convergence of reconstituted yeast replication forks that include all core replisome components and both type I and type II topoisomerases. We found that most converging forks stall at a very late stage, indicating a role for additional factors. We showed that the Pif1 and Rrm3 DNA helicases promote efficient fork convergence and completion of DNA synthesis, even in the absence of type II topoisomerase. Furthermore, Rrm3 and Pif1 are also important for termination of plasmid DNA replication in vivo. These findings identify a eukaryotic pathway for DNA replication termination that is distinct from previously characterized prokaryotic mechanisms.
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Affiliation(s)
- Tom D Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Department of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - María Ángeles Ortiz Bazán
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Joseph T P Yeeles
- The MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Karim P M Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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50
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DNA Replication Through Strand Displacement During Lagging Strand DNA Synthesis in Saccharomyces cerevisiae. Genes (Basel) 2019; 10:genes10020167. [PMID: 30795600 PMCID: PMC6409922 DOI: 10.3390/genes10020167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 01/21/2023] Open
Abstract
This review discusses a set of experimental results that support the existence of extended strand displacement events during budding yeast lagging strand DNA synthesis. Starting from introducing the mechanisms and factors involved in leading and lagging strand DNA synthesis and some aspects of the architecture of the eukaryotic replisome, we discuss studies on bacterial, bacteriophage and viral DNA polymerases with potent strand displacement activities. We describe proposed pathways of Okazaki fragment processing via short and long flaps, with a focus on experimental results obtained in Saccharomyces cerevisiae that suggest the existence of frequent and extended strand displacement events during eukaryotic lagging strand DNA synthesis, and comment on their implications for genome integrity.
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