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Ryu E, Yoo J, Kang MS, Ha NY, Jang Y, Kim J, Kim Y, Kim BG, Kim S, Myung K, Kang S. ATAD5 functions as a regulatory platform for Ub-PCNA deubiquitination. Proc Natl Acad Sci U S A 2024; 121:e2315759121. [PMID: 39145935 PMCID: PMC11348035 DOI: 10.1073/pnas.2315759121] [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: 09/12/2023] [Accepted: 07/11/2024] [Indexed: 08/16/2024] Open
Abstract
Ubiquitination status of proliferating cell nuclear antigen (PCNA) is crucial for regulating DNA lesion bypass. After the resolution of fork stalling, PCNA is subsequently deubiquitinated, but the underlying mechanism remains undefined. We found that the N-terminal domain of ATAD5 (ATAD5-N), the largest subunit of the PCNA-unloading complex, functions as a scaffold for Ub-PCNA deubiquitination. ATAD5 recognizes DNA-loaded Ub-PCNA through distinct DNA-binding and PCNA-binding motifs. Furthermore, ATAD5 forms a heterotrimeric complex with UAF1-USP1 deubiquitinase, facilitating the deubiquitination of DNA-loaded Ub-PCNA. ATAD5 also enhances the Ub-PCNA deubiquitination by USP7 and USP11 through specific interactions. ATAD5 promotes the distinct deubiquitination process of UAF1-USP1, USP7, and USP11 for poly-Ub-PCNA. Additionally, ATAD5 mutants deficient in UAF1-binding had increased sensitivity to DNA-damaging agents. Our results ultimately reveal that ATAD5 and USPs cooperate to efficiently deubiquitinate Ub-PCNA prior to its release from the DNA in order to safely deactivate the DNA repair process.
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Affiliation(s)
- Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Juyeong Yoo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Na Young Ha
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Yewon Jang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Jinwoo Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Yeongjae Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Shinseog Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
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Kang S, Yoo J, Myung K. PCNA cycling dynamics during DNA replication and repair in mammals. Trends Genet 2024; 40:526-539. [PMID: 38485608 DOI: 10.1016/j.tig.2024.02.006] [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: 01/17/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 06/06/2024]
Abstract
Proliferating cell nuclear antigen (PCNA) is a eukaryotic replicative DNA clamp. Furthermore, DNA-loaded PCNA functions as a molecular hub during DNA replication and repair. PCNA forms a closed homotrimeric ring that encircles the DNA, and association and dissociation of PCNA from DNA are mediated by clamp-loader complexes. PCNA must be actively released from DNA after completion of its function. If it is not released, abnormal accumulation of PCNA on chromatin will interfere with DNA metabolism. ATAD5 containing replication factor C-like complex (RLC) is a PCNA-unloading clamp-loader complex. ATAD5 deficiency causes various DNA replication and repair problems, leading to genome instability. Here, we review recent progress regarding the understanding of the action mechanisms of PCNA unloading complex in DNA replication/repair pathways.
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Affiliation(s)
- Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Juyeong Yoo
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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3
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Wei X, Li H, Chen T, Yang X. Histological study of telocytes in mice intrauterine adhesion model and their positive effect on mesenchymal stem cells in vitro. Cell Biol Int 2024; 48:647-664. [PMID: 38353345 DOI: 10.1002/cbin.12137] [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: 11/08/2023] [Revised: 12/31/2023] [Accepted: 01/28/2024] [Indexed: 04/16/2024]
Abstract
Intrauterine adhesions (IUA), the main cause of secondary infertility in women, result from irreversible fibrotic repair of the endometrium due to inflammation or human factors, accompanied by disruptions in the repair function of endometrial stem cells. This significantly impacts the physical and mental health of women in their childbearing years. Telocytes (TCs), a distinctive type of interstitial cells found in various tissues and organs, play diverse repair functions due to their unique spatial structure. In this study, we conduct the inaugural exploration of the changes in TCs in IUA disease and their potential impact on the function of stem cells. Our results show that in vivo, through double immunofluorescence staining (CD34+/Vimentin+; CD34+/CD31-), as endometrial fibrosis deepens, the number of TCs gradually decreases, telopodes shorten, and the three-dimensional structure becomes disrupted in the mouse IUA mode. In vitro, TCs can promote the proliferation and cycle of bone mesenchymal stem cells (BMSCs) by promoting the Wnt/β-catenin signaling pathway, which were inhibited using XAV939. TCs can promote the migrated ability of BMSCs and contribute to the repair of stem cells during endometrial injury. In addition, TCs can inhibit the apoptosis of BMSCs through the Bcl-2/Bax pathway. In conclusion, our study demonstrates, for the first time, the resistance role of TCs in IUA disease, shedding light on their potential involvement in endometrial repair through the modulation of stem cell function.
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Affiliation(s)
- Xiaojiao Wei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
| | - Hui Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
| | - Tianquan Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Yangzhou University, Yangzhou City, Jiangsu Province, People's Republic of China
| | - Xiaojun Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
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Piguet B, Houseley J. Transcription as source of genetic heterogeneity in budding yeast. Yeast 2024; 41:171-185. [PMID: 38196235 DOI: 10.1002/yea.3926] [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: 10/07/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA-bound regulatory factors, G-quadruplexes and RNA-DNA hybrid structures known as R-loops. Here, we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled nucleotide excision repair and of systems that maintain DNA replication fork processivity and integrity. Interactions between DNA replication and transcription have particular potential to induce mutation and structural variation, but we conclude that such interactions must have only minor effects on DNA replication by the replisome with little if any direct mutagenic outcome. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication, which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity, but only under particular conditions and in particular genetic contexts, ensuring that the bulk of the genome remains extremely stable despite the seemingly frequent interactions between transcription and DNA replication.
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 4] [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: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
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Yakoub G, Choi YS, Wong RP, Strauch T, Ann KJ, Cohen RE, Ulrich HD. Avidity-based biosensors for ubiquitylated PCNA reveal choreography of DNA damage bypass. SCIENCE ADVANCES 2023; 9:eadf3041. [PMID: 37672592 PMCID: PMC10482348 DOI: 10.1126/sciadv.adf3041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
In eukaryotes, the posttranslational modifier ubiquitin is used to regulate the amounts, interactions, or activities of proteins in diverse pathways and signaling networks. Its effects are mediated by monoubiquitin or polyubiquitin chains of varying geometries. We describe the design, validation, and application of a series of avidity-based probes against the ubiquitylated forms of the DNA replication clamp, proliferating cell nuclear antigen (PCNA), in budding yeast. Directed against total ubiquitylated PCNA or specifically K63-polyubiquitylated PCNA, the probes are tunable in their activities and can be used either as biosensors or as inhibitors of the PCNA-dependent DNA damage bypass pathway. Used in live cells, the probes revealed the timing of PCNA ubiquitylation during damage bypass and a particular susceptibility of the ribosomal DNA locus to the activation of the pathway. Our approach is applicable to a wide range of ubiquitin-conjugated proteins, thus representing a generalizable strategy for the design of biosensors for specific (poly)ubiquitylated forms of individual substrates.
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Affiliation(s)
- George Yakoub
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Yun-Seok Choi
- Department of Biochemistry and Molecular Biology, Colorado State University, 273 MRB, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA
| | - Ronald P. Wong
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Kezia J. Ann
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, 273 MRB, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA
| | - Helle D. Ulrich
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
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Saha G, Roy S, Basu M, Ghosh MK. USP7 - a crucial regulator of cancer hallmarks. Biochim Biophys Acta Rev Cancer 2023; 1878:188903. [PMID: 37127084 DOI: 10.1016/j.bbcan.2023.188903] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
Over the course of three decades of study, the deubiquitinase Herpesvirus associated Ubiquitin-Specific Protease/Ubiquitin-Specific Protease 7 (HAUSP/USP7) has gradually come to be recognized as a crucially important molecule in cellular physiology. The fact that USP7 is overexpressed in a number of cancers, including breast, prostate, colorectal, and lung cancers, supports the idea that USP7 is also an important regulator of tumorigenesis. In this review, we discuss USP7's function in relation to the cancer hallmarks described by Hanahan and Weinberg. This post-translational modifier can support increased proliferation, block unfavorable growth signals, stop cell death, and support an unstable cellular genome by manipulating key players in the pertinent signalling circuit. It is interesting to note that USP7 also aids in the stabilization of molecules that support angiogenesis and metastasis. Targeting USP7 has now emerged as a crucial component of USP7 research because pharmacological inhibition of USP7 supports p53-mediated cell cycle arrest and apoptosis. Efficacious USP7 inhibition is currently being investigated in both synthetic and natural compounds, but issues with selectivity and a lack of co-crystal structure have hindered USP7 inhibition from being tested in clinical settings. Moreover, the development of new, more effective USP7 inhibitors and their encouraging implications by numerous groups give us a glimmer of hope for USP7-targeting medications as effective substitutes for hazardous cancer chemotherapeutics.
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Affiliation(s)
- Gouranga Saha
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata-700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, PIN - 700032, India
| | - Srija Roy
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata-700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, PIN - 700032, India
| | - Malini Basu
- Department of Microbiology, Dhruba Chand Halder College, University of Calcutta, Kolkata, PIN - 743372, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata-700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, PIN - 700032, India.
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9
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RAD18 opposes transcription-associated genome instability through FANCD2 recruitment. PLoS Genet 2022; 18:e1010309. [DOI: 10.1371/journal.pgen.1010309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/20/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
DNA replication is a vulnerable time for genome stability maintenance. Intrinsic stressors, as well as oncogenic stress, can challenge replication by fostering conflicts with transcription and stabilizing DNA:RNA hybrids. RAD18 is an E3 ubiquitin ligase for PCNA that is involved in coordinating DNA damage tolerance pathways to preserve genome stability during replication. In this study, we show that RAD18 deficient cells have higher levels of transcription-replication conflicts and accumulate DNA:RNA hybrids that induce DNA double strand breaks and replication stress. We find that these effects are driven in part by failure to recruit the Fanconi Anemia protein FANCD2 at difficult to replicate and R-loop prone genomic sites. FANCD2 activation caused by splicing inhibition or aphidicolin treatment is critically dependent on RAD18 activity. Thus, we highlight a RAD18-dependent pathway promoting FANCD2-mediated suppression of R-loops and transcription-replication conflicts.
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Herpesvirus ubiquitin deconjugases. Semin Cell Dev Biol 2022; 132:185-192. [PMID: 34776333 DOI: 10.1016/j.semcdb.2021.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022]
Abstract
The covalent attachment of ubiquitin and ubiquitin-like polypeptides to cellular and viral proteins regulates numerous processes that enable virus infection, viral genome replication, and the spread of viruses to new hosts. The importance of these protein modifications in the regulation of the life cycle of herpesviruses is underscored by the discovery that all known members of this virus family encode at least one protease that specifically recognizes and disassembles ubiquitin conjugates. The structural and functional characterization of the viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infection and increasing evidence suggests that the viral deconjugases may also play a role in malignant transformation.
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Asimaki E, Petriukov K, Renz C, Meister C, Ulrich HD. Fast friends - Ubiquitin-like modifiers as engineered fusion partners. Semin Cell Dev Biol 2022; 132:132-145. [PMID: 34840080 PMCID: PMC9703124 DOI: 10.1016/j.semcdb.2021.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022]
Abstract
Ubiquitin and its relatives are major players in many biological pathways, and a variety of experimental tools based on biological chemistry or protein engineering is available for their manipulation. One popular approach is the use of linear fusions between the modifier and a protein of interest. Such artificial constructs can facilitate the understanding of the role of ubiquitin in biological processes and can be exploited to control protein stability, interactions and degradation. Here we summarize the basic design considerations and discuss the advantages as well as limitations associated with their use. Finally, we will refer to several published case studies highlighting the principles of how they provide insight into pathways ranging from membrane protein trafficking to the control of epigenetic modifications.
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12
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Wang W, Yan T, Guo X, Cai H, Liang C, Huang L, Wang Y, Ma P, Qi S. KAP1 phosphorylation promotes the survival of neural stem cells after ischemia/reperfusion by maintaining the stability of PCNA. Stem Cell Res Ther 2022; 13:290. [PMID: 35799276 PMCID: PMC9264526 DOI: 10.1186/s13287-022-02962-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/17/2022] [Indexed: 11/28/2022] Open
Abstract
Aims To explore the function of phosphorylation of KAP1 (p-KAP1) at the serine-824 site (S824) in the proliferation and apoptosis of endogenous neural stem cells (NSCs) after cerebral ischemic/reperfusion (I/R). Methods The apoptosis and proliferation of C17.2 cells transfected with the p-KAP1-expression plasmids and the expression of proliferation cell nuclear antigen (PCNA) and p-KAP1 were detected by immunofluorescence and Western blotting after the Oxygen Glucose deprivation/reperfusion model (OGD/R). The interaction of p-KAP1 and CUL4A with PCNA was analyzed by immunoprecipitation. In the rats MCAO model, we performed the adeno-associated virus (AAV) 2/9 gene delivery of p-KAP1 mutants to verify the proliferation of endogenous NSCs and the colocalization of PCNA and CUL4A by immunofluorescence. Results The level of p-KAP1 was significantly down-regulated in the stroke model in vivo and in vitro. Simulated p-KAP1(S824) significantly increased the proliferation of C17.2 cells and the expression of PCNA after OGD/R. Simulated p-KAP1(S824) enhanced the binding of p-KAP1 and PCNA and decreased the interaction between PCNA and CUL4A in C17.2 cells subjected to OGD/R. The AAV2/9-mediated p-KAP1(S824) increased endogenous NSCs proliferation, PCNA expression, p-KAP1 binding to PCNA, and improved neurological function in the rat MCAO model. Conclusions Our findings confirmed that simulated p-KAP1(S824) improved the survival and proliferation of endogenous NSCs. The underlying mechanism is that highly expressed p-KAP1(S824) promotes binding to PCNA, and inhibits the binding of CUL4A to PCNA. This reduced CUL4A-mediated ubiquitination degradation to increase the stability of PCNA and promote the survival and proliferation of NSCs. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02962-5.
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Affiliation(s)
- Wan Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Tianqing Yan
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xinjian Guo
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Heng Cai
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Chang Liang
- School of Basic Medical Science, Xuzhou Medical University, Xuzhou, 221004, China
| | - Linyan Huang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yanling Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ping Ma
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
| | - Suhua Qi
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Pharmacology College, Xuzhou Medical University, Xuzhou, 221004, China.
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13
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Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. J Fungi (Basel) 2022; 8:jof8060621. [PMID: 35736104 PMCID: PMC9225081 DOI: 10.3390/jof8060621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
The sliding clamp PCNA is a multifunctional homotrimer mainly linked to DNA replication. During this process, cells must ensure an accurate and complete genome replication when constantly challenged by the presence of DNA lesions. Post-translational modifications of PCNA play a crucial role in channeling DNA damage tolerance (DDT) and repair mechanisms to bypass unrepaired lesions and promote optimal fork replication restart. PCNA ubiquitination processes trigger the following two main DDT sub-pathways: Rad6/Rad18-dependent PCNA monoubiquitination and Ubc13-Mms2/Rad5-mediated PCNA polyubiquitination, promoting error-prone translation synthesis (TLS) or error-free template switch (TS) pathways, respectively. However, the fork protection mechanism leading to TS during fork reversal is still poorly understood. In contrast, PCNA sumoylation impedes the homologous recombination (HR)-mediated salvage recombination (SR) repair pathway. Focusing on Saccharomyces cerevisiae budding yeast, we summarized PCNA related-DDT and repair mechanisms that coordinately sustain genome stability and cell survival. In addition, we compared PCNA sequences from various fungal pathogens, considering recent advances in structural features. Importantly, the identification of PCNA epitopes may lead to potential fungal targets for antifungal drug development.
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14
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Fenteany G, Sharma G, Gaur P, Borics A, Wéber E, Kiss E, Haracska L. A series of xanthenes inhibiting Rad6 function and Rad6-Rad18 interaction in the PCNA ubiquitination cascade. iScience 2022; 25:104053. [PMID: 35355521 PMCID: PMC8958325 DOI: 10.1016/j.isci.2022.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitination of proliferating cell nuclear antigen (PCNA) triggers pathways of DNA damage tolerance, including mutagenic translesion DNA synthesis, and comprises a cascade of reactions involving the E1 ubiquitin-activating enzyme Uba1, the E2 ubiquitin-conjugating enzyme Rad6, and the E3 ubiquitin ligase Rad18. We report here the discovery of a series of xanthenes that inhibit PCNA ubiquitination, Rad6∼ubiquitin thioester formation, and the Rad6–Rad18 interaction. Structure-activity relationship experiments across multiple assays reveal chemical and structural features important for different activities along the pathway to PCNA ubiquitination. The compounds that inhibit these processes are all a subset of the xanthen-3-ones we tested. These small molecules thus represent first-in-class probes of Rad6 function and the association of Rad6 and Rad18, the latter being a new inhibitory activity discovered for a small molecule, in the PCNA ubiquitination cascade and potential therapeutic agents to contain cancer progression. Alpha-based HTS for PCNA ubiquitination modulators Target-based characterization of hits A series of xanthenes that inhibit Rad6 functions and Rad6–Rad18 interaction
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15
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Póti Á, Szikriszt B, Gervai JZ, Chen D, Szüts D. Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis. PLoS Genet 2022; 18:e1010051. [PMID: 35130276 PMCID: PMC8870599 DOI: 10.1371/journal.pgen.1010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/24/2022] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Translesion DNA synthesis (TLS) is a fundamental damage bypass pathway that utilises specialised polymerases with relaxed template specificity to achieve replication through damaged DNA. Misinsertions by low fidelity TLS polymerases may introduce additional mutations on undamaged DNA near the original lesion site, which we termed collateral mutations. In this study, we used whole genome sequencing datasets of chicken DT40 and several human cell lines to obtain evidence for collateral mutagenesis in higher eukaryotes. We found that cisplatin and UVC radiation frequently induce close mutation pairs within 25 base pairs that consist of an adduct-associated primary and a downstream collateral mutation, and genetically linked their formation to TLS activity involving PCNA ubiquitylation and polymerase κ. PCNA ubiquitylation was also indispensable for close mutation pairs observed amongst spontaneously arising base substitutions in cell lines with disrupted homologous recombination. Collateral mutation pairs were also found in melanoma genomes with evidence of UV exposure. We showed that collateral mutations frequently copy the upstream base, and extracted a base substitution signature that describes collateral mutagenesis in the presented dataset regardless of the primary mutagenic process. Using this mutation signature, we showed that collateral mutagenesis creates approximately 10–20% of non-paired substitutions as well, underscoring the importance of the process. DNA base substitutions are the most common form of genomic mutations, formed both spontaneously and in response to environmental mutagens. One of the main mechanisms of base substitution mutagenesis is translesion synthesis, a process that relies on specialised DNA polymerases to replicate damaged DNA templates. In addition to incorrect base insertions at the site of lesions in the template, translesion polymerases may also generate ‘collateral’ mutations away from the lesion due to their lower accuracy in selecting the correct incoming nucleotide. In this study, we surveyed the whole genome sequence of experimental cell clones to examine the extent and genetic dependence of collateral mutagenesis in higher eukaryotes. Looking for close mutation pairs, we found that collateral mutations frequently occur near primary lesions generated by cisplatin or ultraviolet radiation in chicken and human cells, but are restricted to a short distance of approximately 25 base pairs. By analysing their sequence context, we showed that collateral mutations can also occur near correctly bypassed primary lesions and may be responsible for a considerable proportion of all base substitution mutations.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- * E-mail:
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16
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Yoshimura A, Sakakihara T, Enomoto T, Seki M. Functional Domain Mapping of Werner Interacting Protein 1 (WRNIP1). Biol Pharm Bull 2022; 45:200-206. [PMID: 35110507 DOI: 10.1248/bpb.b21-00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Werner helicase-interacting protein 1 (WRNIP1) belongs to the AAA+ ATPase family and is conserved from Escherichia coli to human. In addition to an ATPase domain in the middle region of WRNIP1, WRNIP1 contains a ubiquitin-binding zinc-finger (UBZ) domain and two leucine zipper motifs in the N-terminal and C-terminal regions, respectively. Here, we report that the UBZ domain of WRNIP1 is responsible for the reduced levels of UV-induced proliferating cell nuclear antigen (PCNA) monoubiquitylation in POLH-disrupted (polymerase η (Polη)-deficient) cells, and that the ATPase domain of WRNIP1 is involved in regulating the level of the PrimPol protein. The suppression of UV sensitivity of Polη-deficient cells by deletion of WRNIP1 was abolished by expression of the mutant WRNIP1 lacking the UBZ domain or ATPase domain, but not by the mutant lacking the leucine zipper domain in WRNIP1/POLH double-disrupted cells. The leucine zipper domain of WRNIP1 was required for its interaction with RAD18, a key factor in TLS (DNA translesion synthesis), and DNA polymerase δ catalytic subunit, POLD1. On the basis of these findings, we discuss the possible role of WRNIP1 in TLS.
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Affiliation(s)
- Akari Yoshimura
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University
| | - Tatsuya Sakakihara
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University
| | - Takemi Enomoto
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University
| | - Masayuki Seki
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University
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17
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Zhu T, Wang X, Zheng Z, Quan J, Liu Y, Wang Y, Liu T, Liu X, Wang M, Zhang Z. ZIP12 Contributes to Hypoxic Pulmonary Hypertension by Driving Phenotypic Switching of Pulmonary Artery Smooth Muscle Cells. J Cardiovasc Pharmacol 2022; 79:235-243. [PMID: 34694243 DOI: 10.1097/fjc.0000000000001156] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT ZIP12, a plasmalemmal zinc transporter, reportedly promotes pulmonary vascular remodeling (PVR) by enhancing proliferation of pulmonary artery smooth muscle cells (PASMCs). However, the mechanisms of ZIP12 facilitating PASMCs proliferation remain incompletely appreciated. It has been acknowledged that proliferation-predisposing phenotypic switching of PASMCs can lead to PVR. Given that hypoxia triggers phenotypic switching of PASMCs and ZIP12 mediates PVR, this study aims to explore whether ZIP12-mediated phenotypic switching of PASMCs contributes to hypoxia-induced PVR. Rats were exposed to hypoxia (10% O2) for 3 weeks to induce PVR, and primary rat PASMCs were cultured under hypoxic condition (3% O2) for 48 hours to induce proliferation. Immunofluorescence, quantitative reverse transcription-polymerase chain reaction, and Western blot analysis were performed to detect the expression of target mRNAs and proteins. EdU incorporation and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay were conducted to measure the proliferation of PASMCs. Hypoxia upregulated ZIP12 expression (both mRNA and protein) in pulmonary arteries and PASMCs. Knockdown of ZIP12 inhibited phenotypic switching of PASMCs induced by hypoxia. We propose that HIF-1α/ZIP12/pERK pathway could represent a novel mechanism underlying hypoxia-induced phenotypic switching of PASMCs. Therapeutic targeting of ZIP12 could be exploited to treat PVR.
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Affiliation(s)
- Tiantian Zhu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xuan Wang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China ; and
| | - Zijie Zheng
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China ; and
| | - Jinping Quan
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuhao Liu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuting Wang
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tianheng Liu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xu Liu
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
| | - Mi Wang
- The Department of Cardiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng Zhang
- Department of Clinical Pharmacy, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, China
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China ; and
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18
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Guo CR, Mao Y, Jiang F, Juan CX, Zhou GP, Li N. Computational detection of a genome instability-derived lncRNA signature for predicting the clinical outcome of lung adenocarcinoma. Cancer Med 2021; 11:864-879. [PMID: 34866362 PMCID: PMC8817082 DOI: 10.1002/cam4.4471] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/30/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Evidence has been emerging of the importance of long non-coding RNAs (lncRNAs) in genome instability. However, no study has established how to classify such lncRNAs linked to genomic instability, and whether that connection poses a therapeutic significance. Here, we established a computational frame derived from mutator hypothesis by combining profiles of lncRNA expression and those of somatic mutations in a tumor genome, and identified 185 candidate lncRNAs associated with genomic instability in lung adenocarcinoma (LUAD). Through further studies, we established a six lncRNA-based signature, which assigned patients to the high- and low-risk groups with different prognosis. Further validation of this signature was performed in a number of separate cohorts of LUAD patients. In addition, the signature was found closely linked to genomic mutation rates in patients, indicating it could be a useful way to quantify genomic instability. In summary, this research offered a novel method by through which more studies may explore the function of lncRNAs and presented a possible new way for detecting biomarkers associated with genomic instability in cancers.
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Affiliation(s)
- Chen-Rui Guo
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yan Mao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Jiang
- Department of Neonatology,, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chen-Xia Juan
- Department of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Li
- Department of Abdominal Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
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19
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Zhang Q, Huang L, Leng B, Li Y, Jiao N, Jiang S, Yang W, Yuan X. Zearalenone Affect the Intestinal Villi Associated with the Distribution and the Expression of Ghrelin and Proliferating Cell Nuclear Antigen in Weaned Gilts. Toxins (Basel) 2021; 13:toxins13100736. [PMID: 34679029 PMCID: PMC8537219 DOI: 10.3390/toxins13100736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/10/2021] [Accepted: 10/15/2021] [Indexed: 01/17/2023] Open
Abstract
This study explored and investigated how zearalenone (ZEA) affects the morphology of small intestine and the distribution and expression of ghrelin and proliferating cell nuclear antigen (PCNA) in the small intestine of weaned gilts. A total of 20 weaned gilts (42-day-old, D × L × Y, weighing 12.84 ± 0.26 kg) were divided into the control and ZEA groups (ZEA at 1.04 mg/kg in diet) in a 35-d study. Histological observations of the small intestines revealed that villus injuries of the duodenum, jejunum and ileum, such as atrophy, retardation and branching dysfunction, were observed in the ZEA treatment. The villi branch of the ileum in the ZEA group was obviously decreased compared to that of the ileum, jejunum and duodenum, and the number of lymphoid nodules of the ileum was increased. Additionally, the effect of ZEA (1.04 mg/kg) was decreased by the immunoreactivity and distribution of ghrelin and PCNA in the duodenal and jejunal mucosal epithelial cells. Interestingly, ZEA increased the immunoreactivity of ghrelin in the ileal mucosal epithelial cells and decreased the immunoreactivity expression of PCNA in the gland epithelium of the small intestine. In conclusion, ZEA (1.04 mg/kg) had adverse effects on the development and the absorptive capacity of the villi of the intestines; yet, the small intestine could resist or ameliorate the adverse effects of ZEA by changing the autocrine of ghrelin in intestinal epithelial cells.
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Affiliation(s)
- Quanwei Zhang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
| | - Libo Huang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
| | - Bo Leng
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
| | - Yang Li
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
| | - Ning Jiao
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
| | - Shuzhen Jiang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
| | - Weiren Yang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai’an City 271018, China; (Q.Z.); (L.H.); (B.L.); (Y.L.); (N.J.); (S.J.)
- Correspondence: (W.Y.); (X.Y.); Tel.: +86-186-0548-9796 (W.Y.); +86-134-7538-6175 (X.Y.)
| | - Xuejun Yuan
- College of Life Sciences, Shandong Agricultural University, Tai’an City 271018, China
- Correspondence: (W.Y.); (X.Y.); Tel.: +86-186-0548-9796 (W.Y.); +86-134-7538-6175 (X.Y.)
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20
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Du M, Zhang Y, Chen H, Han R. TaPCNA plays a role in programmed cell death after UV-B exposure in wheat (Triticum aestivum). FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1029-1038. [PMID: 34237246 DOI: 10.1071/fp21013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Ultraviolet (UV)-B is a component of sunlight and shows a significant effect on DNA damage, which can be regulated by proliferating cell nuclear antigen (PCNA). The role of TaPCNA in wheat (Triticum aestivum L.) programmed cell death (PCD) under UV-B has not been investigated previously. Here, we explored the function of TaPCNA in wheat exposed to UV-B utilising Barley Stripe Mosaic Virus-virus-induced gene silencing (VIGS). The results showed that the expression of TaPCNA was downregulated, and curly wheat leaves with several spots were determined by VIGS. The growth rate and mesophyll cell length were significantly inhibited after TaPCNA was silenced. The activity of superoxide dismutase and the contents of soluble sugar and soluble protein decreased, whereas the activities of peroxidase and catalase and malondialdehyde content increased in TaPCNA-silenced and UV-B treatment groups. DNA laddering and propidium iodide staining results showed that DNA fragments and micronucleus accumulated after TaPCNA silencing with or without UV-B. Thus, TaPCNA participates in plant growth and DNA damage and PCD under UV-B. This study suggests an idea for the exploration of the function of certain genes in such complex wheat genomes and offers a theoretical basis to improve wheat agronomic traits.
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Affiliation(s)
- Meiting Du
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Linfen City, Shanxi Province, China
| | - Ying Zhang
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Linfen City, Shanxi Province, China
| | - Huize Chen
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Linfen City, Shanxi Province, China; and Corresponding authors. Emails: ;
| | - Rong Han
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Linfen City, Shanxi Province, China; and Corresponding authors. Emails: ;
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21
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Tibbs J, Ghoneim M, Caldwell CC, Buzynski T, Bowie W, Boehm EM, Washington MT, Tabei SMA, Spies M. KERA: analysis tool for multi-process, multi-state single-molecule data. Nucleic Acids Res 2021; 49:e53. [PMID: 33660771 PMCID: PMC8136784 DOI: 10.1093/nar/gkab087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/17/2021] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular machines within cells dynamically assemble, disassemble and reorganize. Molecular interactions between their components can be observed at the single-molecule level and quantified using colocalization single-molecule spectroscopy, in which individual labeled molecules are seen transiently associating with a surface-tethered partner, or other total internal reflection fluorescence microscopy approaches in which the interactions elicit changes in fluorescence in the labeled surface-tethered partner. When multiple interacting partners can form ternary, quaternary and higher order complexes, the types of spatial and temporal organization of these complexes can be deduced from the order of appearance and reorganization of the components. Time evolution of complex architectures can be followed by changes in the fluorescence behavior in multiple channels. Here, we describe the kinetic event resolving algorithm (KERA), a software tool for organizing and sorting the discretized fluorescent trajectories from a range of single-molecule experiments. KERA organizes the data in groups by transition patterns, and displays exhaustive dwell time data for each interaction sequence. Enumerating and quantifying sequences of molecular interactions provides important information regarding the underlying mechanism of the assembly, dynamics and architecture of the macromolecular complexes. We demonstrate KERA's utility by analyzing conformational dynamics of two DNA binding proteins: replication protein A and xeroderma pigmentosum complementation group D helicase.
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Affiliation(s)
- Joseph Tibbs
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Mohamed Ghoneim
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Colleen C Caldwell
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Troy Buzynski
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Wayne Bowie
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Elizabeth M Boehm
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - M Todd Washington
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - S M Ali Tabei
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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22
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Guilliam TA. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Front Mol Biosci 2021; 8:712971. [PMID: 34295925 PMCID: PMC8290200 DOI: 10.3389/fmolb.2021.712971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic replisome coordinates template unwinding and nascent-strand synthesis to drive DNA replication fork progression and complete efficient genome duplication. During its advancement along the parental template, each replisome may encounter an array of obstacles including damaged and structured DNA that impede its progression and threaten genome stability. A number of mechanisms exist to permit replisomes to overcome such obstacles, maintain their progression, and prevent fork collapse. A combination of recent advances in structural, biochemical, and single-molecule approaches have illuminated the architecture of the replisome during unperturbed replication, rationalised the impact of impediments to fork progression, and enhanced our understanding of DNA damage tolerance mechanisms and their regulation. This review focusses on these studies to provide an updated overview of the mechanisms that support replisomes to maintain their progression on an imperfect template.
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Affiliation(s)
- Thomas A. Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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23
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Activation of DNA Damage Tolerance Pathways May Improve Immunotherapy of Mesothelioma. Cancers (Basel) 2021; 13:cancers13133211. [PMID: 34199066 PMCID: PMC8269013 DOI: 10.3390/cancers13133211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 12/20/2022] Open
Abstract
Immunotherapy based on two checkpoint inhibitors (ICI), programmed cell death 1 (PD-1, Nivolumab) and cytotoxic T-lymphocyte 4 (CTLA-4, Ipilimumab), has provided a significant improvement in overall survival for malignant mesothelioma (MM). Despite this major breakthrough, the median overall survival of patients treated with the two ICIs only reached 18.1 months vs. 14 months in standard chemotherapy. With an objective response rate of 40%, only a subset of patients benefits from immunotherapy. A critical step in the success of immunotherapy is the presentation of tumor-derived peptides by the major histocompatibility complex I (MHC-I) of tumor cells. These neoantigens are potentially immunogenic and trigger immune responses orchestrated by cytotoxic cells. In MM, tumor development is nevertheless characterized by a low mutation rate despite major structural chromosomal rearrangements driving oncogenesis (BAP1, NF2, CDKN2AB). In this opinion, we propose to investigate an approach based on the mechanisms of the DNA damage tolerance (DDT) pathways to increase the frequency of non-synonymous mutations. The idea is to transiently activate the error-prone DDT in order to generate neoantigens while preserving a fully competent antitumor immune response.
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24
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Rossi G, Placidi M, Castellini C, Rea F, D'Andrea S, Alonso GL, Gravina GL, Tatone C, Di Emidio G, D’Alessandro AM. Crocetin Mitigates Irradiation Injury in an In Vitro Model of the Pubertal Testis: Focus on Biological Effects and Molecular Mechanisms. Molecules 2021; 26:molecules26061676. [PMID: 33802807 PMCID: PMC8002482 DOI: 10.3390/molecules26061676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/13/2022] Open
Abstract
Infertility is a potential side effect of radiotherapy and significantly affects the quality of life for adolescent cancer survivors. Very few studies have addressed in pubertal models the mechanistic events that could be targeted to provide protection from gonadotoxicity and data on potential radioprotective treatments in this peculiar period of life are elusive. In this study, we utilized an in vitro model of the mouse pubertal testis to investigate the efficacy of crocetin to counteract ionizing radiation (IR)-induced injury and potential underlying mechanisms. Present experiments provide evidence that exposure of testis fragments from pubertal mice to 2 Gy X-rays induced extensive structural and cellular damage associated with overexpression of PARP1, PCNA, SOD2 and HuR and decreased levels of SIRT1 and catalase. A twenty-four hr exposure to 50 μM crocetin pre- and post-IR significantly reduced testis injury and modulated the response to DNA damage and oxidative stress. Nevertheless, crocetin treatment did not counteract the radiation-induced changes in the expression of SIRT1, p62 and LC3II. These results increase the knowledge of mechanisms underlying radiation damage in pubertal testis and establish the use of crocetin as a fertoprotective agent against IR deleterious effects in pubertal period.
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Affiliation(s)
- Giulia Rossi
- Lab of Reproductive Technologies, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (G.R.); (M.P.); (F.R.); (C.T.)
| | - Martina Placidi
- Lab of Reproductive Technologies, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (G.R.); (M.P.); (F.R.); (C.T.)
| | - Chiara Castellini
- Andrology Unit, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (C.C.); (S.D.)
| | - Francesco Rea
- Lab of Reproductive Technologies, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (G.R.); (M.P.); (F.R.); (C.T.)
| | - Settimio D'Andrea
- Andrology Unit, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (C.C.); (S.D.)
| | - Gonzalo Luis Alonso
- Química Agrícola, E.T.S.I. Agrónomos y Montes, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Avda. de España s/n, 02071 Albacete, Spain;
| | - Giovanni Luca Gravina
- Laboratory of Radiobiology, Division of Radiotherapy, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Carla Tatone
- Lab of Reproductive Technologies, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (G.R.); (M.P.); (F.R.); (C.T.)
| | - Giovanna Di Emidio
- Lab of Reproductive Technologies, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (G.R.); (M.P.); (F.R.); (C.T.)
- Correspondence:
| | - Anna Maria D’Alessandro
- Lab of Nutritional Biochemistry, Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
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25
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Shen M, Young A, Autexier C. PCNA, a focus on replication stress and the alternative lengthening of telomeres pathway. DNA Repair (Amst) 2021; 100:103055. [PMID: 33581499 DOI: 10.1016/j.dnarep.2021.103055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of telomeres, which are specialized stretches of DNA found at the ends of linear chromosomes, is a crucial step for the immortalization of cancer cells. Approximately 10-15 % of cancer cells use a homologous recombination-based mechanism known as the Alternative Lengthening of Telomeres (ALT) pathway to maintain their telomeres. Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures. Telomeres in ALT+ cells especially are subject to elevated levels of replication stress compared to telomeres that are maintained by the enzyme telomerase, in part due to the incorporation of telomeric variant repeats at ALT+ telomeres, their on average longer lengths, and their modified chromatin states. Many DNA metabolic strategies exist to counter replication stress and to protect stalled replication forks. The role of proliferating cell nuclear antigen (PCNA) as a platform for recruiting protein partners that participate in several of these DNA replication and repair pathways has been well-documented. We propose that many of these pathways may be active at ALT+ telomeres, either to facilitate DNA replication, to manage replication stress, or during telomere extension. Here, we summarize recent evidence detailing the role of PCNA in pathways including DNA secondary structure resolution, DNA damage bypass, replication fork restart, and DNA damage synthesis. We propose that an examination of PCNA and its post-translational modifications (PTMs) may offer a unique lens by which we might gain insight into the DNA metabolic landscape that is distinctively present at ALT+ telomeres.
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Affiliation(s)
- Michelle Shen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Adrian Young
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada.
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26
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Paeschke K, Burkovics P. Mgs1 function at G-quadruplex structures during DNA replication. Curr Genet 2020; 67:225-230. [PMID: 33237336 PMCID: PMC8032586 DOI: 10.1007/s00294-020-01128-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/03/2022]
Abstract
The coordinated action of DNA polymerases and DNA helicases is essential at genomic sites that are hard to replicate. Among these are sites that harbour G-quadruplex DNA structures (G4). G4s are stable alternative DNA structures, which have been implicated to be involved in important cellular processes like the regulation of gene expression or telomere maintenance. G4 structures were shown to hinder replication fork progression and cause genomic deletions, mutations and recombination events. Many helicases unwind G4 structures and preserve genome stability, but a detailed understanding of G4 replication and the re-start of stalled replication forks around formed G4 structures is not clear, yet. In our recent study, we identified that Mgs1 preferentially binds to G4 DNA structures in vitro and is associated with putative G4-forming chromosomal regions in vivo. Mgs1 binding to G4 motifs in vivo is partially dependent on the helicase Pif1. Pif1 is the major G4-unwinding helicase in S. cerevisiae. In the absence of Mgs1, we determined elevated gross chromosomal rearrangement (GCR) rates in yeast, similar to Pif1 deletion. Here, we highlight the recent findings and set these into context with a new mechanistic model. We propose that Mgs1's functions support DNA replication at G4-forming regions.
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Affiliation(s)
- Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany.
| | - Peter Burkovics
- Institute of Genetics, Biological Research Centre, Szeged, Hungary.
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27
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Cranford MT, Kaszubowski JD, Trakselis MA. A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine. Nucleic Acids Res 2020; 48:10986-10997. [PMID: 32997110 PMCID: PMC7641752 DOI: 10.1093/nar/gkaa803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/22/2020] [Accepted: 09/16/2020] [Indexed: 01/12/2023] Open
Abstract
During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves ‘on-the-fly’ translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol for lesion bypass. The length of TLS must be long enough for effective bypass, but it must also be regulated to minimize replication errors by the TLS Pol. The exact position where the TLS Pol ends and the HiFi Pol resumes (i.e. the length of the TLS patch) has not been described. We use steady-state and pre-steady-state kinetic assays to characterize lesion bypass intermediates formed by different archaeal polymerase holoenzyme complexes that include PCNA123 and RFC. After bypass of 8-oxoG by TLS PolY, products accumulate at the template position three base pairs beyond the lesion. PolY is catalytically poor for subsequent extension from this +3 position beyond 8-oxoG, but this inefficiency is overcome by rapid extension of HiFi PolB1. The reciprocation of Pol activities at this intermediate indicates a defined position where TLS Pol extension is limited and where the DNA substrate is handed back to the HiFi Pol after bypass of 8-oxoG.
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Affiliation(s)
- Matthew T Cranford
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
| | - Joseph D Kaszubowski
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
| | - Michael A Trakselis
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
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28
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Kondratick CM, Washington MT, Spies M. Making Choices: DNA Replication Fork Recovery Mechanisms. Semin Cell Dev Biol 2020; 113:27-37. [PMID: 33967572 DOI: 10.1016/j.semcdb.2020.10.001] [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] [Indexed: 12/19/2022]
Abstract
DNA replication is laden with obstacles that slow, stall, collapse, and break DNA replication forks. At each obstacle, there is a decision to be made whether to bypass the lesion, repair or restart the damaged fork, or to protect stalled forks from further demise. Each "decision" draws upon multitude of proteins participating in various mechanisms that allow repair and restart of replication forks. Specific functions for many of these proteins have been described and an understanding of how they come together in supporting replication forks is starting to emerge. Many questions, however, remain regarding selection of the mechanisms that enable faithful genome duplication and how "normal" intermediates in these mechanisms are sometimes funneled into "rogue" processes that destabilize the genome and lead to cancer, cell death, and emergence of chemotherapeutic resistance. In this review we will discuss molecular mechanisms of DNA damage bypass and replication fork protection and repair. We will specifically focus on the key players that define which mechanism is employed including: PCNA and its control by posttranslational modifications, translesion synthesis DNA polymerases, molecular motors that catalyze reversal of stalled replication forks, proteins that antagonize fork reversal and protect reversed forks from nucleolytic degradation, and the machinery of homologous recombination that helps to reestablish broken forks. We will also discuss risks to genome integrity inherent in each of these mechanisms.
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Affiliation(s)
- Christine M Kondratick
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.,Department of Radiation Oncology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.,Department of Radiation Oncology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
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29
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Wilkinson NA, Mnuskin KS, Ashton NW, Woodgate R. Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass. Cancers (Basel) 2020; 12:cancers12102848. [PMID: 33023096 PMCID: PMC7600381 DOI: 10.3390/cancers12102848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs). However, due to the lower fidelity of the specialized polymerases involved in TLS, the activation and suppression of these pathways must be tightly regulated by post-translational modifications such as ubiquitination in order to limit the risk of mutagenesis. Many cancer cells rely on the deregulation of DNA damage bypass to promote carcinogenesis and tumor formation, often giving them heightened resistance to DNA damage from chemotherapeutic agents. In this review, we discuss the key functions of ubiquitin and ubiquitin-like proteins in regulating DNA damage bypass in human cells, and highlight ways in which these processes are both deregulated in cancer progression and might be targeted in cancer therapy.
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Affiliation(s)
| | | | - Nicholas W. Ashton
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
| | - Roger Woodgate
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
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30
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Shropshire JD, Leigh B, Bordenstein SR. Symbiont-mediated cytoplasmic incompatibility: what have we learned in 50 years? eLife 2020; 9:61989. [PMID: 32975515 PMCID: PMC7518888 DOI: 10.7554/elife.61989] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, thereby imparting a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally-transmitted bacteria to high frequencies in arthropods worldwide. In the past two decades, CI experienced a boom in interest due to its (i) deployment in worldwide efforts to curb mosquito-borne diseases, (ii) causation by bacteriophage genes, cifA and cifB, that modify sexual reproduction, and (iii) important impacts on arthropod speciation. This review serves as a gateway to experimental, conceptual, and quantitative themes of CI and outlines significant gaps in understanding CI’s mechanism that are ripe for investigation from diverse subdisciplines in the life sciences.
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Affiliation(s)
- J Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, United States
| | - Brittany Leigh
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, United States
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States.,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, United States
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31
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Ripley BM, Reusch DT, Washington MT. Yeast DNA polymerase η possesses two PIP-like motifs that bind PCNA and Rad6-Rad18 with different specificities. DNA Repair (Amst) 2020; 95:102968. [PMID: 32932109 DOI: 10.1016/j.dnarep.2020.102968] [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] [Received: 03/20/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 11/29/2022]
Abstract
In translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) η and Rev1, are recruited to stalled replication forks. These polymerases form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol η interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. Here we report the discovery of a second PIP-like motif in the C-terminal region of pol η, which we have designated as PIP2. We have designated the original PIP motif as PIP1. We show that the pol η PIP1 and PIP2 motifs bind PCNA with different affinities and kinetics. PIP1 binds with higher affinity than does PIP2, and PIP1 dissociates more slowly than does PIP2. In addition, we show that the interaction between pol η and Rad6-Rad18 is also mediated by the pol η PIP1 and PIP2 motifs. Again, we show that the affinity and kinetics by which these motifs bind Rad6-Rad18 is different. These findings are significant, because the multiple PIP-like motifs on pol η likely play quite different roles within the multi-protein complex formed at stalled replication forks. PIP1 likely plays a critical role in the recruiting pol η to this multi-protein complex. PIP2, by contrast, likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of TLS.
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Affiliation(s)
- Brittany M Ripley
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - Devin T Reusch
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States.
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32
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Mansilla SF, De La Vega MB, Calzetta NL, Siri SO, Gottifredi V. CDK-Independent and PCNA-Dependent Functions of p21 in DNA Replication. Genes (Basel) 2020; 11:genes11060593. [PMID: 32481484 PMCID: PMC7349641 DOI: 10.3390/genes11060593] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
p21Waf/CIP1 is a small unstructured protein that binds and inactivates cyclin-dependent kinases (CDKs). To this end, p21 levels increase following the activation of the p53 tumor suppressor. CDK inhibition by p21 triggers cell-cycle arrest in the G1 and G2 phases of the cell cycle. In the absence of exogenous insults causing replication stress, only residual p21 levels are prevalent that are insufficient to inhibit CDKs. However, research from different laboratories has demonstrated that these residual p21 levels in the S phase control DNA replication speed and origin firing to preserve genomic stability. Such an S-phase function of p21 depends fully on its ability to displace partners from chromatin-bound proliferating cell nuclear antigen (PCNA). Vice versa, PCNA also regulates p21 by preventing its upregulation in the S phase, even in the context of robust p21 induction by irradiation. Such a tight regulation of p21 in the S phase unveils the potential that CDK-independent functions of p21 may have for the improvement of cancer treatments.
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