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Baranowska G, Misiorna D, Białek W, Kramarz K, Dziadkowiec D. Replication stress response in fission yeast differentially depends on maintaining proper levels of Srs2 helicase and Rrp1, Rrp2 DNA translocases. PLoS One 2024; 19:e0300434. [PMID: 38905307 PMCID: PMC11192394 DOI: 10.1371/journal.pone.0300434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/27/2024] [Indexed: 06/23/2024] Open
Abstract
Homologous recombination is a key process that governs the stability of eukaryotic genomes during DNA replication and repair. Multiple auxiliary factors regulate the choice of homologous recombination pathway in response to different types of replication stress. Using Schizosaccharomyces pombe we have previously suggested the role of DNA translocases Rrp1 and Rrp2, together with Srs2 helicase, in the common synthesis-dependent strand annealing sub-pathway of homologous recombination. Here we show that all three proteins are important for completion of replication after hydroxyurea exposure and provide data comparing the effect of overproduction of Srs2 with Rrp1 and Rrp2. We demonstrate that Srs2 localises to rDNA region and is required for proper replication of rDNA arrays. Upregulation of Srs2 protein levels leads to enhanced replication stress, chromosome instability and viability loss, as previously reported for Rrp1 and Rrp2. Interestingly, our data suggests that dysregulation of Srs2, Rrp1 and Rrp2 protein levels differentially affects checkpoint response: overproduction of Srs2 activates simultaneously DNA damage and replication stress response checkpoints, while cells overproducing Rrp1 mainly launch DNA damage checkpoint. On the other hand, upregulation of Rrp2 primarily leads to replication stress response checkpoint activation. Overall, we propose that Srs2, Rrp1 and Rrp2 have important and at least partially independent functions in the maintenance of distinct difficult to replicate regions of the genome.
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Affiliation(s)
| | - Dorota Misiorna
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Wojciech Białek
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Karol Kramarz
- Faculty of Biological Sciences, Academic Excellence Hub—Research Centre for DNA Repair and Replication, University of Wrocław, Wrocław, Poland
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2
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [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: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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3
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Budden AM, Eravci M, Watson AT, Campillo-Funollet E, Oliver AW, Naiman K, Carr AM. Schizosaccharomyces pombe Rtf2 is important for replication fork barrier activity of RTS1 via splicing of Rtf1. eLife 2023; 12:e78554. [PMID: 37615341 PMCID: PMC10473836 DOI: 10.7554/elife.78554] [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: 03/11/2022] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
Arrested replication forks, when restarted by homologous recombination, result in error-prone DNA syntheses and non-allelic homologous recombination. Fission yeast RTS1 is a model fork barrier used to probe mechanisms of recombination-dependent restart. RTS1 barrier activity is entirely dependent on the DNA binding protein Rtf1 and partially dependent on a second protein, Rtf2. Human RTF2 was recently implicated in fork restart, leading us to examine fission yeast Rtf2's role in more detail. In agreement with previous studies, we observe reduced barrier activity upon rtf2 deletion. However, we identified Rtf2 to be physically associated with mRNA processing and splicing factors and rtf2 deletion to cause increased intron retention. One of the most affected introns resided in the rtf1 transcript. Using an intronless rtf1, we observed no reduction in RFB activity in the absence of Rtf2. Thus, Rtf2 is essential for correct rtf1 splicing to allow optimal RTS1 barrier activity.
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Affiliation(s)
- Alice M Budden
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | - Murat Eravci
- Department of Biochemistry and Biomedicine, University of SussexBrightonUnited Kingdom
| | - Adam T Watson
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | | | - Antony W Oliver
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | - Karel Naiman
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | - Antony M Carr
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
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4
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Conti BA, Smogorzewska A. Mechanisms of direct replication restart at stressed replisomes. DNA Repair (Amst) 2020; 95:102947. [PMID: 32853827 PMCID: PMC7669714 DOI: 10.1016/j.dnarep.2020.102947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/09/2023]
Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA.
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5
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Loss of the Nuclear Protein RTF2 Enhances Influenza Virus Replication. J Virol 2020; 94:JVI.00319-20. [PMID: 32878895 PMCID: PMC7592231 DOI: 10.1128/jvi.00319-20] [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: 02/25/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
Viral infection triggers the secretion of type I interferons, which in turn induce the expression of hundreds of antiviral genes. However, the roles of these induced genes in controlling viral infections remain largely unknown, limiting our ability to develop host-based antiviral therapeutics against pathogenic viruses, such as influenza virus. Here, we performed a loss-of-function genetic CRISPR screen in cells prestimulated with type I interferon to identify antiviral genes that restrict influenza A virus replication. Besides finding key components of the interferon signaling pathway, we discovered a new restriction factor, RTF2, which acts in the nucleus, restricts influenza virus transcription, and contributes to the interferon-induced upregulation of known restriction factors. Our work contributes to the field of antiviral immunology by discovering and characterizing a novel restriction factor of influenza virus and may ultimately be useful for understanding how to control a virus that causes significant morbidity and mortality worldwide. While hundreds of genes are induced by type I interferons, their roles in restricting the influenza virus life cycle remain mostly unknown. Using a loss-of-function CRISPR screen in cells prestimulated with interferon beta (IFN-β), we identified a small number of factors required for restricting influenza A virus replication. In addition to known components of the interferon signaling pathway, we found that replication termination factor 2 (RTF2) restricts influenza virus at the nuclear stage (and perhaps other stages) of the viral life cycle, based on several lines of evidence. First, a deficiency in RTF2 leads to higher levels of viral primary transcription, even in the presence of cycloheximide to block genome replication and secondary transcription. Second, cells that lack RTF2 have enhanced activity of a viral reporter that depends solely on four viral proteins that carry out replication and transcription in the nucleus. Third, when the RTF2 protein is mislocalized outside the nucleus, it is not able to restrict replication. Finally, the absence of RTF2 leads not only to enhanced viral transcription but also to reduced expression of antiviral factors in response to interferon. RTF2 thus inhibits primary influenza virus transcription, likely acts in the nucleus, and contributes to the upregulation of antiviral effectors in response to type I interferons. IMPORTANCE Viral infection triggers the secretion of type I interferons, which in turn induce the expression of hundreds of antiviral genes. However, the roles of these induced genes in controlling viral infections remain largely unknown, limiting our ability to develop host-based antiviral therapeutics against pathogenic viruses, such as influenza virus. Here, we performed a loss-of-function genetic CRISPR screen in cells prestimulated with type I interferon to identify antiviral genes that restrict influenza A virus replication. Besides finding key components of the interferon signaling pathway, we discovered a new restriction factor, RTF2, which acts in the nucleus, restricts influenza virus transcription, and contributes to the interferon-induced upregulation of known restriction factors. Our work contributes to the field of antiviral immunology by discovering and characterizing a novel restriction factor of influenza virus and may ultimately be useful for understanding how to control a virus that causes significant morbidity and mortality worldwide.
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Suo D, Wang L, Zeng T, Zhang H, Li L, Liu J, Yun J, Guan XY, Li Y. NRIP3 upregulation confers resistance to chemoradiotherapy in ESCC via RTF2 removal by accelerating ubiquitination and degradation of RTF2. Oncogenesis 2020; 9:75. [PMID: 32839439 PMCID: PMC7445249 DOI: 10.1038/s41389-020-00260-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 12/01/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignant cancer worldwide. Despite recent improvements in surgical techniques and adjuvant therapies, the prognosis of patients with advanced ESCC remains poor. Resistance to chemoradiotherapy (CRT) remains a major cause of treatment failure for advanced ESCC patients. Here, we report that NRIP3 (nuclear receptor interacting protein 3) promotes ESCC tumor cell growth and resistance to CRT in ESCC cells by increasing and binding to DDI1 (DNA-damage inducible 1 homolog 1) and RTF2 (homologous to Schizosaccharomyces pombe Rtf2), and accelerating the removal of RTF2, which is a key determinant for the ability of cells to manage replication stress. In addition, we found that NRIP3 could increase DDI1 expression via PPARα. The NRIP3-PPARα-DDI1-RTF2 axis represents a protective molecular pathway in ESCC cells that mediates resistance to replication stress signals induced by chemoradiotherapy. In addition, elevated NRIP3 is associated with the poor clinical outcome of ESCC patients receiving radiotherapy and/or cisplatin-based chemotherapy. Our study therefore reveals that NRIP3 is a prognostic factor in ESCC and could have some predictive value to select patients who benefit from CRT treatment. A common mechanism that protects ESCC tumor cells from DNA damage induced by CRT is also revealed in this study.
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Affiliation(s)
- Daqin Suo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ling Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tingting Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hui Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Metabolic Innovation Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Clinical Oncology, University of Hong Kong, Hong Kong, China
| | - Jinyun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Metabolic Innovation Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingping Yun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
- Department of Clinical Oncology, University of Hong Kong, Hong Kong, China.
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
- Guangdong Esophageal Cancer Institute, Guangdong, China.
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7
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [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: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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8
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Jalan M, Oehler J, Morrow CA, Osman F, Whitby MC. Factors affecting template switch recombination associated with restarted DNA replication. eLife 2019; 8:41697. [PMID: 30667359 PMCID: PMC6358216 DOI: 10.7554/elife.41697] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination helps ensure the timely completion of genome duplication by restarting collapsed replication forks. However, this beneficial function is not without risk as replication restarted by homologous recombination is prone to template switching (TS) that can generate deleterious genome rearrangements associated with diseases such as cancer. Previously we established an assay for studying TS in Schizosaccharomyces pombe (Nguyen et al., 2015). Here, we show that TS is detected up to 75 kb downstream of a collapsed replication fork and can be triggered by head-on collision between the restarted fork and RNA Polymerase III transcription. The Pif1 DNA helicase, Pfh1, promotes efficient restart and also suppresses TS. A further three conserved helicases (Fbh1, Rqh1 and Srs2) strongly suppress TS, but there is no change in TS frequency in cells lacking Fml1 or Mus81. We discuss how these factors likely influence TS.
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Affiliation(s)
- Manisha Jalan
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Oehler
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Carl A Morrow
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Fekret Osman
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Liao H, Ji F, Helleday T, Ying S. Mechanisms for stalled replication fork stabilization: new targets for synthetic lethality strategies in cancer treatments. EMBO Rep 2018; 19:embr.201846263. [PMID: 30108055 DOI: 10.15252/embr.201846263] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Accepted: 07/20/2018] [Indexed: 01/24/2023] Open
Abstract
Timely and faithful duplication of the entire genome depends on completion of replication. Replication forks frequently encounter obstacles that may cause genotoxic fork stalling. Nevertheless, failure to complete replication rarely occurs under normal conditions, which is attributed to an intricate network of proteins that serves to stabilize, repair and restart stalled forks. Indeed, many of the components in this network are encoded by tumour suppressor genes, and their loss of function by mutation or deletion generates genomic instability, a hallmark of cancer. Paradoxically, the same fork-protective network also confers resistance of cancer cells to chemotherapeutic drugs that induce high-level replication stress. Here, we review the mechanisms and major pathways rescuing stalled replication forks, with a focus on fork stabilization preventing fork collapse. A coherent understanding of how cells protect their replication forks will not only provide insight into how cells maintain genome stability, but also unravel potential therapeutic targets for cancers refractory to conventional chemotherapies.
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Affiliation(s)
- Hongwei Liao
- Department of Pharmacology & Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | - Fang Ji
- Department of Pharmacology & Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou, China
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden .,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Songmin Ying
- Department of Pharmacology & Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou, China
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10
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Kottemann MC, Conti BA, Lach FP, Smogorzewska A. Removal of RTF2 from Stalled Replisomes Promotes Maintenance of Genome Integrity. Mol Cell 2017; 69:24-35.e5. [PMID: 29290612 DOI: 10.1016/j.molcel.2017.11.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
Abstract
The protection and efficient restart of stalled replication forks is critical for the maintenance of genome integrity. Here, we identify a regulatory pathway that promotes stalled forks recovery from replication stress. We show that the mammalian replisome component C20orf43/RTF2 (homologous to S. pombe Rtf2) must be removed for fork restart to be optimal. We further show that the proteasomal shuttle proteins DDI1 and DDI2 are required for RTF2 removal from stalled forks. Persistence of RTF2 at stalled forks results in fork restart defects, hyperactivation of the DNA damage signal, accumulation of single-stranded DNA (ssDNA), sensitivity to replication drugs, and chromosome instability. These results establish that RTF2 removal is a key determinant for the ability of cells to manage replication stress and maintain genome integrity.
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Affiliation(s)
- Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA.
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11
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Yadav P, Tripathi RK, Singh RK, Mohindra V. Expression profile and in silico characterization of novel RTF2h gene under oxidative stress in Indian catfish, Clarias magur (Hamilton 1822). Mol Biol Rep 2016; 44:63-77. [PMID: 27743114 DOI: 10.1007/s11033-016-4081-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 09/12/2016] [Indexed: 12/19/2022]
Abstract
During the investigation of genes involved in the hypoxia tolerance, novel transcript, Replication Termination Factor 2 homologue (RTF2h), was found to be differentially expressed in brain of Clarias magur (previous name, C. batrachus) whose function was still undefined. Thus, present study was aimed to examine the transcriptional response of novel RTF2h gene, for its possible involvement in hypoxia tolerance in C. magur. Novel transcripts expressed under hypoxic stress were identified from ESTs obtained from SSH libraries of C. magur. Homology analysis of novel transcript (JK487668) revealed it to have RING superfamily signature and was closely related with RTF2 homologue. To characterize the expression pattern of CmRTF2h gene in different tissues of C. magur, qRT-PCR analysis was performed which showed significant increased expression, in spleen following short-term hypoxia exposure (12 H; 2.33-fold), while after long-term hypoxia exposure, significant up-regulation was found three tissues: in spleen (6.57-fold), liver (2.31-fold) and head kidney (2.99-fold) and was down-regulated in brain (3.52-fold). Further, the consensus sequence, obtained from SSH EST sequence and transcripts from hypoxia induced transcriptome data, through multiple sequence alignments, homology modeling and phylogentic analysis together, confirmed it as a novel CmRTF2h gene. In-silico protein-protein interaction and docking studies suggested its closely related function to that of RTF2. The present study reports the expression pattern of CmRTF2h under hypoxia. The up-regulated expression of CmRTF2h under hypoxic conditions may contribute to defense mechanism against induced DNA damage, which in turn may of adaptive significance for hypoxia tolerance in C. magur.
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Affiliation(s)
- Prabhaker Yadav
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P. O. Dilkusha, Lucknow, 226002, U.p., India
| | - Ratnesh K Tripathi
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P. O. Dilkusha, Lucknow, 226002, U.p., India
- Imperial Life Sciences (P) Limited, Gurgaon, 122001, Haryana, India
| | - Rajeev K Singh
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P. O. Dilkusha, Lucknow, 226002, U.p., India
| | - Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P. O. Dilkusha, Lucknow, 226002, U.p., India.
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Zech J, Godfrey EL, Masai H, Hartsuiker E, Dalgaard JZ. The DNA-Binding Domain of S. pombe Mrc1 (Claspin) Acts to Enhance Stalling at Replication Barriers. PLoS One 2015. [PMID: 26201080 PMCID: PMC4511789 DOI: 10.1371/journal.pone.0132595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During S-phase replication forks can stall at specific genetic loci. At some loci, the stalling events depend on the replisome components Schizosaccharomyces pombe Swi1 (Saccharomyces cerevisiae Tof1) and Swi3 (S. cerevisiae Csm3) as well as factors that bind DNA in a site-specific manner. Using a new genetic screen we identified Mrc1 (S. cerevisiae Mrc1/metazoan Claspin) as a replisome component involved in replication stalling. Mrc1 is known to form a sub-complex with Swi1 and Swi3 within the replisome and is required for the intra-S phase checkpoint activation. This discovery is surprising as several studies show that S. cerevisiae Mrc1 is not required for replication barrier activity. In contrast, we show that deletion of S. pombe mrc1 leads to an approximately three-fold reduction in barrier activity at several barriers and that Mrc1’s role in replication fork stalling is independent of its role in checkpoint activation. Instead, S. pombe Mrc1 mediated fork stalling requires the presence of a functional copy of its phylogenetically conserved DNA binding domain. Interestingly, this domain is on the sequence level absent from S. cerevisiae Mrc1. Our study indicates that direct interactions between the eukaryotic replisome and the DNA are important for site-specific replication stalling.
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Affiliation(s)
- Juergen Zech
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
- * E-mail: (JZ); (JZD)
| | - Emma Louise Godfrey
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
| | - Hisao Masai
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156–8613, Japan
| | - Edgar Hartsuiker
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Wales, LI57 2UW, United Kingdom
| | - Jacob Zeuthen Dalgaard
- Warwick Medical School, University of Warwick, Gibbet Hill Campus, CV47AL Coventry, United Kingdom
- * E-mail: (JZ); (JZD)
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13
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An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana. Genetics 2015; 200:523-35. [PMID: 25819795 DOI: 10.1534/genetics.115.176438] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/25/2015] [Indexed: 01/01/2023] Open
Abstract
Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-messengerRNA (mRNA) splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. In addition to the known spliceosomal component PRP8, the screen recovered Arabidopsis RTF2 (AtRTF2), a previously uncharacterized, evolutionarily conserved protein containing a replication termination factor 2 (Rtf2) domain. A homozygous null mutation in AtRTF2 is embryo lethal, indicating that AtRTF2 is an essential protein. Quantitative RT-PCR demonstrated that impaired expression of GFP in atrtf2 and prp8 mutants is due to inefficient splicing of the GFP pre-mRNA. A genome-wide analysis using RNA sequencing indicated that 13-16% of total introns are retained to a significant degree in atrtf2 mutants. Considering these results and previous suggestions that Rtf2 represents an ubiquitin-related domain, we discuss the possible role of AtRTF2 in ubiquitin-based regulation of pre-mRNA splicing.
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14
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Chavdarova M, Marini V, Sisakova A, Sedlackova H, Vigasova D, Brill SJ, Lisby M, Krejci L. Srs2 promotes Mus81-Mms4-mediated resolution of recombination intermediates. Nucleic Acids Res 2015; 43:3626-42. [PMID: 25765656 PMCID: PMC4402524 DOI: 10.1093/nar/gkv198] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/26/2015] [Indexed: 11/26/2022] Open
Abstract
A variety of DNA lesions, secondary DNA structures or topological stress within the DNA template may lead to stalling of the replication fork. Recovery of such forks is essential for the maintenance of genomic stability. The structure-specific endonuclease Mus81–Mms4 has been implicated in processing DNA intermediates that arise from collapsed forks and homologous recombination. According to previous genetic studies, the Srs2 helicase may play a role in the repair of double-strand breaks and ssDNA gaps together with Mus81–Mms4. In this study, we show that the Srs2 and Mus81–Mms4 proteins physically interact in vitro and in vivo and we map the interaction domains within the Srs2 and Mus81 proteins. Further, we show that Srs2 plays a dual role in the stimulation of the Mus81–Mms4 nuclease activity on a variety of DNA substrates. First, Srs2 directly stimulates Mus81–Mms4 nuclease activity independent of its helicase activity. Second, Srs2 removes Rad51 from DNA to allow access of Mus81–Mms4 to cleave DNA. Concomitantly, Mus81–Mms4 inhibits the helicase activity of Srs2. Taken together, our data point to a coordinated role of Mus81–Mms4 and Srs2 in processing of recombination as well as replication intermediates.
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Affiliation(s)
- Melita Chavdarova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic
| | - Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic
| | - Alexandra Sisakova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Hana Sedlackova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic
| | - Dana Vigasova
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Steven J Brill
- Department of Genetics, Cancer Research Institute, Vlarska 7, 833 91 Bratislava, Slovakia
| | - Michael Lisby
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, Brno 625 00, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
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15
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Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
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Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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16
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Bastia D, Zaman S. Mechanism and physiological significance of programmed replication termination. Semin Cell Dev Biol 2014; 30:165-73. [PMID: 24811316 DOI: 10.1016/j.semcdb.2014.04.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 11/26/2022]
Abstract
Replication forks in both prokaryotic and eukaryotic systems pause at random sites due to depletion of dNTP pools, DNA damage, tight binding nonhistone proteins or unusual DNA sequences and/or structures, in a mostly non-polar fashion. However, there is also physiologically programmed replication termination at sequence-specific authentic replication termini. Here, the structure and functions of programmed replication termini, their mechanism of action and their diverse physiological functions in prokaryotes and eukaryotes have been reviewed.
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Affiliation(s)
- Deepak Bastia
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States.
| | - Shamsu Zaman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States
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17
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Choy A, Severo MS, Sun R, Girke T, Gillespie JJ, Pedra JHF. Decoding the ubiquitin-mediated pathway of arthropod disease vectors. PLoS One 2013; 8:e78077. [PMID: 24205097 PMCID: PMC3804464 DOI: 10.1371/journal.pone.0078077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Protein regulation by ubiquitin has been extensively described in model organisms. However, characterization of the ubiquitin machinery in disease vectors remains mostly unknown. This fundamental gap in knowledge presents a concern because new therapeutics are needed to control vector-borne diseases, and targeting the ubiquitin machinery as a means for disease intervention has been already adopted in the clinic. In this study, we employed a bioinformatics approach to uncover the ubiquitin-mediated pathway in the genomes of Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus and Rhodnius prolixus. We observed that (1) disease vectors encode a lower percentage of ubiquitin-related genes when compared to Drosophila melanogaster, Mus musculus and Homo sapiens but not Saccharomyces cerevisiae; (2) overall, there are more proteins categorized as E3 ubiquitin ligases when compared to E2-conjugating or E1-activating enzymes; (3) the ubiquitin machinery within the three mosquito genomes is highly similar; (4) ubiquitin genes are more than doubled in the Chagas disease vector (R. prolixus) when compared to other arthropod vectors; (5) the deer tick I. scapularis and the body louse (P. humanus) genomes carry low numbers of E1-activating enzymes and HECT-type E3 ubiquitin ligases; (6) R. prolixus have low numbers of RING-type E3 ubiquitin ligases; and (7) C. quinquefasciatus present elevated numbers of predicted F-box E3 ubiquitin ligases, JAB and UCH deubiquitinases. Taken together, these findings provide novel opportunities to study the interaction between a pathogen and an arthropod vector.
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Affiliation(s)
- Anthony Choy
- Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Maiara S. Severo
- Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Ruobai Sun
- "Institute for Integrative Genome Biology, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Thomas Girke
- "Institute for Integrative Genome Biology, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joao H. F. Pedra
- Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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18
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Slx8 removes Pli1-dependent protein-SUMO conjugates including SUMOylated topoisomerase I to promote genome stability. PLoS One 2013; 8:e71960. [PMID: 23936535 PMCID: PMC3735562 DOI: 10.1371/journal.pone.0071960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 07/10/2013] [Indexed: 11/19/2022] Open
Abstract
The SUMO-dependent ubiquitin ligase Slx8 plays key roles in promoting genome stability, including the processing of trapped Topoisomerase I (Top1) cleavage complexes and removal of toxic SUMO conjugates. We show that it is the latter function that constitutes Slx8's primary role in fission yeast. The SUMO conjugates in question are formed by the SUMO ligase Pli1, which is necessary for limiting spontaneous homologous recombination when Top1 is present. Surprisingly there is no requirement for Pli1 to limit recombination in the vicinity of a replication fork blocked at the programmed barrier RTS1. Notably, once committed to Pli1-mediated SUMOylation Slx8 becomes essential for genotoxin resistance, limiting both spontaneous and RTS1 induced recombination, and promoting normal chromosome segregation. We show that Slx8 removes Pli1-dependent Top1-SUMO conjugates and in doing so helps to constrain recombination at RTS1. Overall our data highlight how SUMOylation and SUMO-dependent ubiquitylation by the Pli1-Slx8 axis contribute in different ways to maintain genome stability.
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19
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Lambert S, Carr AM. Impediments to replication fork movement: stabilisation, reactivation and genome instability. Chromosoma 2013; 122:33-45. [DOI: 10.1007/s00412-013-0398-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 02/11/2013] [Accepted: 02/11/2013] [Indexed: 01/02/2023]
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20
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Sofueva S, Osman F, Lorenz A, Steinacher R, Castagnetti S, Ledesma J, Whitby MC. Ultrafine anaphase bridges, broken DNA and illegitimate recombination induced by a replication fork barrier. Nucleic Acids Res 2011; 39:6568-84. [PMID: 21576223 PMCID: PMC3159475 DOI: 10.1093/nar/gkr340] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most DNA double-strand breaks (DSBs) in S- and G2-phase cells are repaired accurately by Rad51-dependent sister chromatid recombination. However, a minority give rise to gross chromosome rearrangements (GCRs), which can result in disease/death. What determines whether a DSB is repaired accurately or inaccurately is currently unclear. We provide evidence that suggests that perturbing replication by a non-programmed protein-DNA replication fork barrier results in the persistence of replication intermediates (most likely regions of unreplicated DNA) into mitosis, which results in anaphase bridge formation and ultimately to DNA breakage. However, unlike previously characterised replication-associated DSBs, these breaks are repaired mainly by Rad51-independent processes such as single-strand annealing, and are therefore prone to generate GCRs. These data highlight how a replication-associated DSB can be predisposed to give rise to genome rearrangements in eukaryotes.
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Affiliation(s)
- Sevil Sofueva
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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21
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Branzei D. Ubiquitin family modifications and template switching. FEBS Lett 2011; 585:2810-7. [PMID: 21539841 DOI: 10.1016/j.febslet.2011.04.053] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/21/2011] [Accepted: 04/21/2011] [Indexed: 12/21/2022]
Abstract
Homologous recombination plays an important role in the maintenance of genome integrity. Arrested forks and DNA lesions trigger strand annealing events, called template switching, which can provide for accurate damage bypass, but can also lead to chromosome rearrangements. Advances have been made in understanding the underlying mechanisms for these events and in elucidating the factors involved. Ubiquitin- and SUMO-mediated modification pathways have emerged as key players in regulating damage-induced template switching. Here I review the biological significance of template switching at the nexus of DNA replication and recombination, and the role of ubiquitin-like modifications in mediating and controlling this process.
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Affiliation(s)
- Dana Branzei
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
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22
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Lambert S, Mizuno K, Blaisonneau J, Martineau S, Chanet R, Fréon K, Murray JM, Carr AM, Baldacci G. Homologous Recombination Restarts Blocked Replication Forks at the Expense of Genome Rearrangements by Template Exchange. Mol Cell 2010; 39:346-59. [DOI: 10.1016/j.molcel.2010.07.015] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 03/31/2010] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
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23
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Branzei D, Foiani M. Maintaining genome stability at the replication fork. Nat Rev Mol Cell Biol 2010; 11:208-19. [PMID: 20177396 DOI: 10.1038/nrm2852] [Citation(s) in RCA: 610] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aberrant DNA replication is a major source of the mutations and chromosome rearrangements that are associated with pathological disorders. When replication is compromised, DNA becomes more prone to breakage. Secondary structures, highly transcribed DNA sequences and damaged DNA stall replication forks, which then require checkpoint factors and specialized enzymatic activities for their stabilization and subsequent advance. These mechanisms ensure that the local DNA damage response, which enables replication fork progression and DNA repair in S phase, is coupled with cell cycle transitions. The mechanisms that operate in eukaryotic cells to promote replication fork integrity and coordinate replication with other aspects of chromosome maintenance are becoming clear.
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Affiliation(s)
- Dana Branzei
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, 20139 Milan, Italy.
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24
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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