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Wang F, He Q, Yao NY, O'Donnell ME, Li H. The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Nat Struct Mol Biol 2024:10.1038/s41594-024-01332-4. [PMID: 38871854 DOI: 10.1038/s41594-024-01332-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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2
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Yu R, Wu X, Qian F, Yang Q. RFC3 drives the proliferation, migration, invasion and angiogenesis of colorectal cancer cells by binding KIF14. Exp Ther Med 2024; 27:222. [PMID: 38590579 PMCID: PMC11000453 DOI: 10.3892/etm.2024.12510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/26/2024] [Indexed: 04/10/2024] Open
Abstract
Colorectal cancer (CRC) is a deadly and aggressive type of cancer that has a high fatality rate. The expression levels of replication factor C subunit 3 (RFC3) and kinesin family member 14 (KIF14) have been reported to be increased in CRC. The current study aimed to explore the effects of RFC3 on the malignant behaviors of CRC cells and its possible underlying mechanism involving KIF14. RFC3 and KIF14 expression levels in CRC tissues were analyzed using TNMplot database and Gene Expression Profiling Interactive Analysis database bioinformatics tools. RFC3 and KIF14 levels in CRC cells were examined using reverse transcription-quantitative PCR and western blotting. Cell Counting Kit-8 and 5-ethynyl-2'-deoxyuridine assays were performed to assess cell proliferation. Cell apoptosis was determined using flow cytometric analysis. Wound healing and Transwell assays were adopted for the evaluation of cell migration and invasion. Tube formation assay in human umbilical vein endothelial cells was used to measure angiogenesis. Western blotting analysis was performed to determine the expression of apoptosis-, migration- and angiogenesis-associated proteins. Additionally, bioinformatics tools predicted the co-expression and interaction of RFC3 and KIF14, which was verified by a co-immunoprecipitation assay. RFC3 displayed elevated expression in CRC tissues and cells, and depletion of RFC3 halted the proliferation, migration, invasion and angiogenesis, while increasing the apoptosis of CRC cells; this was accompanied by changes in the expression levels of related proteins. In addition, RFC3 bound to KIF14 and interference with RFC3 reduced KIF14 expression. Moreover, KIF14 upregulation reversed the effects of RFC3 depletion on the aggressive cellular behaviors in CRC. In conclusion, RFC3 might interact with KIF14 to function as a contributor to the malignant development of CRC.
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Affiliation(s)
- Rong Yu
- Department of General Surgery, Quzhou Kecheng People's Hospital, Quzhou, Zhejiang 324000, P.R. China
| | - Xinxin Wu
- Department of General Surgery, Yancheng Dafeng Hospital of Traditional Chinese Medicine, Yancheng, Jiangsu 224110, P.R. China
| | - Fang Qian
- Department of Radiology, Wuxi Xinwu Hospital of Traditional Chinese Medicine, Wuxi, Jiangsu 214000, P.R. China
| | - Qian Yang
- Department of Radiology, Maternal and Child Health Hospital of Huaiyin District, Huai'an, Jiangsu 223300, P.R. China
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3
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Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA. Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. J Biol Chem 2024; 300:107166. [PMID: 38490435 PMCID: PMC11044049 DOI: 10.1016/j.jbc.2024.107166] [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: 01/10/2024] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
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Affiliation(s)
- Jacob T Landeck
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emily K Norman
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emma L Sedivy
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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4
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Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
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5
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Olsen JG, Prestel A, Kassem N, Broendum SS, Shamim HM, Simonsen S, Grysbæk M, Mortensen J, Rytkjær LL, Haxholm GW, Marabini R, Holmberg C, Carr AM, Crehuet R, Nielsen O, Kragelund BB. Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs. Nucleic Acids Res 2024; 52:2030-2044. [PMID: 38261971 PMCID: PMC10939359 DOI: 10.1093/nar/gkae011] [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: 05/11/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Noah Kassem
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sebastian S Broendum
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hossain Mohammad Shamim
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Signe Simonsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Grysbæk
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Josefine Mortensen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Louise Lund Rytkjær
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Gitte W Haxholm
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Holmberg
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex, John Maynard Smith Building, Falmer, BN1 9RQ, Brighton
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, c/ Jordi Girona 18-26, 08034 Barcelona
| | - Olaf Nielsen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
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6
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Tyagi N, Uppili B, Sharma P, Parveen S, Saifi S, Jain A, Sonakar A, Ahmed I, Sahni S, Shamim U, Anand A, Suroliya V, Asokachandran V, Srivastava A, Sivasubbu S, Scaria V, Faruq M. Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort. Neurogenetics 2024; 25:13-25. [PMID: 37917284 DOI: 10.1007/s10048-023-00736-6] [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: 06/02/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
An intronic bi-allelic pentanucleotide repeat expansion mutation, (AAGGG)400-2000, at AAAAG repeat locus in RFC1 gene, is known as underlying genetic cause in cases with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and late-onset sporadic ataxia. Biallelic positive cases carry a common recessive risk haplotype, "AAGA," spanning RFC1 gene. In this study, our aim is to find prevalence of bi-allelic (AAGGG)exp in Indian ataxia and other neurological disorders and investigate the complexity of RFC1 repeat locus and its potential association with neurodegenerative diseases in Indian population-based cohorts. We carried out repeat number and repeat type estimation using flanking PCR and repeat primed PCR (AAAAG/AAAGG/AAGGG) in four Indian disease cohorts and healthy controls. Haplotype assessment of suspected cases was done by genotyping and confirmed by Sanger sequencing. Blood samples and consent of all the cases and detailed clinical details of positive cases were collected in collaboration with A.I.I.M.S. Furthermore, comprehension of RFC1 repeat locus and risk haplotype analysis in Indian background was performed on the NGS data of Indian healthy controls by ExpansionHunter, ExpansionHunter Denovo, and PHASE analysis, respectively. Genetic screening of RFC1-TNR locus in 1998 uncharacterized cases (SCA12: 87; uncharacterized ataxia: 1818, CMT: 93) and 564 heterogenous controls showed that the frequency of subjects with bi-allelic (AAGGG)exp are 1.15%, < 0.05%, 2.15%, and 0% respectively. Two RFC1 positive sporadic late-onset ataxia cases, one bi-allelic (AAGGG)exp and another, (AAAGG)~700/(AAGGG)exp, had recessive risk haplotype and CANVAS symptoms. Long normal alleles, 15-27, are significantly rare in ataxia cohort. In IndiGen control population (IndiGen; N = 1029), long normal repeat range, 15-27, is significantly associated with A3G3 and some rare repeat motifs, AGAGG, AACGG, AAGAG, and AAGGC. Risk-associated "AAGA" haplotype of the original pathogenic expansion of A2G3 was found associated with the A3G3 representing alleles in background population. Apart from bi-allelic (AAGGG)exp, we report cases with a new pathogenic expansion of (AAAGG)exp/(AAGGG)exp in RFC1 and recessive risk haplotype. We found different repeat motifs at RFC1 TNR locus, like AAAAG, AAAGG, AAAGGG, AAAAGG, AAGAG, AACGG, AAGGC, AGAGG, and AAGGG, in Indian background population except ACAGG and (AAAGG)n/(AAGGG)n. Our findings will help in further understanding the role of long normal repeat size and different repeat motifs, specifically AAAGG, AAAGGG, and other rare repeat motifs, at the RFC1 locus.
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Affiliation(s)
- Nishu Tyagi
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bharathram Uppili
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Sharma
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shaista Parveen
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Sheeba Saifi
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Abhinav Jain
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akhilesh Sonakar
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Istaq Ahmed
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Shweta Sahni
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Uzma Shamim
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Avni Anand
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Varun Suroliya
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Vivekanand Asokachandran
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Achal Srivastava
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Vinod Scaria
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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7
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Maltby CJ, Krans A, Grudzien SJ, Palacios Y, Muiños J, Suárez A, Asher M, Khurana V, Barmada SJ, Dijkstra AA, Todd PK. AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571345. [PMID: 38168171 PMCID: PMC10760133 DOI: 10.1101/2023.12.13.571345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by biallelic, non-reference pentameric AAGGG(CCCTT) repeat expansions within the second intron of replication factor complex subunit 1 (RFC1). To investigate how these repeats cause disease, we generated CANVAS patient induced pluripotent stem cell (iPSC) derived neurons (iNeurons) and utilized calcium imaging and transcriptomic analysis to define repeat-elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in CANVAS patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons, and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. These phenotypic deficits were not replicated by knockdown of RFC1 in control neurons and were not rescued by ectopic expression of RFC1. These findings support a repeat-dependent but RFC1-independent cause of neuronal dysfunction in CANVAS, with important implications for therapeutic development in this currently untreatable condition.
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Affiliation(s)
- Connor J. Maltby
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
| | - Samantha J. Grudzien
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yomira Palacios
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Muiños
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- UM SMART Undergraduate Summer Program, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Suárez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Asher
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Vikram Khurana
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sami J. Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Anke A. Dijkstra
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter K. Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
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8
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Kumar M, Tyagi N, Faruq M. The molecular mechanisms of spinocerebellar ataxias for DNA repeat expansion in disease. Emerg Top Life Sci 2023; 7:289-312. [PMID: 37668011 DOI: 10.1042/etls20230013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023]
Abstract
Spinocerebellar ataxias (SCAs) are a heterogenous group of neurodegenerative disorders which commonly inherited in an autosomal dominant manner. They cause muscle incoordination due to degeneration of the cerebellum and other parts of nervous system. Out of all the characterized (>50) SCAs, 14 SCAs are caused due to microsatellite repeat expansion mutations. Repeat expansions can result in toxic protein gain-of-function, protein loss-of-function, and/or RNA gain-of-function effects. The location and the nature of mutation modulate the underlying disease pathophysiology resulting in varying disease manifestations. Potential toxic effects of these mutations likely affect key major cellular processes such as transcriptional regulation, mitochondrial functioning, ion channel dysfunction and synaptic transmission. Involvement of several common pathways suggests interlinked function of genes implicated in the disease pathogenesis. A better understanding of the shared and distinct molecular pathogenic mechanisms in these diseases is required to develop targeted therapeutic tools and interventions for disease management. The prime focus of this review is to elaborate on how expanded 'CAG' repeats contribute to the common modes of neurotoxicity and their possible therapeutic targets in management of such devastating disorders.
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Affiliation(s)
- Manish Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Nishu Tyagi
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
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9
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Vandborg B, Holroyd DL, Pukala T, Bruning JB. Production of recombinant human proliferating cellular nuclear antigen (PCNA) for structural and biophysical characterization. Protein Expr Purif 2023; 212:106353. [PMID: 37597793 DOI: 10.1016/j.pep.2023.106353] [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: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023]
Abstract
Human proliferating cell nuclear antigen (hPCNA) is a DNA replication processivity factor, which acts as a docking platform, allowing proteins to have access to the replication fork and increasing the affinity of DNA interacting proteins, making it critical for cell survival. The trimer forms a ring-shaped oligomer allowing DNA to pass through the middle and interacting proteins to dock on the outside of the ring. Without this structural formation, there is a loss of DNA replication and repair in the cell. Due to the location of subunit-subunit termini, the addition of a purification tag can hamper crystallography and biophysical experiments, as the trimer complex folding can be impeded. To avoid these complications, a tag-less, step-wise purification was implemented, which resulted in 17.6 mg from 2 L culture of pure hPCNA with a 260 nm/280 nm value of 0.43. The produced crystal structure reveals a correctly formed oligomer. The clear depletion of the tracer binding and probe protein interaction in a fluorescence polarisation competition-based assay demonstrates the purification method produces a protein structure with a functional binding site. This purification method presents a reliable and simple method for producing hPCNA for biophysical characterisation.
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Affiliation(s)
- B Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - D L Holroyd
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - T Pukala
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - J B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
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10
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Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA. Differences in clamp loader mechanism between bacteria and eukaryotes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569468. [PMID: 38076975 PMCID: PMC10705477 DOI: 10.1101/2023.11.30.569468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp, and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader Replication Factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the E. coli clamp loader at high resolution using cryo-electron microscopy (cryo-EM). We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
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Affiliation(s)
- Jacob T. Landeck
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Emily K. Norman
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Emma L. Sedivy
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Brian A. Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
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11
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Avs KR, Pandi C, Kannan B, Pandi A, Jayaseelan VP, Arumugam P. RFC3 serves as a novel prognostic biomarker and target for head and neck squamous cell carcinoma. Clin Oral Investig 2023; 27:6961-6969. [PMID: 37861747 DOI: 10.1007/s00784-023-05316-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVE Head and neck squamous cell carcinoma (HNSCC) is a prevalent cancer that originates from the squamous cells. The role of the replication factor C subunit 3 (RFC3) in HNSCC progression remains elusive. The aim of this study was to uncover RFC3 significance in HNSCC. METHODS The Cancer Genome Atlas (TCGA-HNSCC) dataset was initially used to assess RFC3 expression and its association with HNSCC clinical features. Subsequently, quantitative reverse transcription PCR (RT-qPCR) confirmed RFC3 mRNA expression in oral squamous cell carcinoma (OSCC), a primary HNSCC type. Survival rates were evaluated using the Kaplan-Meier plot, while the Tumor Immune Estimation Resource (TIMER) database probed RFC3-immune cell interaction. Additionally, in silico tools were used to examine the RFC3 protein network and engagement in HNSCC pathways. RESULTS RFC3 expression is significantly upregulated in HNSCC, including OSCC. Upregulated RFC3 expression was significantly correlated with the clinicopathological features of HNSCC, including tumor stage, grade, metastasis, and patient survival. RFC3 is also associated with immune cell infiltration. Functional analysis has highlighted its involvement in DNA replication, mismatch repair, and cell cycle pathways. Interestingly, RFC3 high expression is linked to well-known oncogenic signaling pathways, such as MYC/MYCN, HIPPO, and mTOR. CONCLUSIONS In conclusion, RFC3 can be considered a novel prognostic biomarker for HNSCC, and further studies on its functional mechanisms may help to use RFC3 as a therapeutic target for HNSCC. CLINICAL RELEVANCE The clinical relevance of this study lies in identifying RFC3 as a novel biomarker and prognostic indicator for HNSCC, offering insights that could impact future clinical approaches.
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Affiliation(s)
- Keerthana Reddy Avs
- Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Chandra Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Balachander Kannan
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Anitha Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Vijayashree Priyadharsini Jayaseelan
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Paramasivam Arumugam
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India.
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12
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Park SH, Kim N, Kang N, Ryu E, Lee EA, Ra JS, Gartner A, Kang S, Myung K, Lee KY. Short-range end resection requires ATAD5-mediated PCNA unloading for faithful homologous recombination. Nucleic Acids Res 2023; 51:10519-10535. [PMID: 37739427 PMCID: PMC10602867 DOI: 10.1093/nar/gkad776] [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: 05/11/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Homologous recombination (HR) requires bidirectional end resection initiated by a nick formed close to a DNA double-strand break (DSB), dysregulation favoring error-prone DNA end-joining pathways. Here we investigate the role of the ATAD5, a PCNA unloading protein, in short-range end resection, long-range resection not being affected by ATAD5 deficiency. Rapid PCNA loading onto DNA at DSB sites depends on the RFC PCNA loader complex and MRE11-RAD50-NBS1 nuclease complexes bound to CtIP. Based on our cytological analyses and on an in vitro system for short-range end resection, we propose that PCNA unloading by ATAD5 is required for the completion of short-range resection. Hampering PCNA unloading also leads to failure to remove the KU70/80 complex from the termini of DSBs hindering DNA repair synthesis and the completion of HR. In line with this model, ATAD5-depleted cells are defective for HR, show increased sensitivity to camptothecin, a drug forming protein-DNA adducts, and an augmented dependency on end-joining pathways. Our study highlights the importance of PCNA regulation at DSB for proper end resection and HR.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Namwoo Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Anton Gartner
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Kyoo-young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Korea
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon 24252, Korea
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13
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Shao Z, Yang J, Gao Y, Zhang Y, Zhao X, Shao Q, Zhang W, Cao C, Liu H, Gan J. Structural and functional studies of PCNA from African swine fever virus. J Virol 2023; 97:e0074823. [PMID: 37534905 PMCID: PMC10506467 DOI: 10.1128/jvi.00748-23] [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: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) belongs to the DNA sliding clamp family. Via interacting with various partner proteins, PCNA plays critical roles in DNA replication, DNA repair, chromatin assembly, epigenetic inheritance, chromatin remodeling, and many other fundamental biological processes. Although PCNA and PCNA-interacting partner networks are conserved across species, PCNA of a given species is rarely functional in heterologous systems, emphasizing the importance of more representative PCNA studies. Here, we report two crystal structures of PCNA from African swine fever virus (ASFV), which is the only member of the Asfarviridae family. Compared to the eukaryotic and archaeal PCNAs and the sliding clamp structural homologs from other viruses, AsfvPCNA possesses unique sequences and/or conformations at several regions, such as the J-loop, interdomain-connecting loop (IDCL), P-loop, and C-tail, which are involved in partner recognition or modification of sliding clamps. In addition to double-stranded DNA binding, we also demonstrate that AsfvPCNA can modestly enhance the ligation activity of the AsfvLIG protein. The unique structural features of AsfvPCNA can serve as a potential target for the development of ASFV-specific inhibitors and help combat the deadly virus. IMPORTANCE Two high-resolution crystal structures of African swine fever virus proliferating cell nuclear antigen (AsfvPCNA) are presented here. Structural comparison revealed that AsfvPCNA is unique at several regions, such as the J-loop, the interdomain-connecting loop linker, and the P-loop, which may play important roles in ASFV-specific partner selection of AsfvPCNA. Unlike eukaryotic and archaeal PCNAs, AsfvPCNA possesses high double-stranded DNA-binding affinity. Besides DNA binding, AsfvPCNA can also modestly enhance the ligation activity of the AsfvLIG protein, which is essential for the replication and repair of ASFV genome. The unique structural features make AsfvPCNA a potential target for drug development, which will help combat the deadly virus.
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Affiliation(s)
- Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Zhao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weizhen Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chulei Cao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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14
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Horsfall AJ, Chav T, Pederick JL, Kikhtyak Z, Vandborg BC, Kowalczyk W, Scanlon DB, Tilley WD, Hickey TE, Abell AD, Bruning JB. Designing Fluorescent Nuclear Permeable Peptidomimetics to Target Proliferating Cell Nuclear Antigen. J Med Chem 2023; 66:10354-10363. [PMID: 37489955 DOI: 10.1021/acs.jmedchem.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Human proliferating cell nuclear antigen (PCNA) is a critical mediator of DNA replication and repair, acting as a docking platform for replication proteins. Disrupting these interactions with a peptidomimetic agent presents as a promising avenue to limit proliferation of cancerous cells. Here, a p21-derived peptide was employed as a starting scaffold to design a modular peptidomimetic that interacts with PCNA and is cellular and nuclear permeable. Ultimately, a peptidomimetic was produced which met these criteria, consisting of a fluorescein tag and SV40 nuclear localization signal conjugated to the N-terminus of a p21 macrocycle derivative. Attachment of the fluorescein tag was found to directly affect cellular uptake of the peptidomimetic, with fluorescein being requisite for nuclear permeability. This work provides an important step forward in the development of PCNA targeting peptidomimetics for use as anti-cancer agents or as cancer diagnostics.
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Affiliation(s)
- Aimee J Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Theresa Chav
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bethiney C Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Denis B Scanlon
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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15
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Chen H, Xie H, Zhang Y, Wang G. Construction of a prognostic signature of RFC5 immune-related genes in patients with cervical cancer. Cancer Biomark 2023:CBM220347. [PMID: 37302025 DOI: 10.3233/cbm-220347] [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: 06/12/2023]
Abstract
BACKGROUND Cervical cancer (CC) is a malignant tumor threatening women's health. Replication factor C (RFC) 5 is significantly highly expressed in CC tissues, and the immune microenvironment plays a crucial role in tumor initiation, progression, and metastasis. OBJECTIVE To determine the prognostic role of RFC5 in CC, analyze the immune genes significantly associated with RFC5, and establish a nomogram to evaluate the prognosis of patients with CC. METHODS High RFC5 expression in patients with CC was analyzed and verified through TCGA GEO, TIMER2.0, and HPA databases. A risk score model was constructed using RFC5-related immune genes identified using R packages. Combining the risk score model and clinical information of patients with CC, a nomogram was constructed to evaluate the prognosis of patients with CC. RESULTS Comprehensive analysis showed that the risk score was a prognostic factor for CC. The nomogram could predict the 3-year overall survival of patients with CC. CONCLUSIONS RFC5 was validated as a biomarker for CC. The RFC5 related immune genes were used to establish a new prognostic model of CC.
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Affiliation(s)
- Huaqiu Chen
- School of Clinical Medicine, Dali University, Dali, Yunnan, China
- Xichang People's Hospital, Xichang, Sichuan, China
- Affiliated Hospital of Xichang College, Xichang, Sichuan, China
| | - Huanyu Xie
- Xichang People's Hospital, Xichang, Sichuan, China
- Affiliated Hospital of Xichang College, Xichang, Sichuan, China
| | - Yuanyuan Zhang
- School of Clinical Medicine, Dali University, Dali, Yunnan, China
| | - Guangming Wang
- School of Clinical Medicine, Dali University, Dali, Yunnan, China
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16
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Bhandari SK, Wiest N, Sallmyr A, Du R, Ferry L, Defossez PA, Tomkinson AE. Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1. Sci Rep 2023; 13:4363. [PMID: 36928068 PMCID: PMC10020546 DOI: 10.1038/s41598-023-31367-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol δ. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIα (LigIIIα)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol ε, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIα/XRCC1 and Pol δ at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is enriched in the chromatin of LigI-deficient mouse CH12F3 and human 46BR.1G1 cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a relatively stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome.
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Affiliation(s)
- Seema Khattri Bhandari
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nathaniel Wiest
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Annahita Sallmyr
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ruofei Du
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Laure Ferry
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, 750013, Paris, France
| | | | - Alan E Tomkinson
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
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17
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Welter AL, Machida YJ. Functions and evolution of FAM111 serine proteases. Front Mol Biosci 2022; 9:1081166. [PMID: 36589246 PMCID: PMC9798293 DOI: 10.3389/fmolb.2022.1081166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Proteolysis plays fundamental and regulatory roles in diverse cellular processes. The serine protease FAM111A (FAM111 trypsin-like peptidase A) emerged recently as a protease involved in two seemingly distinct processes: DNA replication and antiviral defense. FAM111A localizes to nascent DNA and plays a role at the DNA replication fork. At the fork, FAM111A is hypothesized to promote DNA replication at DNA-protein crosslinks (DPCs) and protein obstacles. On the other hand, FAM111A has also been identified as a host restriction factor for mutants of SV40 and orthopoxviruses. FAM111A also has a paralog, FAM111B, a serine protease with unknown cellular functions. Furthermore, heterozygous missense mutations in FAM111A and FAM111B cause distinct genetic disorders. In this review, we discuss possible models that could explain how FAM111A can function as a protease in both DNA replication and antiviral defense. We also review the consequences of FAM111A and FAM111B mutations and explore possible mechanisms underlying the diseases. Additionally, we propose a possible explanation for what drove the evolution of FAM111 proteins and discuss why some species have two FAM111 proteases. Altogether, studies of FAM111 proteases in DNA repair, antiviral defense, and genetic diseases will help us elucidate their functions and the regulatory mechanisms.
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Affiliation(s)
- Allison L. Welter
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States,Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Yuichi J. Machida
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States,*Correspondence: Yuichi J. Machida,
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18
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Thakar T, Dhoonmoon A, Straka J, Schleicher EM, Nicolae CM, Moldovan GL. Lagging strand gap suppression connects BRCA-mediated fork protection to nucleosome assembly through PCNA-dependent CAF-1 recycling. Nat Commun 2022; 13:5323. [PMID: 36085347 PMCID: PMC9463168 DOI: 10.1038/s41467-022-33028-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The inability to protect stalled replication forks from nucleolytic degradation drives genome instability and underlies chemosensitivity in BRCA-deficient tumors. An emerging hallmark of BRCA-deficiency is the inability to suppress replication-associated single-stranded DNA (ssDNA) gaps. Here, we report that lagging strand ssDNA gaps interfere with the ASF1-CAF-1 nucleosome assembly pathway, and drive fork degradation in BRCA-deficient cells. We show that CAF-1 function at replication forks is lost in BRCA-deficient cells, due to defects in its recycling during replication stress. This CAF-1 recycling defect is caused by lagging strand gaps which preclude PCNA unloading, causing sequestration of PCNA-CAF-1 complexes on chromatin. Importantly, correcting PCNA unloading defects in BRCA-deficient cells restores CAF-1-dependent fork stability. We further show that the activation of a HIRA-dependent compensatory histone deposition pathway restores fork stability to BRCA-deficient cells. We thus define lagging strand gap suppression and nucleosome assembly as critical enablers of BRCA-mediated fork stability. Efficient DNA replication is crucial for genome stability. Here, Thakar et al. report that accumulation of lagging strand ssDNA gaps during replication interferes with nucleosome assembly and drives replication fork degradation in BRCA-deficient cells.
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Affiliation(s)
- Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Joshua Straka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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19
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Wei L, Cafiero TR, Tseng A, Gertje HP, Berneshawi A, Crossland NA, Ploss A. Conversion of hepatitis B virus relaxed circular to covalently closed circular DNA is supported in murine cells. JHEP Rep 2022; 4:100534. [PMID: 36035363 PMCID: PMC9403495 DOI: 10.1016/j.jhepr.2022.100534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/26/2022] [Accepted: 07/04/2022] [Indexed: 11/05/2022] Open
Abstract
Background & Aims HBV has a narrow host restriction, with humans and chimpanzees representing the only known natural hosts. The molecular correlates of resistance in species that are commonly used in biomedical research, such as mice, are currently incompletely understood. Expression of human NTCP (hNTCP) in mouse hepatocytes enables HBV entry, but subsequently covalently closed circular (cccDNA) does not form in most murine cells. It is unknown if this blockade in cccDNA formation is due to deficiency in repair of relaxed circular DNA (rcDNA) to cccDNA. Methods Here, we deployed both in vivo and in vitro virological and biochemical approaches to investigate if murine cells contain a complete set of repair factors capable of converting HBV rcDNA to cccDNA. Results We demonstrate that HBV cccDNA does form in murine cell culture or in mice when recombinant rcDNA without a protein adduct is directly introduced into cells. We further show that the murine orthologues of core components in DNA lagging strand synthesis, required for the repair of rcDNA to cccDNA in human cells, can support this crucial step in the HBV life cycle. It is worth noting that recombinant HBV rcDNA substrates, either without a protein adduct or containing neutravidin to mimic HBV polymerase, were used in our study; it remains unclear if the HBV polymerase removal processes are the same in mouse and human cells. Conclusions Collectively, our data suggest that the HBV life cycle is blocked post entry and likely before the repair stage in mouse cells, which yields critical insights that will aid in the construction of a mouse model with inbred susceptibility to HBV infection. Lay summary Hepatitis B virus (HBV) is only known to infect humans and chimpanzees in nature. Mouse models are often used in modeling disease pathogenesis and preclinical research to assess the efficacy and safety of interventions before they are then tested in human participants. However, because mice are not susceptible to HBV infection it is difficult to accurately model human infection (and test potential treatments) in mouse models. Herein, we have shown that mice are able to perform a key step in the HBV life cycle, tightening the net around the possible reason why HBV can not efficiently infect and replicate in mice.
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Key Words
- FEN-1, flap endonuclease 1
- HCC, hepatocellular carcinoma
- HDD, hydrodynamic delivery
- LIG1, DNA ligase 1
- NA-RrcDNA, neutravidin-recombinant relaxed circular DNA
- PCNA, proliferating cell nuclear antigen
- POLδ, DNA polymerase delta
- RFC, replication factor C
- RrcDNA, recombinant relaxed circular DNA
- animal model
- cccDNA, covalently closed circular DNA
- hNTCP, human sodium taurocholate co-transporting polypeptide
- hepatitis B virus
- rcDNA, relaxed circular DNA
- species tropism
- ssDNA, single-stranded DNA
- viral hepatitis
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Affiliation(s)
- Lei Wei
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Thomas R Cafiero
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Anna Tseng
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Andrew Berneshawi
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Alexander Ploss
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ, 08544, USA
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20
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Day M, Oliver AW, Pearl LH. Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction. Nucleic Acids Res 2022; 50:8279-8289. [PMID: 35819203 PMCID: PMC9371934 DOI: 10.1093/nar/gkac588] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5'-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5' DNA end and fixes the orientation of 9-1-1 on the ssDNA.
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Affiliation(s)
- Matthew Day
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW1E 6BT, UK
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21
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Liu X, Gaubitz C, Pajak J, Kelch BA. A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA. eLife 2022; 11:77483. [PMID: 35731107 PMCID: PMC9293009 DOI: 10.7554/elife.77483] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Clamp loaders place circular sliding clamp proteins onto DNA so that clamp-binding partner proteins can synthesize, scan, and repair the genome. DNA with nicks or small single-stranded gaps are common clamp-loading targets in DNA repair, yet these substrates would be sterically blocked given the known mechanism for binding of primer-template DNA. Here, we report the discovery of a second DNA binding site in the yeast clamp loader replication factor C (RFC) that aids in binding to nicked or gapped DNA. This DNA binding site is on the external surface and is only accessible in the open conformation of RFC. Initial DNA binding at this site thus provides access to the primary DNA binding site in the central chamber. Furthermore, we identify that this site can partially unwind DNA to create an extended single-stranded gap for DNA binding in RFC’s central chamber and subsequent ATPase activation. Finally, we show that deletion of the BRCT domain, a major component of the external DNA binding site, results in defective yeast growth in the presence of DNA damage where nicked or gapped DNA intermediates occur. We propose that RFC’s external DNA binding site acts to enhance DNA binding and clamp loading, particularly at DNA architectures typically found in DNA repair.
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Affiliation(s)
- Xingchen Liu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Christl Gaubitz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
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22
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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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23
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Cui K, Qin L, Tang X, Nong J, Chen J, Wu N, Gong X, Yi L, Yang C, Xia S. A Single Amino Acid Substitution in RFC4 Leads to Endoduplication and Compromised Resistance to DNA Damage in Arabidopsis thaliana. Genes (Basel) 2022; 13:genes13061037. [PMID: 35741798 PMCID: PMC9223238 DOI: 10.3390/genes13061037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Replication factor C (RFC) is a heteropentameric ATPase associated with the diverse cellular activities (AAA+ATPase) protein complex, which is composed of one large subunit, known as RFC1, and four small subunits, RFC2/3/4/5. Among them, RFC1 and RFC3 were previously reported to mediate genomic stability and resistance to pathogens in Arabidopsis. Here, we generated a viable rfc4e (rfc4-1/RFC4G54E) mutant with a single amino acid substitution by site-directed mutagenesis. Three of six positive T2 mutants with the same amino acid substitution, but different insertion loci, were sequenced to identify homozygotes, and the three homozygote mutants showed dwarfism, early flowering, and a partially sterile phenotype. RNA sequencing revealed that genes related to DNA repair and replication were highly upregulated. Moreover, the frequency of DNA lesions was found to be increased in rfc4e mutants. Consistent with this, the rfc4e mutants were very sensitive to DSB-inducing genotoxic agents. In addition, the G54E amino acid substitution in AtRFC4 delayed cell cycle progression and led to endoduplication. Overall, our study provides evidence supporting the notion that RFC4 plays an important role in resistance to genotoxicity and cell proliferation by regulating DNA damage repair in Arabidopsis thaliana.
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Affiliation(s)
- Kan Cui
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Jieying Nong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Jin Chen
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (J.C.); (L.Y.)
- Changsha Technology Innovation Center for Phytoremediation of Heavy Metal Contaminated Soil, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Nan Wu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Xin Gong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Lixiong Yi
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (J.C.); (L.Y.)
| | - Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
- Correspondence:
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24
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Bhardwaj VK, Purohit R. A lesson for the maestro of the replication fork: Targeting the protein-binding interface of proliferating cell nuclear antigen for anticancer therapy. J Cell Biochem 2022; 123:1091-1102. [PMID: 35486518 DOI: 10.1002/jcb.30265] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022]
Abstract
The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA replication that regulates a diverse range of cellular functions and pathways through a comprehensive list of protein-protein interactions. The hydrophobic binding pocket on PCNA offers an opportunity for the development of inhibitors to target various types of cancers and modulate protein-protein interactions. In the present study, we explored the binding modes and affinity of molecule I1 (standard molecule) with the previously suggested dimer interface pocket and the hydrophobic pocket present on the frontal side of the PCNA monomer. We also identified potential lead molecules from the library of in-house synthesized 3-methylenisoindolin-1-one based molecules to inhibit the protein-protein interactions of PCNA. Our results were based on robust computational methods, including molecular docking, conventional, steered, and umbrella sampling molecular dynamics simulations. Our results suggested that the standard inhibitor I1 interacts with the hydrophobic pocket of PCNA with a higher affinity than the previously suggested binding site. Also, the proposed molecules showed better or comparable binding free energies as calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach and further validated by enhanced umbrella sampling simulations. In vitro and in vivo methods could test the computationally suggested molecules for advancement in the drug discovery pipeline.
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Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Division of Biotechnology, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Division of Biotechnology, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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25
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Wu G, Zhou J, Zhu X, Tang X, Liu J, Zhou Q, Chen Z, Liu T, Wang W, Xiao X, Wu T. Integrative analysis of expression, prognostic significance and immune infiltration of RFC family genes in human sarcoma. Aging (Albany NY) 2022; 14:3705-3719. [PMID: 35483337 PMCID: PMC9085243 DOI: 10.18632/aging.204039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/13/2022] [Indexed: 11/25/2022]
Abstract
Objective: To reveal the expression and prognostic value of replication factor C family genes (RFCs) in patients with sarcoma. Results: The results showed that the mRNA expression levels of RFC2, RFC3, RFC4, and RFC5 were increased in sarcoma tissues. In addition, Cancer Cell Line Encyclopedia (CCLE) dataset analysis indicated that RFC1, RFC2, RFC3, RFC4, and RFC5 were elevated expressed in sarcoma cell lines. Moreover, Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan-Meier Plotter showed that highly expressed RFC2-5 were associated with poor overall survival (OS) or relapse-free survival (RFS) in sarcoma patients. The results of the Tumor Immune Estimation Resource (TIMER) database indicated that the expression of RFCs was negatively correlated with the infiltration of CD4+ T cells and macrophages. Conclusions: There were significant differences in the expression of RFCs between normal tissue and sarcoma tissue, and RFC2, RFC3, RFC4, and RFC5 might be promising prognostic biomarkers for sarcoma. Methods: The expression of RFCs was analyzed using the ONCOMINE dataset and GEPIA dataset. CCLE dataset was used to assess the expression of RFCs in the cancer cell line. The prognostic value of RFCs was evaluated by GEPIA and Kaplan-Meier analysis. Furthermore, the association between RFCs and their co-expressed genes were explored via ONCOMINE and GEPIA datasets. We used the TIMER dataset to analyze the immune cell infiltration of RFCs in sarcoma.
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Affiliation(s)
- Gen Wu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.,Clinical Medicine Eight-Year Program, 02 Class, 2014 Grade, Central South University, Changsha 410013, Hunan Province, China
| | - Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Xi Zhu
- Department of Internal Medicine III, University Hospital, Ludwig Maximilian University, Munich 81377, Germany
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou No.1 People's Hospital, Chenzhou 423000, Hunan, China
| | - Jie Liu
- Department of Cardiology, The Fourth Hospital of Changsha, Changsha 410006, Hunan, China
| | - Qiong Zhou
- Department of Cardiology, The Fourth Hospital of Changsha, Changsha 410006, Hunan, China
| | - Ziyuan Chen
- Department of Orthopedics, The First People's Hospital of Changde City, Changde 415003, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Xungang Xiao
- Department of Orthopedics, Chenzhou No.1 People's Hospital, Chenzhou 423000, Hunan, China
| | - Tong Wu
- Department of Emergency, The First Hospital of Changsha, Changsha 410005, Hunan, China
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26
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Hou K, Yu Y, Li D, Zhang Y, Zhang K, Tong J, Yang K, Jia S. Alternative Lengthening of Telomeres and Mediated Telomere Synthesis. Cancers (Basel) 2022; 14:cancers14092194. [PMID: 35565323 PMCID: PMC9105334 DOI: 10.3390/cancers14092194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Alternative lengthing of telomere (ALT) is an important mechanism for maintaining telomere length and cell proliferation in telomerase-negative tumor cells. However, the molecular mechanism of ALT is still poorly understood. ALT occurs in a wide range of tumor types and usually associated with a worse clinical consequence. Here, we review the recent findings of ALT mechanisms, which promise ALT could be a valuable drug target for clinical telomerase-negative tumor treatment. Abstract Telomeres are DNA–protein complexes that protect eukaryotic chromosome ends from being erroneously repaired by the DNA damage repair system, and the length of telomeres indicates the replicative potential of the cell. Telomeres shorten during each division of the cell, resulting in telomeric damage and replicative senescence. Tumor cells tend to ensure cell proliferation potential and genomic stability by activating telomere maintenance mechanisms (TMMs) for telomere lengthening. The alternative lengthening of telomeres (ALT) pathway is the most frequently activated TMM in tumors of mesenchymal and neuroepithelial origin, and ALT also frequently occurs during experimental cellular immortalization of mesenchymal cells. ALT is a process that relies on homologous recombination (HR) to elongate telomeres. However, some processes in the ALT mechanism remain poorly understood. Here, we review the most recent understanding of ALT mechanisms and processes, which may help us to better understand how the ALT pathway is activated in cancer cells and determine the potential therapeutic targets in ALT pathway-stabilized tumors.
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Affiliation(s)
- Kailong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China;
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
| | - Yuyang Yu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Duda Li
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Yanduo Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Ke Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Jinkai Tong
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Kunxian Yang
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
- Correspondence: (K.Y.); (S.J.)
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- Correspondence: (K.Y.); (S.J.)
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27
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The partner-swapping sliding clamp loader exposed. Nat Struct Mol Biol 2022; 29:283-286. [PMID: 35410371 DOI: 10.1038/s41594-022-00761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Zhang Y, Chen Q, Zhu G, Zhang D, Liang W. Chromatin-remodeling factor CHR721 with non-canonical PIP-box interacts with OsPCNA in Rice. BMC PLANT BIOLOGY 2022; 22:164. [PMID: 35365089 PMCID: PMC8974069 DOI: 10.1186/s12870-022-03532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Proliferating cell nuclear antigen (PCNA) is one of the key factors for the DNA replication process and DNA damage repair. Most proteins interacting with PCNA have a common binding motif: PCNA interacting protein box (PIP box). However, some proteins with non-canonical PIP-box have also been reported to be the key factors that interacted with PCNA. RESULTS Here we discovered the C terminal of a chromatin-remodeling factor CHR721 with non-canonical PIP-box was essential for interacting with OsPCNA in rice. Both OsPCNA and CHR721 were localized in the nuclei and function in response to DNA damages. CONCLUSIONS Based on the results and previous work, we proposed a working model that CHR721 with non-canonical PIP-box interacted with OsPCNA and both of them probably participate in the DNA damage repair process.
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Affiliation(s)
- Yushun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China.
| | - Qiong Chen
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Guanlin Zhu
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Beijing, 100101, China
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, Hubei, 443002, China
| | - Weihong Liang
- College of Life Sciences, Henan Normal University, Xinxiang, China.
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29
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Gaubitz C, Liu X, Pajak J, Stone NP, Hayes JA, Demo G, Kelch BA. Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader. eLife 2022; 11:74175. [PMID: 35179493 PMCID: PMC8893722 DOI: 10.7554/elife.74175] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Sliding clamps are ring-shaped protein complexes that are integral to the DNA replication machinery of all life. Sliding clamps are opened and installed onto DNA by clamp loader AAA+ ATPase complexes. However, how a clamp loader opens and closes the sliding clamp around DNA is still unknown. Here, we describe structures of the Saccharomyces cerevisiae clamp loader Replication Factor C (RFC) bound to its cognate sliding clamp Proliferating Cell Nuclear Antigen (PCNA) en route to successful loading. RFC first binds to PCNA in a dynamic, closed conformation that blocks both ATPase activity and DNA binding. RFC then opens the PCNA ring through a large-scale ‘crab-claw’ expansion of both RFC and PCNA that explains how RFC prefers initial binding of PCNA over DNA. Next, the open RFC:PCNA complex binds DNA and interrogates the primer-template junction using a surprising base-flipping mechanism. Our structures indicate that initial PCNA opening and subsequent closure around DNA do not require ATP hydrolysis, but are driven by binding energy. ATP hydrolysis, which is necessary for RFC release, is triggered by interactions with both PCNA and DNA, explaining RFC’s switch-like ATPase activity. Our work reveals how a AAA+ machine undergoes dramatic conformational changes for achieving binding preference and substrate remodeling.
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Affiliation(s)
- Christl Gaubitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Xingchen Liu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Joshua Pajak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Nicholas P Stone
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Janelle A Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Gabriel Demo
- Central European Institute of Technology - Masaryk University, Brno, Czech Republic
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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30
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Park SH, Kim Y, Ra JS, Wie MW, Kang MS, Kang S, Myung K, Lee KY. Timely termination of repair DNA synthesis by ATAD5 is important in oxidative DNA damage-induced single-strand break repair. Nucleic Acids Res 2021; 49:11746-11764. [PMID: 34718749 PMCID: PMC8599757 DOI: 10.1093/nar/gkab999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) generate oxidized bases and single-strand breaks (SSBs), which are fixed by base excision repair (BER) and SSB repair (SSBR), respectively. Although excision and repair of damaged bases have been extensively studied, the function of the sliding clamp, proliferating cell nuclear antigen (PCNA), including loading/unloading, remains unclear. We report that, in addition to PCNA loading by replication factor complex C (RFC), timely PCNA unloading by the ATPase family AAA domain-containing protein 5 (ATAD5)-RFC-like complex is important for the repair of ROS-induced SSBs. We found that PCNA was loaded at hydrogen peroxide (H2O2)-generated direct SSBs after the 3'-terminus was converted to the hydroxyl moiety by end-processing enzymes. However, PCNA loading rarely occurred during BER of oxidized or alkylated bases. ATAD5-depleted cells were sensitive to acute H2O2 treatment but not methyl methanesulfonate treatment. Unexpectedly, when PCNA remained on DNA as a result of ATAD5 depletion, H2O2-induced repair DNA synthesis increased in cancerous and normal cells. Based on higher H2O2-induced DNA breakage and SSBR protein enrichment by ATAD5 depletion, we propose that extended repair DNA synthesis increases the likelihood of DNA polymerase stalling, shown by increased PCNA monoubiquitination, and consequently, harmful nick structures are more frequent.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Youyoung Kim
- 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 (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Min Woo Wie
- 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 (UNIST), Ulsan 44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), 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 (UNIST), Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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31
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PCNA Loaders and Unloaders-One Ring That Rules Them All. Genes (Basel) 2021; 12:genes12111812. [PMID: 34828416 PMCID: PMC8618651 DOI: 10.3390/genes12111812] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
During each cell duplication, the entirety of the genomic DNA in every cell must be accurately and quickly copied. Given the short time available for the chore, the requirement of many proteins, and the daunting amount of DNA present, DNA replication poses a serious challenge to the cell. A high level of coordination between polymerases and other DNA and chromatin-interacting proteins is vital to complete this task. One of the most important proteins for maintaining such coordination is PCNA. PCNA is a multitasking protein that forms a homotrimeric ring that encircles the DNA. It serves as a processivity factor for DNA polymerases and acts as a landing platform for different proteins interacting with DNA and chromatin. Therefore, PCNA is a signaling hub that influences the rate and accuracy of DNA replication, regulates DNA damage repair, controls chromatin formation during the replication, and the proper segregation of the sister chromatids. With so many essential roles, PCNA recruitment and turnover on the chromatin is of utmost importance. Three different, conserved protein complexes are in charge of loading/unloading PCNA onto DNA. Replication factor C (RFC) is the canonical complex in charge of loading PCNA during the S-phase. The Ctf18 and Elg1 (ATAD5 in mammalian) proteins form complexes similar to RFC, with particular functions in the cell’s nucleus. Here we summarize our current knowledge about the roles of these important factors in yeast and mammals.
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32
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Abramzon Y, Dewan R, Cortese A, Resnick S, Ferrucci L, Houlden H, Traynor BJ. Investigating RFC1 expansions in sporadic amyotrophic lateral sclerosis. J Neurol Sci 2021; 430:118061. [PMID: 34537679 DOI: 10.1016/j.jns.2021.118061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
A homozygous AAGGG repeat expansion within the RFC1 gene was recently described as a common cause of CANVAS syndrome. We examined 1069 sporadic ALS patients for the presence of this repeat expansion. We did not discover any carriers of the homozygous AAGGG expansion in our ALS cohort, indicating that this form of RFC1 repeat expansions is not a common cause of sporadic ALS. However, our study did identify a novel repeat conformation and further expanded on the highly polymorphic nature of the RFC1 locus.
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Affiliation(s)
- Yevgenya Abramzon
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London WC1N 1PJ, UK.
| | - Ramita Dewan
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Andrea Cortese
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Susan Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London WC1N 1PJ, UK; Neurology Department, Johns Hopkins University, Baltimore, MD 21205, USA
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Park SH, Kim SJ, Myung K, Lee KY. Characterization of subcellular localization of eukaryotic clamp loader/unloader and its regulatory mechanism. Sci Rep 2021; 11:21817. [PMID: 34751190 PMCID: PMC8575788 DOI: 10.1038/s41598-021-01336-w] [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: 05/18/2021] [Accepted: 10/13/2021] [Indexed: 11/27/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) plays a critical role as a processivity clamp for eukaryotic DNA polymerases and a binding platform for many DNA replication and repair proteins. The enzymatic activities of PCNA loading and unloading have been studied extensively in vitro. However, the subcellular locations of PCNA loaders, replication complex C (RFC) and CTF18-RFC-like-complex (RLC), and PCNA unloader ATAD5-RLC remain elusive, and the role of their subunits RFC2-5 is unknown. Here we used protein fractionation to determine the subcellular localization of RFC and RLCs and affinity purification to find molecular requirements for the newly defined location. All RFC/RLC proteins were detected in the nuclease-resistant pellet fraction. RFC1 and ATAD5 were not detected in the non-ionic detergent-soluble and nuclease-susceptible chromatin fractions, independent of cell cycle or exogenous DNA damage. We found that small RFC proteins contribute to maintaining protein levels of the RFC/RLCs. RFC1, ATAD5, and RFC4 co-immunoprecipitated with lamina-associated polypeptide 2 (LAP2) α which regulates intranuclear lamin A/C. LAP2α knockout consistently reduced detection of RFC/RLCs in the pellet fraction, while marginally affecting total protein levels. Our findings strongly suggest that PCNA-mediated DNA transaction occurs through regulatory machinery associated with nuclear structures, such as the nuclear matrix.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Korea
| | - Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Korea.
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34
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Dragašević-Mišković N, Stanković I, Milovanović A, Kostić VS. Autosomal recessive adult onset ataxia. J Neurol 2021; 269:504-533. [PMID: 34499204 DOI: 10.1007/s00415-021-10763-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]
Abstract
Autosomal recessive ataxias (ARCA) represent a complex group of diseases ranging from primary ataxias to rare and complex metabolic disorders in which ataxia is a part of the clinical picture. Small number of ARCA manifest exclusively in adulthood, while majority of typical childhood onset ARCA may also start later with atypical clinical presentation. We have systematically searched the literature for ARCA with adult onset, both in the group of primary ataxias including those that are less frequently described in isolated or in a small number of families, and also in the group of complex and metabolic diseases in which ataxia is only part of the clinical picture. We propose an algorithm that could be used when encountering a patient with adult onset sporadic or recessive ataxia in whom the acquired causes are excluded. ARCA are frequently neglected in the differential diagnosis of adult-onset ataxias. Rising awareness of their clinical significance is important, not only because some of these disorders may be potentially treatable, but also for prognostic implications and inclusion of patients to future clinical trials with disease modifying agents.
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Affiliation(s)
- Nataša Dragašević-Mišković
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia.
| | - Iva Stanković
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia
| | - Andona Milovanović
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia
| | - Vladimir S Kostić
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia
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35
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Wei L, Ploss A. Mechanism of Hepatitis B Virus cccDNA Formation. Viruses 2021; 13:v13081463. [PMID: 34452329 PMCID: PMC8402782 DOI: 10.3390/v13081463] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) remains a major medical problem affecting at least 257 million chronically infected patients who are at risk of developing serious, frequently fatal liver diseases. HBV is a small, partially double-stranded DNA virus that goes through an intricate replication cycle in its native cellular environment: human hepatocytes. A critical step in the viral life-cycle is the conversion of relaxed circular DNA (rcDNA) into covalently closed circular DNA (cccDNA), the latter being the major template for HBV gene transcription. For this conversion, HBV relies on multiple host factors, as enzymes capable of catalyzing the relevant reactions are not encoded in the viral genome. Combinations of genetic and biochemical approaches have produced findings that provide a more holistic picture of the complex mechanism of HBV cccDNA formation. Here, we review some of these studies that have helped to provide a comprehensive picture of rcDNA to cccDNA conversion. Mechanistic insights into this critical step for HBV persistence hold the key for devising new therapies that will lead not only to viral suppression but to a cure.
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36
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PCNA inhibition enhances the cytotoxicity of β-lapachone in NQO1-Positive cancer cells by augmentation of oxidative stress-induced DNA damage. Cancer Lett 2021; 519:304-314. [PMID: 34329742 DOI: 10.1016/j.canlet.2021.07.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 12/25/2022]
Abstract
β-Lapachone is a classic quinone-containing antitumor NQO1-bioactivatable drug that directly kills NQO1-overexpressing cancer cells. However, the clinical applications of β-lapachone are primarily limited by its high toxicity and modest lethality. To overcome this side effect and expand the therapeutic utility of β-lapachone, we demonstrate the effects of a novel combination therapy including β-lapachone and the proliferating cell nuclear antigen (PCNA) inhibitor T2 amino alcohol (T2AA) on various NQO1+ cancer cells. PCNA has DNA clamp processivity activity mediated by encircling double-stranded DNA to recruit proteins involved in DNA replication and DNA repair. In this study, we found that compared to monotherapy, a nontoxic dose of the T2AA synergized with a sublethal dose of β-lapachone in an NQO1-dependent manner and that combination therapy prevented DNA repair, increased double-strand break (DSB) formation and promoted programmed necrosis and G1 phase cell cycle arrest. We further determined that combination therapy enhanced antitumor efficacy and prolonged survival in Lewis lung carcinoma (LLC) xenografts model. Our findings show novel evidence for a new therapeutic approach that combines of β-lapachone treatment with PCNA inhibition that is highly effective in treating NQO1+ solid tumor cells.
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37
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Su J, Xu R, Mongia P, Toyofuku N, Nakagawa T. Fission yeast Rad8/HLTF facilitates Rad52-dependent chromosomal rearrangements through PCNA lysine 107 ubiquitination. PLoS Genet 2021; 17:e1009671. [PMID: 34292936 PMCID: PMC8297803 DOI: 10.1371/journal.pgen.1009671] [Citation(s) in RCA: 3] [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: 03/11/2021] [Accepted: 06/18/2021] [Indexed: 11/19/2022] Open
Abstract
Gross chromosomal rearrangements (GCRs), including translocation, deletion, and inversion, can cause cell death and genetic diseases such as cancer in multicellular organisms. Rad51, a DNA strand exchange protein, suppresses GCRs by repairing spontaneous DNA damage through a conservative way of homologous recombination, gene conversion. On the other hand, Rad52 that catalyzes single-strand annealing (SSA) causes GCRs using homologous sequences. However, the detailed mechanism of Rad52-dependent GCRs remains unclear. Here, we provide genetic evidence that fission yeast Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) of PCNA, a DNA sliding clamp. In rad51Δ cells, loss of Rad8 eliminated 75% of the isochromosomes resulting from centromere inverted repeat recombination, showing that Rad8 is essential for the formation of the majority of isochromosomes in rad51Δ cells. Rad8 HIRAN and RING finger mutations reduced GCRs, suggesting that Rad8 facilitates GCRs through 3’ DNA-end binding and ubiquitin ligase activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating enzymes were required for GCRs. Consistent with this, mutating PCNA K107 rather than the well-studied PCNA K164 reduced GCRs. Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, rad8, and rad52 mutations epistatically reduced GCRs. In contrast to GCRs, PCNA K107R did not significantly change gene conversion rates, suggesting a specific role of PCNA K107 ubiquitination in GCRs. PCNA K107R enhanced temperature-sensitive growth defects of DNA ligase I cdc17-K42 mutant, implying that PCNA K107 ubiquitination occurs when Okazaki fragment maturation fails. Remarkably, K107 is located at the interface between PCNA subunits, and an interface mutation D150E bypassed the requirement of PCNA K107 and Rad8 ubiquitin ligase for GCRs. These data suggest that Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs by changing the PCNA clamp structure. Gross chromosomal rearrangements (GCRs), including translocation, can alter gene dosage and activity, resulting in genetic diseases such as cancer. However, GCRs can occur by some enzymes, including Rad52 recombinase, and result in chromosomal evolution. Therefore, GCRs are not only pathological but also physiological phenomena from an evolutionary point of view. However, the detailed mechanism of GCRs remains unclear. Here, using fission yeast, we show that the homolog of human HLTF, Rad8 causes GCRs through noncanonical ubiquitination of proliferating cellular nuclear antigen (PCNA) at a lysine 107 (K107). Rad51, a DNA strand exchange protein, suppresses the formation of isochromosomes whose arms mirror each another and chromosomal truncation. We found that, like Rad52, Rad8 is required for isochromosome formation but not chromosomal truncation in rad51Δ cells, showing a specific role of Rad8 in homology-mediated GCRs. Mutations in Rad8 ubiquitin E3 ligase RING finger domain, Mms2-Ubc4 ubiquitin-conjugating enzymes, and PCNA K107 reduced GCRs in rad51Δ cells, suggesting that Rad8-Mms2-Ubc4-dependent PCNA K107 ubiquitination facilitates GCRs. PCNA trimers form a DNA sliding clamp. The K107 residue is located at the PCNA-PCNA interface, and an interface mutation D150E restored GCRs in PCNA K107R mutant cells. This study provides genetic evidence that Rad8-dependent PCNA K107 ubiquitination facilitates GCRs by changing the PCNA clamp structure.
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Affiliation(s)
- Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Piyusha Mongia
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
- * E-mail:
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38
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Tu S, Zhang H, Yang X, Wen W, Song K, Yu X, Qu X. Screening of cervical cancer-related hub genes based on comprehensive bioinformatics analysis. Cancer Biomark 2021; 32:303-315. [PMID: 34151839 DOI: 10.3233/cbm-203262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Since the molecular mechanisms of cervical cancer (CC) have not been completely discovered, it is of great significance to identify the hub genes and pathways of this disease to reveal the molecular mechanisms of cervical cancer. OBJECTIVE The study aimed to identify the biological functions and prognostic value of hub genes in cervical cancer. METHODS The gene expression data of CC patients were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. The core genes were screened out by differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). R software, the STRING online tool and Cytoscape software were used to screen out the hub genes. The GEPIA public database was used to further verify the expression levels of the hub genes in normal tissues and tumour tissues and determine the disease-free survival (DFS) rates of the hub genes. The protein expression of the survival-related hub genes was identified with the Human Protein Atlas (HPA) database. RESULTS A total of 64 core genes were screened, and 10 genes, including RFC5, POLE3, RAD51, RMI1, PALB2, HDAC1, MCM4, ESR1, FOS and E2F1, were identified as hub genes. Compared with that in normal tissues, RFC5, POLE3, RAD51,RMI1, PALB2, MCM4 and E2F1 were all significantly upregulated in cervical cancer, ESR1 was significantly downregulated in cervical cancer, and RFC5 expression in CC patients was significantly related to OS. In the DFS analysis, no significant difference was observed in the expression level of RFC5 in cervical cancer patients. Finally, RFC5 protein levels verified by the HPA database were consistently upregulated with mRNA levels in CC samples. CONCLUSIONS RFC5 may play important roles in the occurrence and prognosis of CC. It could be further explored and validated as a potential predictor and therapeutic target for CC.
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Horsfall AJ, Vandborg BA, Kowalczyk W, Chav T, Scanlon DB, Abell AD, Bruning JB. Unlocking the PIP-box: A peptide library reveals interactions that drive high-affinity binding to human PCNA. J Biol Chem 2021; 296:100773. [PMID: 33984330 PMCID: PMC8191301 DOI: 10.1016/j.jbc.2021.100773] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/02/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022] Open
Abstract
The human sliding clamp, Proliferating Cell Nuclear Antigen (hPCNA), interacts with over 200 proteins through a conserved binding motif, the PIP-box, to orchestrate DNA replication and repair. It is not clear how changes to the features of a PIP-box modulate protein binding and thus how they fine-tune downstream processes. Here, we present a systematic study of each position within the PIP-box to reveal how hPCNA-interacting peptides bind with drastically varied affinities. We synthesized a series of 27 peptides derived from the native protein p21 with small PIP-box modifications and another series of 19 peptides containing PIP-box binding motifs from other proteins. The hPCNA-binding affinity of all peptides, characterized as KD values determined by surface plasmon resonance, spanned a 4000-fold range, from 1.83 nM to 7.59 μM. The hPCNA-bound peptide structures determined by X-ray crystallography and modeled computationally revealed intermolecular and intramolecular interaction networks that correlate with high hPCNA affinity. These data informed rational design of three new PIP-box sequences, testing of which revealed the highest affinity hPCNA-binding partner to date, with a KD value of 1.12 nM, from a peptide with PIP-box QTRITEYF. This work showcases the sequence-specific nuances within the PIP-box that are responsible for high-affinity hPCNA binding, which underpins our understanding of how nature tunes hPCNA affinity to regulate DNA replication and repair processes. In addition, these insights will be useful to future design of hPCNA inhibitors.
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Affiliation(s)
- Aimee J Horsfall
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Beth A Vandborg
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Theresa Chav
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Denis B Scanlon
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - John B Bruning
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
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40
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Gray S, Santiago ER, Chappie JS, Cohen PE. Cyclin N-Terminal Domain-Containing-1 Coordinates Meiotic Crossover Formation with Cell-Cycle Progression in a Cyclin-Independent Manner. Cell Rep 2021; 32:107858. [PMID: 32640224 PMCID: PMC7341696 DOI: 10.1016/j.celrep.2020.107858] [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: 11/25/2019] [Revised: 05/14/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
During mammalian meiotic prophase I, programmed DNA double-strand breaks are repaired by non-crossover or crossover events, the latter predominantly occurring via the class I crossover pathway and requiring the cyclin N-terminal domain-containing 1(CNTD1) protein. Using an epitope-tagged Cntd1 allele, we detect a short isoform of CNTD1 in vivo that lacks a predicted N-terminal cyclin domain and does not bind cyclin-dependent kinases. Instead, we find that the short-form CNTD1 variant associates with components of the replication factor C (RFC) machinery to facilitate crossover formation, and with the E2 ubiquitin conjugating enzyme, CDC34, to regulate ubiquitylation and subsequent degradation of the WEE1 kinase, thereby modulating cell-cycle progression. We propose that these interactions facilitate a role for CNTD1 as a stop-go regulator during prophase I, ensuring accurate and complete crossover formation before allowing metaphase progression and the first meiotic division. CNTD1 associates with sites of crossing over in meiosis, co-localizing with MutLγ In the testis, CNTD1 does not interact with CDKs or with known crossover regulators CNTD1 regulates crossing over via interactions with the replication factor C complex CNTD1 regulates cell-cycle progression via interactions with the SCF complex
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Affiliation(s)
- Stephen Gray
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA.
| | - Emerson R Santiago
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Paula E Cohen
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA.
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41
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Hepatitis B virus cccDNA is formed through distinct repair processes of each strand. Nat Commun 2021; 12:1591. [PMID: 33707452 PMCID: PMC7952586 DOI: 10.1038/s41467-021-21850-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is a highly contagious pathogen that afflicts over a third of the world’s population, resulting in close to a million deaths annually. The formation and persistence of the HBV covalently closed circular DNA (cccDNA) is the root cause of HBV chronicity. However, the detailed molecular mechanism of cccDNA formation from relaxed circular DNA (rcDNA) remains opaque. Here we show that the minus and plus-strand lesions of HBV rcDNA require different sets of human repair factors in biochemical repair systems. We demonstrate that the plus-strand repair resembles DNA lagging strand synthesis, and requires proliferating cell nuclear antigen (PCNA), the replication factor C (RFC) complex, DNA polymerase delta (POLδ), flap endonuclease 1 (FEN-1), and DNA ligase 1 (LIG1). Only FEN-1 and LIG1 are required for the repair of the minus strand. Our findings provide a detailed mechanistic view of how HBV rcDNA is repaired to form cccDNA in biochemical repair systems. HBV covalently closed circular DNA (cccDNA) enables and persists in chronic infection, but the molecular mechanism of its formation is unclear. Here, Wei and Ploss elucidate the detailed kinetics and biochemical steps by which the relaxed circular DNA is converted into cccDNA.
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Boavida A, Santos D, Mahtab M, Pisani FM. Functional Coupling between DNA Replication and Sister Chromatid Cohesion Establishment. Int J Mol Sci 2021; 22:2810. [PMID: 33802105 PMCID: PMC8001024 DOI: 10.3390/ijms22062810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 12/28/2022] Open
Abstract
Several lines of evidence suggest the existence in the eukaryotic cells of a tight, yet largely unexplored, connection between DNA replication and sister chromatid cohesion. Tethering of newly duplicated chromatids is mediated by cohesin, an evolutionarily conserved hetero-tetrameric protein complex that has a ring-like structure and is believed to encircle DNA. Cohesin is loaded onto chromatin in telophase/G1 and converted into a cohesive state during the subsequent S phase, a process known as cohesion establishment. Many studies have revealed that down-regulation of a number of DNA replication factors gives rise to chromosomal cohesion defects, suggesting that they play critical roles in cohesion establishment. Conversely, loss of cohesin subunits (and/or regulators) has been found to alter DNA replication fork dynamics. A critical step of the cohesion establishment process consists in cohesin acetylation, a modification accomplished by dedicated acetyltransferases that operate at the replication forks. Defects in cohesion establishment give rise to chromosome mis-segregation and aneuploidy, phenotypes frequently observed in pre-cancerous and cancerous cells. Herein, we will review our present knowledge of the molecular mechanisms underlying the functional link between DNA replication and cohesion establishment, a phenomenon that is unique to the eukaryotic organisms.
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Affiliation(s)
- Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
| | - Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
| | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Francesca M. Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
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Deng J, Zhong F, Gu W, Qiu F. Exploration of Prognostic Biomarkers among Replication Factor C Family in the Hepatocellular Carcinoma. Evol Bioinform Online 2021; 17:1176934321994109. [PMID: 33628006 PMCID: PMC7885030 DOI: 10.1177/1176934321994109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/19/2021] [Indexed: 01/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the common cancers with a high incidence and mortality. The human replication factor C (RFC) family contains 5 subunits that play an important role in DNA replication and DNA damage repair. RFCs are abnormally expressed in a variety of cancers; some of them are differentially expressed in HCC tissues and related to tumor growth. However, the expression, prognostic value, and effect targets of the whole RFC family in HCC are still unclear. To address these issues, we performed a multidimensional analysis of RFCs in HCC patients by Oncomine, UALCAN, GEPIA, Human protein atlas, Kaplan-Meier plotter, cBioPortal, GeneMANIA, String, and LinkedOmics. mRNA expression of RFCs was significantly increased in HCC tissues. There was a significant correlation between the expression of RFC2/3/4/5 and tumor stage of HCC patients. Besides, high mRNA expression of RFC2/4 was associated with worse overall survival (OS). Moreover, genetic alterations of RFCs were associated with worse OS in HCC patients. We found that genes co-expressed with RFC2/4 were mainly involved in biological processes, such as chromosome segregation, mitotic cell cycle phase transition, and telomere organization and they activated the cell cycle and spliceosome pathways. The gene set is mainly enriched in cancer-related kinases AURKA, ATR, CDK1, PLK1, and CHEK1. E2F family members were the key transcription factors for RFCs. Our results suggest that differentially expressed RFC2 and RFC4 are potential prognostic biomarkers in HCC and may act on E2F transcription factors and some kinase targets to dysregulate the cell cycle pathway. These efforts may provide new research directions for prognostic biomarkers and therapeutic targets in HCC.
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Affiliation(s)
- Jianxiong Deng
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Fangyan Zhong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Weiguo Gu
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
| | - Feng Qiu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
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44
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Chang HR, Jung E, Cho S, Jeon YJ, Kim Y. Targeting Non-Oncogene Addiction for Cancer Therapy. Biomolecules 2021; 11:129. [PMID: 33498235 PMCID: PMC7909239 DOI: 10.3390/biom11020129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
While Next-Generation Sequencing (NGS) and technological advances have been useful in identifying genetic profiles of tumorigenesis, novel target proteins and various clinical biomarkers, cancer continues to be a major global health threat. DNA replication, DNA damage response (DDR) and repair, and cell cycle regulation continue to be essential systems in targeted cancer therapies. Although many genes involved in DDR are known to be tumor suppressor genes, cancer cells are often dependent and addicted to these genes, making them excellent therapeutic targets. In this review, genes implicated in DNA replication, DDR, DNA repair, cell cycle regulation are discussed with reference to peptide or small molecule inhibitors which may prove therapeutic in cancer patients. Additionally, the potential of utilizing novel synthetic lethal genes in these pathways is examined, providing possible new targets for future therapeutics. Specifically, we evaluate the potential of TONSL as a novel gene for targeted therapy. Although it is a scaffold protein with no known enzymatic activity, the strategy used for developing PCNA inhibitors can also be utilized to target TONSL. This review summarizes current knowledge on non-oncogene addiction, and the utilization of synthetic lethality for developing novel inhibitors targeting non-oncogenic addiction for cancer therapy.
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Affiliation(s)
- Hae Ryung Chang
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Eunyoung Jung
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Soobin Cho
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Young-Jun Jeon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea;
| | - Yonghwan Kim
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
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45
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Lee KY, Park SH. Eukaryotic clamp loaders and unloaders in the maintenance of genome stability. Exp Mol Med 2020; 52:1948-1958. [PMID: 33339954 PMCID: PMC8080817 DOI: 10.1038/s12276-020-00533-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic sliding clamp proliferating cell nuclear antigen (PCNA) plays a critical role as a processivity factor for DNA polymerases and as a binding and acting platform for many proteins. The ring-shaped PCNA homotrimer and the DNA damage checkpoint clamp 9-1-1 are loaded onto DNA by clamp loaders. PCNA can be loaded by the pentameric replication factor C (RFC) complex and the CTF18-RFC-like complex (RLC) in vitro. In cells, each complex loads PCNA for different purposes; RFC-loaded PCNA is essential for DNA replication, while CTF18-RLC-loaded PCNA participates in cohesion establishment and checkpoint activation. After completing its tasks, PCNA is unloaded by ATAD5 (Elg1 in yeast)-RLC. The 9-1-1 clamp is loaded at DNA damage sites by RAD17 (Rad24 in yeast)-RLC. All five RFC complex components, but none of the three large subunits of RLC, CTF18, ATAD5, or RAD17, are essential for cell survival; however, deficiency of the three RLC proteins leads to genomic instability. In this review, we describe recent findings that contribute to the understanding of the basic roles of the RFC complex and RLCs and how genomic instability due to deficiency of the three RLCs is linked to the molecular and cellular activity of RLC, particularly focusing on ATAD5 (Elg1). The attachment and removal of clamp proteins that encircle DNA as it is copied and assist its replication and maintenance is mediated by DNA clamp loader and unloader proteins; defects in loading and unloading can increase the rate of damaging mutations. Kyoo-young Lee and Su Hyung Park at the Institute for Basic Science in Ulsan, South Korea, review current understanding of the activity of clamp loading and unloading proteins. They examine research on the proteins in eukaryotic cells, those containing a cell nucleus, making their discussion relevant to understanding the stability of the human genome. They focus particular attention on a protein called ATAD5, which is involved in unloading the clamp proteins. Deficiencies in ATAD5 function have been implicated in genetic instability that might lead to several different types of cancer.
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Affiliation(s)
- Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
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Sheriff O, Yaw A, Lai SK, Loo HL, Sze SK, Preiser PR. Plasmodium falciparum replication factor C subunit 1 is involved in genotoxic stress response. Cell Microbiol 2020; 23:e13277. [PMID: 33040440 DOI: 10.1111/cmi.13277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 02/03/2023]
Abstract
About half the world's population is at risk of malaria, with Plasmodium falciparum malaria being responsible for the most malaria related deaths globally. Antimalarial drugs such as chloroquine and artemisinin are directed towards the proliferating intra-erythrocytic stages of the parasite, which is responsible for all the clinical symptoms of the disease. These antimalarial drugs have been reported to function via multiple pathways, one of which induces DNA damage via the generation of free radicals and reactive oxygen species. An urgent need to understand the mechanistic details of drug response and resistance is highlighted by the decreasing clinical efficacy of the front line drug, Artemisinin. The replication factor C subunit 1 is an important component of the DNA replication machinery and DNA damage response mechanism. Here we show the translocation of PfRFC1 from an intranuclear localisation to the nuclear periphery, indicating an orchestrated progression of distinct patterns of replication in the developing parasites. PfRFC1 responds to genotoxic stress via elevated protein levels in soluble and chromatin bound fractions. Reduction of PfRFC1 protein levels upon treatment with antimalarials suggests an interplay of replication, apoptosis and DNA repair pathways leading to cell death. Additionally, mislocalisation of the endogenously tagged protein confirmed its essential role in parasites' replication and DNA repair. This study provides key insights into DNA replication, DNA damage response and cell death in P. falciparum.
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Affiliation(s)
- Omar Sheriff
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Aniweh Yaw
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Hooi Linn Loo
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Peter Rainer Preiser
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore.,Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
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Jin G, Wang W, Cheng P, Tian Y, Zhang L, Niu H. DNA replication and sister chromatid cohesion 1 promotes breast carcinoma progression by modulating the Wnt/β-catenin signaling and p53 protein. J Biosci 2020. [DOI: 10.1007/s12038-020-00100-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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48
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Wan L, Chen Z, Wan N, Liu M, Xue J, Chen H, Zhang Y, Peng Y, Tang Z, Gong Y, Yuan H, Wang S, Deng Q, Hou X, Wang C, Peng H, Shi Y, Peng L, Lei L, Duan R, Xia K, Qiu R, Shen L, Tang B, Ashizawa T, Jiang H. Biallelic Intronic AAGGG Expansion of RFC1 is Related to Multiple System Atrophy. Ann Neurol 2020; 88:1132-1143. [PMID: 32939785 DOI: 10.1002/ana.25902] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE A recessive biallelic repeat expansion, (AAGGG)exp , in the RFC1 gene has been reported to be a frequent cause of late-onset ataxia. For cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), the recessive biallelic (AAGGG)exp genotype was present in ~92% of cases. This study aimed to examine whether the pentanucleotide repeat (PNR) was related to multiple system atrophy (MSA), which shares a spectrum of symptoms with CANVAS. METHODS In this study, we screened the pathogenic (AAGGG)exp repeat and 5 other PNRs in 104 Chinese sporadic adult-onset ataxia of unknown aetiology (SAOA) patients, 282 MSA patients, and 203 unaffected individuals. Multiple molecular genetic tests were used, including long-range polymerase chain reaction (PCR), repeat-primed PCR (RP-PCR), Sanger sequencing, and Southern blot. Comprehensive clinical assessments were conducted, including neurological examination, neuroimaging, nerve electrophysiology, and examination of vestibular function. RESULTS We identified biallelic (AAGGG)exp in 1 SAOA patient and 3 MSA patients. Additionally, 1 MSA patient had the (AAGGG)exp /(AAAGG)exp genotype with uncertain pathogenicity. We also described the carrier frequency for different PNRs in our cohorts. Furthermore, we summarized the distinct phenotypes of affected patients, suggesting that biallelic (AAGGG)exp in RFC1 could be associated with MSA and should be screened routinely in the MSA diagnostic workflow. INTERPRETATION Our results expanded the clinical phenotypic spectrum of RFC1-related disorders and raised the possibility that MSA might share the same genetic background as CANVAS, which is crucial for re-evaluating the current CANVAS and MSA diagnostic criteria. ANN NEUROL 2020;88:1132-1143.
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Affiliation(s)
- Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jin Xue
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Hongsheng Chen
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Youming Zhang
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yiqing Gong
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Shang Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qi Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xuan Hou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Huirong Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Linliu Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lijing Lei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Ranhui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Tetsuo Ashizawa
- Neuroscience Research Program, Methodist Hospital Research Institute, Houston, TX, USA
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Structure of the human clamp loader reveals an autoinhibited conformation of a substrate-bound AAA+ switch. Proc Natl Acad Sci U S A 2020; 117:23571-23580. [PMID: 32907938 DOI: 10.1073/pnas.2007437117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DNA replication requires the sliding clamp, a ring-shaped protein complex that encircles DNA, where it acts as an essential cofactor for DNA polymerases and other proteins. The sliding clamp needs to be opened and installed onto DNA by a clamp loader ATPase of the AAA+ family. The human clamp loader replication factor C (RFC) and sliding clamp proliferating cell nuclear antigen (PCNA) are both essential and play critical roles in several diseases. Despite decades of study, no structure of human RFC has been resolved. Here, we report the structure of human RFC bound to PCNA by cryogenic electron microscopy to an overall resolution of ∼3.4 Å. The active sites of RFC are fully bound to adenosine 5'-triphosphate (ATP) analogs, which is expected to induce opening of the sliding clamp. However, we observe the complex in a conformation before PCNA opening, with the clamp loader ATPase modules forming an overtwisted spiral that is incapable of binding DNA or hydrolyzing ATP. The autoinhibited conformation observed here has many similarities to a previous yeast RFC:PCNA crystal structure, suggesting that eukaryotic clamp loaders adopt a similar autoinhibited state early on in clamp loading. Our results point to a "limited change/induced fit" mechanism in which the clamp first opens, followed by DNA binding, inducing opening of the loader to release autoinhibition. The proposed change from an overtwisted to an active conformation reveals an additional regulatory mechanism for AAA+ ATPases. Finally, our structural analysis of disease mutations leads to a mechanistic explanation for the role of RFC in human health.
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50
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Amir M, Alam A, Ishrat R, Alajmi MF, Hussain A, Rehman MT, Islam A, Ahmad F, Hassan MI, Dohare R. A Systems View of the Genome Guardians: Mapping the Signaling Circuitry Underlying Oligonucleotide/Oligosaccharide-Binding Fold Proteins. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:518-530. [PMID: 32780668 DOI: 10.1089/omi.2020.0072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The oligonucleotide/oligosaccharide-binding (OB)-fold domain proteins are considered as genome guardians, whose functions are extending beyond genomic stability. The broad functional diversity of the OB-fold proteins is attributed to their protein-DNA, protein-RNA, and protein-protein interactions (PPI). To understand the connectivity of the human OB-fold proteins, we report here a systems-level approach. Specifically, we mapped all human OB-fold PPI networks and evaluated topological features such as network robustness and network hub, among others. We found that the OB-fold network comprised of 227 nodes forming 5523 interactions, and has a scale-free topology having UBA52, ATR, and TP53 as leading hub proteins that control efficient communication within the network. Furthermore, four different clusters and subclusters have been identified, which are implicated in diverse cellular processes, including DNA replication, repair, maintenance of genomic stability, RNA processing, spermatogenesis, complement system, and telomere maintenance. The importance of these clusters is further strengthened by knockout studies, which showed a significant decrease in topological properties. In summary, this study provides new insights on the role of OB-fold protein as genome guardians in regard to the underlying mechanism of signaling pathways, the roles of key regulators, and thus, offers new prospects as potential targets for diagnostics and therapeutics purposes.
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Affiliation(s)
- Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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