1
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Li X, Perdomo IMM, Rodrigues Alves Barbosa V, Diao C, Tarailo-Graovac M. The critical role of the iron-sulfur cluster and CTC components in DOG-1/BRIP1 function in Caenorhabditis elegans. Nucleic Acids Res 2024:gkae617. [PMID: 39011897 DOI: 10.1093/nar/gkae617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
FANCJ/BRIP1, initially identified as DOG-1 (Deletions Of G-rich DNA) in Caenorhabditis elegans, plays a critical role in genome integrity by facilitating DNA interstrand cross-link repair and resolving G-quadruplex structures. Its function is tightly linked to a conserved [4Fe-4S] cluster-binding motif, mutations of which contribute to Fanconi anemia and various cancers. This study investigates the critical role of the iron-sulfur (Fe-S) cluster in DOG-1 and its relationship with the cytosolic iron-sulfur protein assembly targeting complex (CTC). We found that a DOG-1 mutant, expected to be defective in Fe-S cluster binding, is primarily localized in the cytoplasm, leading to heightened DNA damage sensitivity and G-rich DNA deletions. We further discovered that the deletion of mms-19, a nonessential CTC component, also resulted in DOG-1 sequestered in cytoplasm and increased DNA damage sensitivity. Additionally, we identified that CIAO-1 and CIAO-2B are vital for DOG-1's stability and repair functions but unlike MMS-19 have essential roles in C. elegans. These findings confirm the CTC and Fe-S cluster as key elements in regulating DOG-1, crucial for genome integrity. Additionally, this study advances our understanding of the CTC's role in Fe-S protein regulation and development in C. elegans, offering a model to study its impact on multicellular organism development.
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Affiliation(s)
- Xiao Li
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Ivette Maria Menendez Perdomo
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Victoria Rodrigues Alves Barbosa
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Catherine Diao
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
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2
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Teh MR, Armitage AE, Drakesmith H. Why cells need iron: a compendium of iron utilisation. Trends Endocrinol Metab 2024:S1043-2760(24)00109-7. [PMID: 38760200 DOI: 10.1016/j.tem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Iron deficiency is globally prevalent, causing an array of developmental, haematological, immunological, neurological, and cardiometabolic impairments, and is associated with symptoms ranging from chronic fatigue to hair loss. Within cells, iron is utilised in a variety of ways by hundreds of different proteins. Here, we review links between molecular activities regulated by iron and the pathophysiological effects of iron deficiency. We identify specific enzyme groups, biochemical pathways, cellular functions, and cell lineages that are particularly iron dependent. We provide examples of how iron deprivation influences multiple key systems and tissues, including immunity, hormone synthesis, and cholesterol metabolism. We propose that greater mechanistic understanding of how cellular iron influences physiological processes may lead to new therapeutic opportunities across a range of diseases.
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Affiliation(s)
- Megan R Teh
- MRC Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew E Armitage
- MRC Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hal Drakesmith
- MRC Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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3
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Gale SE, Willeford A, Sandquist K, Watson K. Intravenous iron in patients with iron deficiency and heart failure: a review of modern evidence. Curr Opin Cardiol 2024; 39:178-187. [PMID: 38353280 DOI: 10.1097/hco.0000000000001121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PURPOSE OF REVIEW Iron deficiency is common in patients with heart failure, affecting up to half of ambulatory patients and an even greater percentage of patients admitted for acute decompensation. Iron deficiency in this population is also associated with poor outcomes, including worse quality of life in addition to increased hospitalizations for heart failure and mortality. Evidence suggests that patients with iron deficiency in heart failure may benefit from repletion with IV iron. RECENT FINDINGS In this review, we outline the etiology and pathophysiology of iron deficiency in heart failure as well as various iron formulations available. We discuss evidence for intravenous iron repletion with a particular focus on recent studies that have evaluated its effects on hospitalizations and mortality. Finally, we discuss areas of uncertainty and future study and provide practical guidance for iron repletion. SUMMARY In summary, there is overwhelming evidence that intravenous iron repletion in patients with iron deficiency in heart failure is both beneficial and safe. However, further evidence is needed to better identify which patients would most benefit from iron repletion as well as the ideal repletion strategy.
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Affiliation(s)
- Stormi E Gale
- Novant Health Heart and Vascular Institute, Huntersville, North Carolina
| | - Andrew Willeford
- University of California San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, California
| | | | - Kristin Watson
- University of Maryland School of Pharmacy, Baltimore, Maryland, USA
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4
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Zhang DD. Ironing out the details of ferroptosis. Nat Cell Biol 2024:10.1038/s41556-024-01361-7. [PMID: 38429476 DOI: 10.1038/s41556-024-01361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024]
Abstract
Ferroptosis, spurred by excess labile iron and lipid peroxidation, is implicated in various diseases. Advances have been made in comprehending the lipid-peroxidation side of ferroptosis, but the exact role of iron in driving ferroptosis remains unknown. Although iron overload is characterized in multiple disease states, the potential role of ferroptosis within them remains undefined. This overview focuses on the 'ferro' side of ferroptosis, highlighting iron dysregulation in human diseases and potential therapeutic strategies targeting iron regulation and metabolism.
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Affiliation(s)
- Donna D Zhang
- Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA.
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5
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Liu Y, Luo X, Chen Y, Dang J, Zeng D, Guo X, Weng W, Zhao J, Shi X, Chen J, Dong B, Zhong S, Ren J, Li Y, Wang J, Zhang J, Sun J, Xu H, Lu Y, Brand D, Zheng SG, Pan Y. Heterogeneous ferroptosis susceptibility of macrophages caused by focal iron overload exacerbates rheumatoid arthritis. Redox Biol 2024; 69:103008. [PMID: 38142586 PMCID: PMC10788633 DOI: 10.1016/j.redox.2023.103008] [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: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023] Open
Abstract
Focal iron overload is frequently observed in patients with rheumatoid arthritis (RA), yet its functional significance remains elusive. Herein, we report that iron deposition in lesion aggravates arthritis by inducing macrophage ferroptosis. We show that excessive iron in synovial fluid positively correlates with RA disease severity as does lipid hyperoxidation of focal monocyte/macrophages. Further study reveals high susceptibility to iron induced ferroptosis of the anti-inflammatory macrophages M2, while pro-inflammatory M1 are less affected. Distinct glutathione peroxidase 4 (GPX4) degradation depending on p62/SQSTM1 in the two cell types make great contribution mechanically. Of note, ferroptosis inhibitor liproxstatin-1 (LPX-1) can alleviate the progression of K/BxN serum-transfer induced arthritis (STIA) mice accompanied with increasing M2 macrophages proportion. We thus propose that the heterogeneous ferroptosis susceptibility of macrophage subtypes as well as consequent inflammation and immune disorders are potential biomarkers and therapeutic targets in RA.
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Affiliation(s)
- Yan Liu
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China; Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiqing Luo
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ye Chen
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China; Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Junlong Dang
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Donglan Zeng
- Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xinghua Guo
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Weizhen Weng
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jun Zhao
- Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaoyi Shi
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China; Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jingrong Chen
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China; Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Bo Dong
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shuyuan Zhong
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jianhua Ren
- Department of Joint and Trauma Surgery, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yuhang Li
- Department of Joint and Trauma Surgery, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Julie Wang
- Division of Rheumatology and Immunology, Department of Immunology, School of Cell and Gene Therapy, Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jingwen Zhang
- Department of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jianbo Sun
- Department of Clinical Research, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, Guangdong, China
| | - Hanshi Xu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yan Lu
- Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - David Brand
- The Lt. Col. Luke Weathers, Jr. VA Medical Center, Memphis, TN, 38163, United States
| | - Song Guo Zheng
- Division of Rheumatology and Immunology, Department of Immunology, School of Cell and Gene Therapy, Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Yunfeng Pan
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China.
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6
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Mao C, Mills M. Characterization of human XPD helicase activity with single-molecule magnetic tweezers. Biophys J 2024; 123:260-271. [PMID: 38111195 PMCID: PMC10808040 DOI: 10.1016/j.bpj.2023.12.014] [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: 03/13/2023] [Revised: 06/02/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023] Open
Abstract
XPD helicase is a DNA-unwinding enzyme involved in DNA repair. As part of TFIIH, XPD opens a repair bubble in DNA for access by proteins in the nucleotide excision repair pathway. XPD uses the energy from ATP hydrolysis to translocate in the 5' to 3' direction on one strand of duplex DNA, displacing the opposite strand in the process. We used magnetic tweezers assays to measure the double-stranded DNA unwinding and single-stranded DNA translocation activities of human XPD in isolation. In our experimental setup, hXPD exhibited low unwinding processivity of ∼14 bp and slow unwinding rate of ∼0.3 bp/s. Measurements of the ssDNA translocation activity demonstrated that hXPD translocated on ssDNA at a similar rate as unwinding, revealing that slow rate was an intrinsic property of the hXPD translocation. Individual unwinding and translocation events were composed of pauses and runs with a distribution of lengths and rates. Analysis of these events unveiled similar mean run lengths and rates for unwinding and translocation, indicating that the unwinding behavior was a direct reflection of the translocation activity. The analysis also revealed that hXPD spent similar time stalling and unwinding/translocating. The detailed basal activity of hXPD reported here provides a baseline for future studies on how hXPD activity is regulated by other TFIIH components.
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Affiliation(s)
- Chunfeng Mao
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri
| | - Maria Mills
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.
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7
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Kulikowicz T, Sommers JA, Fuchs KF, Wu Y, Brosh RM. Purification and biochemical characterization of the G4 resolvase and DNA helicase FANCJ. Methods Enzymol 2024; 695:1-27. [PMID: 38521581 DOI: 10.1016/bs.mie.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplex (G4) DNA or RNA poses a unique nucleic acid structure in genomic transactions. Because of the unique topology presented by G4, cells have exquisite mechanisms and pathways to metabolize G4 that arise in guanine-rich regions of the genome such as telomeres, promoter regions, ribosomal DNA, and other chromosomal elements. G4 resolvases are often represented by a class of molecular motors known as helicases that disrupt the Hoogsteen hydrogen bonds in G4 by harnessing the chemical energy of nucleoside triphosphate hydrolysis. Of special interest to researchers in the field, including us, is the human FANCJ DNA helicase that efficiently resolves G4 DNA structures. Notably, FANCJ mutations are linked to Fanconi Anemia and are prominent in breast and ovarian cancer. Since our discovery that FANCJ efficiently resolves G4 DNA structures 15 years ago, we and other labs have characterized mechanistic aspects of FANCJ-catalyzed G4 resolution and its biological importance in genomic integrity and cellular DNA replication. In addition to its G4 resolvase function, FANCJ is also a classic DNA helicase that acts on conventional duplex DNA structures, which are relevant to the enzyme's role in interstrand cross link repair, double-strand break repair via homologous recombination, and response to replication stress. Here, we describe detailed procedures for the purification of recombinant FANCJ protein and characterization of its G4 resolvase and duplex DNA helicase activity.
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Affiliation(s)
- Tomasz Kulikowicz
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States.
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8
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Fu I, Geacintov NE, Broyde S. Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase. Nucleic Acids Res 2023; 51:12261-12274. [PMID: 37933861 PMCID: PMC10711554 DOI: 10.1093/nar/gkad974] [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: 08/03/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
Ultraviolet light generates cyclobutane pyrimidine dimer (CPD) and pyrimidine 6-4 pyrimidone (6-4PP) photoproducts that cause skin malignancies if not repaired by nucleotide excision repair (NER). While the faster repair of the more distorting 6-4PPs is attributed mainly to more efficient recognition by XPC, the XPD lesion verification helicase may play a role, as it directly scans the damaged DNA strand. With extensive molecular dynamics simulations of XPD-bound single-strand DNA containing each lesion outside the entry pore of XPD, we elucidate strikingly different verification processes for these two lesions that have very different topologies. The open book-like CPD thymines are sterically blocked from pore entry and preferably entrapped by sensors that are outside the pore; however, the near-perpendicular 6-4PP thymines can enter, accompanied by a displacement of the Arch domain toward the lesion, which is thereby tightly accommodated within the pore. This trapped 6-4PP may inhibit XPD helicase activity to foster lesion verification by locking the Arch to other domains. Furthermore, the movement of the Arch domain, only in the case of 6-4PP, may trigger signaling to the XPG nuclease for subsequent lesion incision by fostering direct contact between the Arch domain and XPG, and thereby facilitating repair of 6-4PP.
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Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 24 Waverly Place, 6th Floor, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- Department of Biology, New York University, 24 Waverly Place, 6th Floor, New York, NY 10003, USA
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9
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Domgaard H, Cahoon C, Armbrust MJ, Redman O, Jolley A, Thomas A, Jackson R. CasDinG is a 5'-3' dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity. Nucleic Acids Res 2023; 51:8115-8132. [PMID: 37395408 PMCID: PMC10450177 DOI: 10.1093/nar/gkad546] [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: 08/17/2022] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5'-3' DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5'-GNAWN-3' on the 5'-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.
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Affiliation(s)
- Hannah Domgaard
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Christian Cahoon
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Matthew J Armbrust
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Olivine Redman
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Alivia Jolley
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Aaron Thomas
- Center for Integrated Biosystems, Utah State University, Logan, UT, USA
| | - Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
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10
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Sewell KE, Gola GF, Pignataro MF, Herrera MG, Noguera ME, Olmos J, Ramírez JA, Capece L, Aran M, Santos J. Direct Cysteine Desulfurase Activity Determination by NMR and the Study of the Functional Role of Key Structural Elements of Human NFS1. ACS Chem Biol 2023; 18:1534-1547. [PMID: 37410592 DOI: 10.1021/acschembio.3c00147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The mitochondrial cysteine desulfurase NFS1 is an essential PLP-dependent enzyme involved in iron-sulfur cluster assembly. The enzyme catalyzes the desulfurization of the l-Cys substrate, producing a persulfide and l-Ala as products. In this study, we set the measurement of the product l-Ala by NMR in vitro by means of 1H NMR spectra acquisition. This methodology provided us with the possibility of monitoring the reaction in both fixed-time and real-time experiments, with high sensitivity and accuracy. By studying I452A, W454A, Q456A, and H457A NFS1 variants, we found that the C-terminal stretch (CTS) of the enzyme is critical for function. Specifically, mutation of the extremely conserved position W454 resulted in highly decreased activity. Additionally, we worked on two singular variants: "GGG" and C158A. In the former, the catalytic Cys-loop was altered by including two Gly residues to increase the flexibility of this loop. This variant had significantly impaired activity, indicating that the Cys-loop motions are fine-tuned in the wild-type enzyme. In turn, for C158A, we found an unanticipated increase in l-Cys desulfurase activity. Furthermore, we carried out molecular dynamics simulations of the supercomplex dedicated to iron-sulfur cluster biosynthesis, which includes NFS1, ACP, ISD11, ISCU2, and FXN subunits. We identified CTS as a key element that established interactions with ISCU2 and FXN concurrently; we found specific interactions that are established when FXN is present, reinforcing the idea that FXN not only forms part of the iron-sulfur cluster assembly site but also modulates the internal motions of ISCU2.
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Affiliation(s)
- Karl E Sewell
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - Gabriel F Gola
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET─Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - María Florencia Pignataro
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - María Georgina Herrera
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - Martín E Noguera
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Junín 956, Buenos Aires 1113AAD, Argentina
| | - Justo Olmos
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - Javier A Ramírez
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET─Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), Universidad de Buenos Aires. Buenos Aires C1428EGA, Argentina
| | - Martín Aran
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Javier Santos
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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11
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Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N. Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment. Mol Cell 2023:S1097-2765(23)00420-3. [PMID: 37343553 DOI: 10.1016/j.molcel.2023.05.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/19/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023]
Abstract
Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic details of their function remain unknown. Here, we provide high-resolution functional snapshots of type IV-A Csf complexes before and after target dsDNA binding, either in the absence or presence of CasDinG, revealing the mechanisms underlying CsfcrRNA complex assembly, "DWN" PAM-dependent dsDNA targeting, R-loop formation, and CasDinG recruitment. Furthermore, we establish that CasDinG, a signature DinG family helicase, harbors ssDNA-stimulated ATPase activity and ATP-dependent 5'-3' DNA helicase activity. In addition, we show that CasDinG unwinds the non-target strand (NTS) and target strand (TS) of target dsDNA from the CsfcrRNA complex. These molecular details advance our mechanistic understanding of type IV-A CRISPR-Csf function and should enable Csf complexes to be harnessed as genome-engineering tools for biotechnological applications.
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Affiliation(s)
- Ning Cui
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yongrui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yanhong Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao-Yu Liu
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chongyuan Wang
- Faculty of Pharmaceutical Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China; Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China
| | - Hongda Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China.
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12
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Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature 2023; 617:170-175. [PMID: 37076618 PMCID: PMC10416759 DOI: 10.1038/s41586-023-05959-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts1. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases2. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported3-7. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
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Affiliation(s)
- Jinseok Kim
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Chia-Lung Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- School of Life Sciences, Anhui University, Hefei, China
| | - Yanxiang Cui
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Filip M Golebiowski
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- Roche Polska, Warsaw, Poland
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Fumio Hanaoka
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe, Japan.
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.
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13
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Metformin inhibits oral squamous cell carcinoma progression through regulating RNA alternative splicing. Life Sci 2023; 315:121274. [PMID: 36509195 DOI: 10.1016/j.lfs.2022.121274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
AIMS Oral squamous cell carcinoma (OSCC) is considered as the sixth most common cancer worldwide characterized by high invasiveness, high metastasis rate and high mortality. It is urgent to explore novel therapeutic strategies to overcome this feature. Metformin is currently a strong candidate anti-tumor drug in multiple cancers. However, whether metformin could inhibit cancer progression by regulating RNA alternative splicing remains largely unknown. MAIN METHODS Cell proliferation and growth ability of CAL-27 and UM-SCC6 were analyzed by CCK8 and colony formation assays. Cell migration was judged by wound healing assay. Mechanistically, RNA-seq was applied to systematically identify genes that are regulated by metformin. The expression of metformin-regulated genes was determined by real-time quantitative PCR (RT-qPCR). Metformin-regulated alternative splicing events were confirmed by RT-PCR. KEY FINDINGS We demonstrated that metformin could significantly inhibit the proliferation and migration of oral squamous cell carcinoma cells. Mechanistically, in addition to transcriptional regulation, metformin induces a wide range of alternative splicing alteration, including genes involved in centrosome, cellular response to DNA damage stimulus, GTPase binding, histone modification, catalytic activity, regulation of cell cycle process and ATPase complex. Notably, metformin specifically modulates the splicing of NUBP2, a component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA). Briefly, metformin favors the production of NUBP2-L, the long splicing isoform of NUBP2, thereby inhibiting cancer cell proliferation. SIGNIFICANCE Our findings provide mechanistic insights of metformin on RNA alternative splicing regulation, thus to offer a potential novel route for metformin to inhibit cancer progression.
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14
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Quick and Spontaneous Transformation between [3Fe-4S] and [4Fe-4S] Iron-Sulfur Clusters in the tRNA-Thiolation Enzyme TtuA. Int J Mol Sci 2023; 24:ijms24010833. [PMID: 36614280 PMCID: PMC9821441 DOI: 10.3390/ijms24010833] [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: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential cofactors for enzyme activity. These Fe-S clusters are present in structurally diverse forms, including [4Fe-4S] and [3Fe-4S]. Type-identification of the Fe-S cluster is indispensable in understanding the catalytic mechanism of enzymes. However, identifying [4Fe-4S] and [3Fe-4S] clusters in particular is challenging because of their rapid transformation in response to oxidation-reduction events. In this study, we focused on the relationship between the Fe-S cluster type and the catalytic activity of a tRNA-thiolation enzyme (TtuA). We reconstituted [4Fe-4S]-TtuA, prepared [3Fe-4S]-TtuA by oxidizing [4Fe-4S]-TtuA under strictly anaerobic conditions, and then observed changes in the Fe-S clusters in the samples and the enzymatic activity in the time-course experiments. Electron paramagnetic resonance analysis revealed that [3Fe-4S]-TtuA spontaneously transforms into [4Fe-4S]-TtuA in minutes to one hour without an additional free Fe source in the solution. Although the TtuA immediately after oxidation of [4Fe-4S]-TtuA was inactive [3Fe-4S]-TtuA, its activity recovered to a significant level compared to [4Fe-4S]-TtuA after one hour, corresponding to an increase of [4Fe-4S]-TtuA in the solution. Our findings reveal that [3Fe-4S]-TtuA is highly inactive and unstable. Moreover, time-course analysis of structural changes and activity under strictly anaerobic conditions further unraveled the Fe-S cluster type used by the tRNA-thiolation enzyme.
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15
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Petronek MS, Allen BG. Maintenance of genome integrity by the late-acting cytoplasmic iron-sulfur assembly (CIA) complex. Front Genet 2023; 14:1152398. [PMID: 36968611 PMCID: PMC10031043 DOI: 10.3389/fgene.2023.1152398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.
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16
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Weeks-Pollenz SJ, Ali Y, Morris LA, Sutera VA, Dudenhausen EE, Hibnick M, Lovett ST, Bloom LB. Characterization of the Escherichia coli XPD/Rad3 iron-sulfur helicase YoaA in complex with the DNA polymerase III clamp loader subunit chi (χ). J Biol Chem 2023; 299:102786. [PMID: 36509145 PMCID: PMC9826845 DOI: 10.1016/j.jbc.2022.102786] [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: 06/17/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli YoaA aids in the resolution of DNA damage that halts DNA synthesis in vivo in conjunction with χ, an accessory subunit of DNA polymerase III. YoaA and χ form a discrete complex separate from the DNA polymerase III holoenzyme, but little is known about how YoaA and χ work together to help the replication fork overcome damage. Although YoaA is predicted to be an iron-sulfur helicase in the XPD/Rad3 helicase family based on sequence analysis, the biochemical activities of YoaA have not been described. Here, we characterize YoaA and show that purified YoaA contains iron. YoaA and χ form a complex that is stable through three chromatographic steps, including gel filtration chromatography. When overexpressed in the absence of χ, YoaA is mostly insoluble. In addition, we show the YoaA-χ complex has DNA-dependent ATPase activity. Our measurement of the YoaA-χ helicase activity illustrates for the first time YoaA-χ translocates on ssDNA in the 5' to 3' direction and requires a 5' single-stranded overhang, or ssDNA gap, for DNA/DNA unwinding. Furthermore, YoaA-χ preferentially unwinds forked duplex DNA that contains both 3' and 5' single-stranded overhangs versus duplex DNA with only a 5' overhang. Finally, we demonstrate YoaA-χ can unwind damaged DNA that contains an abasic site or damage on 3' ends that stall replication extension. These results are the first biochemical evidence demonstrating YoaA is a bona fide iron-sulfur helicase, and we further propose the physiologically relevant form of the helicase is YoaA-χ.
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Affiliation(s)
- Savannah J Weeks-Pollenz
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Yasmin Ali
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Leslie A Morris
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Vincent A Sutera
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Elizabeth E Dudenhausen
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Margaret Hibnick
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Susan T Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.
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17
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Nieken KJ, O’Brien K, McDonnell A, Zhaunova L, Ohkura H. A large-scale RNAi screen reveals that mitochondrial function is important for meiotic chromosome organization in oocytes. Chromosoma 2023; 132:1-18. [PMID: 36648541 PMCID: PMC9981535 DOI: 10.1007/s00412-023-00784-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
In prophase of the first meiotic division, chromatin forms a compact spherical cluster called the karyosome within the enlarged oocyte nucleus in Drosophila melanogaster. Similar clustering of chromatin has been widely observed in oocytes in many species including humans. It was previously shown that the proper karyosome formation is required for faithful chromosome segregation, but knowledge about its formation and maintenance is limited. To identify genes involved in karyosome formation, we carried out a large-scale cytological screen using Drosophila melanogaster oocytes. This screen comprised 3916 genes expressed in ovaries, of which 106 genes triggered reproducible karyosome defects upon knockdown. The karyosome defects in 24 out of these 106 genes resulted from activation of the meiotic recombination checkpoint, suggesting possible roles in DNA repair or piRNA processing. The other genes identified in this screen include genes with functions linked to chromatin, nuclear envelope, and actin. We also found that silencing of genes with mitochondrial functions, including electron transport chain components, induced a distinct karyosome defect typically with de-clustered chromosomes located close to the nuclear envelope. Furthermore, mitochondrial dysfunction not only impairs karyosome formation and maintenance, but also delays synaptonemal complex disassembly in cells not destined to become the oocyte. These karyosome defects do not appear to be mediated by apoptosis. This large-scale unbiased study uncovered a set of genes required for karyosome formation and revealed a new link between mitochondrial dysfunction and chromatin organization in oocytes.
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Affiliation(s)
- Karen Jule Nieken
- grid.4305.20000 0004 1936 7988Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Kathryn O’Brien
- grid.4305.20000 0004 1936 7988Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Alexander McDonnell
- grid.4305.20000 0004 1936 7988Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Liudmila Zhaunova
- grid.4305.20000 0004 1936 7988Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF UK
| | - Hiroyuki Ohkura
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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18
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Tesfay L, Paul BT, Hegde P, Brewer M, Habbani S, Jellison E, Moore T, Wu H, Torti SV, Torti FM. Complementary anti-cancer pathways triggered by inhibition of sideroflexin 4 in ovarian cancer. Sci Rep 2022; 12:19936. [PMID: 36402786 PMCID: PMC9675821 DOI: 10.1038/s41598-022-24391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
DNA damaging agents are a mainstay of standard chemotherapy for ovarian cancer. Unfortunately, resistance to such DNA damaging agents frequently develops, often due to increased activity of DNA repair pathways. Sideroflexin 4 (SFXN4) is a little-studied inner mitochondrial membrane protein. Here we demonstrate that SFXN4 plays a role in synthesis of iron sulfur clusters (Fe-S) in ovarian cancer cells and ovarian cancer tumor-initiating cells, and that knockdown of SFXN4 inhibits Fe-S biogenesis in ovarian cancer cells. We demonstrate that this has two important consequences that may be useful in anti-cancer therapy. First, inhibition of Fe-S biogenesis triggers the accumulation of excess iron, leading to oxidative stress. Second, because enzymes critical to multiple DNA repair pathways require Fe-S clusters for their function, DNA repair enzymes and DNA repair itself are inhibited by reduction of SFXN4. Through this dual mechanism, SFXN4 inhibition heightens ovarian cancer cell sensitivity to DNA-damaging drugs and DNA repair inhibitors used in ovarian cancer therapy, such as cisplatin and PARP inhibitors. Sensitization is achieved even in drug resistant ovarian cancer cells. Further, knockout of SFXN4 decreases DNA repair and profoundly inhibits tumor growth in a mouse model of ovarian cancer metastasis. Collectively, these results suggest that SFXN4 may represent a new target in ovarian cancer therapy.
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Affiliation(s)
- Lia Tesfay
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Bibbin T Paul
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Poornima Hegde
- Department of Pathology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Molly Brewer
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Samrin Habbani
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, 47907, USA
| | - Evan Jellison
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Timothy Moore
- Statistical Consulting Services, Center for Open Research Resources, University of Connecticut, Storrs, CT, 06269, USA
| | - Hao Wu
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Suzy V Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
| | - Frank M Torti
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
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19
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Iron-Sulfur Clusters: A Key Factor of Regulated Cell Death in Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7449941. [PMID: 36338346 PMCID: PMC9629928 DOI: 10.1155/2022/7449941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 11/21/2022]
Abstract
Iron-sulfur clusters are ancient cofactors that play crucial roles in myriad cellular functions. Recent studies have shown that iron-sulfur clusters are closely related to the mechanisms of multiple cell death modalities. In addition, numerous previous studies have demonstrated that iron-sulfur clusters play an important role in the development and treatment of cancer. This review first summarizes the close association of iron-sulfur clusters with cell death modalities such as ferroptosis, cuprotosis, PANoptosis, and apoptosis and their potential role in cancer activation and drug resistance. This review hopes to generate new cancer therapy ideas and overcome drug resistance by modulating iron-sulfur clusters.
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20
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NCOA4 links iron bioavailability to DNA metabolism. Cell Rep 2022; 40:111207. [PMID: 35977492 DOI: 10.1016/j.celrep.2022.111207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/20/2022] [Accepted: 07/22/2022] [Indexed: 12/22/2022] Open
Abstract
Iron is essential for deoxyribonucleotides production and for enzymes containing an Fe-S cluster involved in DNA replication and repair. How iron bioavailability and DNA metabolism are coordinated remains poorly understood. NCOA4 protein mediates autophagic degradation of ferritin to maintain iron homeostasis and inhibits DNA replication origin activation via hindrance of the MCM2-7 DNA helicase. Here, we show that iron deficiency inhibits DNA replication, parallel to nuclear NCOA4 stabilization. In iron-depleted cells, NCOA4 knockdown leads to unscheduled DNA synthesis, with replication stress, genome instability, and cell death. In mice, NCOA4 genetic inactivation causes defective intestinal regeneration upon dextran sulfate sodium-mediated injury, with DNA damage, defective cell proliferation, and cell death; in intestinal organoids, this is fostered by iron depletion. In summary, we describe a NCOA4-dependent mechanism that coordinates iron bioavailability and DNA replication. This function prevents replication stress, maintains genome integrity, and sustains high rates of cell proliferation during tissue regeneration.
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21
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Fu I, Mu H, Geacintov NE, Broyde S. Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair. Nucleic Acids Res 2022; 50:6837-6853. [PMID: 35713557 PMCID: PMC9262607 DOI: 10.1093/nar/gkac496] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 01/19/2023] Open
Abstract
In nucleotide excision repair (NER), the xeroderma pigmentosum D helicase (XPD) scans DNA searching for bulky lesions, stalls when encountering such damage to verify its presence, and allows repair to proceed. Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6-4) pyrimidone UV photoproduct (6-4PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215-221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.
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Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Hong Mu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- To whom correspondence should be addressed. Tel: +1 212 998 8231;
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22
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Mitochondrial De Novo Assembly of Iron–Sulfur Clusters in Mammals: Complex Matters in a Complex That Matters. INORGANICS 2022. [DOI: 10.3390/inorganics10030031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Iron–sulfur clusters (Fe–S or ISC) are essential cofactors that function in a wide range of biological pathways. In mammalian cells, Fe–S biosynthesis primarily relies on mitochondria and involves a concerted group of evolutionary-conserved proteins forming the ISC pathway. In the early stage of the ISC pathway, the Fe–S core complex is required for de novo assembly of Fe–S. In humans, the Fe–S core complex comprises the cysteine desulfurase NFS1, the scaffold protein ISCU2, frataxin (FXN), the ferredoxin FDX2, and regulatory/accessory proteins ISD11 and Acyl Carrier Protein (ACP). In recent years, the field has made significant advances in unraveling the structure of the Fe–S core complex and the mechanism underlying its function. Herein, we review the key recent findings related to the Fe–S core complex and its components. We highlight some of the unanswered questions and provide a model of the Fe–S assembly within the complex. In addition, we briefly touch on the genetic diseases associated with mutations in the Fe–S core complex components.
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23
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So M, Stiban J, Ciesielski GL, Hovde SL, Kaguni LS. Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase. Front Genet 2021; 12:790521. [PMID: 34950192 PMCID: PMC8688847 DOI: 10.3389/fgene.2021.790521] [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: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Recent evidence suggests that iron-sulfur clusters (ISCs) in DNA replicative proteins sense DNA-mediated charge transfer to modulate nuclear DNA replication. In the mitochondrial DNA replisome, only the replicative DNA helicase (mtDNA helicase) from Drosophila melanogaster (Dm) has been shown to contain an ISC in its N-terminal, primase-like domain (NTD). In this report, we confirm the presence of the ISC and demonstrate the importance of a metal cofactor in the structural stability of the Dm mtDNA helicase. Further, we show that the NTD also serves a role in membrane binding. We demonstrate that the NTD binds to asolectin liposomes, which mimic phospholipid membranes, through electrostatic interactions. Notably, membrane binding is more specific with increasing cardiolipin content, which is characteristically high in the mitochondrial inner membrane (MIM). We suggest that the N-terminal domain of the mtDNA helicase interacts with the MIM to recruit mtDNA and initiate mtDNA replication. Furthermore, Dm NUBPL, the known ISC donor for respiratory complex I and a putative donor for Dm mtDNA helicase, was identified as a peripheral membrane protein that is likely to execute membrane-mediated ISC delivery to its target proteins.
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Affiliation(s)
- Minyoung So
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland.,Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States
| | - Stacy L Hovde
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
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24
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Campos OA, Attar N, Cheng C, Vogelauer M, Mallipeddi NV, Schmollinger S, Matulionis N, Christofk HR, Merchant SS, Kurdistani SK. A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich's ataxia. SCIENCE ADVANCES 2021; 7:eabj9889. [PMID: 34919435 PMCID: PMC8682991 DOI: 10.1126/sciadv.abj9889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Disruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. A source of damage to Fe-S clusters is cuprous (Cu1+) ions. Since histone H3 enzymatically produces Cu1+ for copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3–mediated Cu1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, due to diminished assembly as occurs in Friedreich’s ataxia or defective distribution, causes severe metabolic and growth defects in Saccharomyces cerevisiae. Decreasing Cu1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster–dependent metabolism and growth. Our findings reveal an interplay between chromatin and mitochondria in Fe-S cluster homeostasis and a potential pathogenic role for histone enzyme activity and Cu1+ in diseases with Fe-S cluster dysfunction.
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Affiliation(s)
- Oscar A. Campos
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Narsis Attar
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan V. Mallipeddi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Nedas Matulionis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sabeeha S. Merchant
- QB3-Berkeley, University of California, Berkeley, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Siavash K. Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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25
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Redwood AB, Zhang X, Seth SB, Ge Z, Bindeman WE, Zhou X, Sinha VC, Heffernan TP, Piwnica-Worms H. The cytosolic iron-sulfur cluster assembly (CIA) pathway is required for replication stress tolerance of cancer cells to Chk1 and ATR inhibitors. NPJ Breast Cancer 2021; 7:152. [PMID: 34857765 PMCID: PMC8639742 DOI: 10.1038/s41523-021-00353-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
The relationship between ATR/Chk1 activity and replication stress, coupled with the development of potent and tolerable inhibitors of this pathway, has led to the clinical exploration of ATR and Chk1 inhibitors (ATRi/Chk1i) as anticancer therapies for single-agent or combinatorial application. The clinical efficacy of these therapies relies on the ability to ascertain which patient populations are most likely to benefit, so there is intense interest in identifying predictive biomarkers of response. To comprehensively evaluate the components that modulate cancer cell sensitivity to replication stress induced by Chk1i, we performed a synthetic-lethal drop-out screen in a cell line derived from a patient with triple-negative breast cancer (TNBC), using a pooled barcoded shRNA library targeting ~350 genes involved in DNA replication, DNA damage repair, and cycle progression. In addition, we sought to compare the relative requirement of these genes when DNA fidelity is challenged by clinically relevant anticancer breast cancer drugs, including cisplatin and PARP1/2 inhibitors, that have different mechanisms of action. This global comparison is critical for understanding not only which agents should be used together for combinatorial therapies in breast cancer patients, but also the genetic context in which these therapies will be most effective, and when a single-agent therapy will be sufficient to provide maximum therapeutic benefit to the patient. We identified unique potentiators of response to ATRi/Chk1i and describe a new role for components of the cytosolic iron-sulfur assembly (CIA) pathway, MMS19 and CIA2B-FAM96B, in replication stress tolerance of TNBC.
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Affiliation(s)
- Abena B. Redwood
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xiaomei Zhang
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Sahil B. Seth
- grid.240145.60000 0001 2291 4776Institute of Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.240145.60000 0001 2291 4776TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Zhongqi Ge
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Wendy E. Bindeman
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.152326.10000 0001 2264 7217Present Address: Vanderbilt University, Department of Cancer Biology, Nashville, TN 37235 USA
| | - Xinhui Zhou
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Vidya C. Sinha
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Timothy P. Heffernan
- grid.240145.60000 0001 2291 4776Institute of Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.240145.60000 0001 2291 4776TRACTION Platform, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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26
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Shi R, Hou W, Wang ZQ, Xu X. Biogenesis of Iron-Sulfur Clusters and Their Role in DNA Metabolism. Front Cell Dev Biol 2021; 9:735678. [PMID: 34660592 PMCID: PMC8514734 DOI: 10.3389/fcell.2021.735678] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
Iron–sulfur (Fe/S) clusters (ISCs) are redox-active protein cofactors that their synthesis, transfer, and insertion into target proteins require many components. Mitochondrial ISC assembly is the foundation of all cellular ISCs in eukaryotic cells. The mitochondrial ISC cooperates with the cytosolic Fe/S protein assembly (CIA) systems to accomplish the cytosolic and nuclear Fe/S clusters maturation. ISCs are needed for diverse cellular functions, including nitrogen fixation, oxidative phosphorylation, mitochondrial respiratory pathways, and ribosome assembly. Recent research advances have confirmed the existence of different ISCs in enzymes that regulate DNA metabolism, including helicases, nucleases, primases, DNA polymerases, and glycosylases. Here we outline the synthesis of mitochondrial, cytosolic and nuclear ISCs and highlight their functions in DNA metabolism.
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Affiliation(s)
- Ruifeng Shi
- Shenzhen University-Friedrich Schiller Universität Jena Joint Ph.D. Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Wenya Hou
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
| | - Xingzhi Xu
- Shenzhen University-Friedrich Schiller Universität Jena Joint Ph.D. Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
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27
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Petronek MS, Spitz DR, Allen BG. Iron-Sulfur Cluster Biogenesis as a Critical Target in Cancer. Antioxidants (Basel) 2021; 10:1458. [PMID: 34573089 PMCID: PMC8465902 DOI: 10.3390/antiox10091458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Cancer cells preferentially accumulate iron (Fe) relative to non-malignant cells; however, the underlying rationale remains elusive. Iron-sulfur (Fe-S) clusters are critical cofactors that aid in a wide variety of cellular functions (e.g., DNA metabolism and electron transport). In this article, we theorize that a differential need for Fe-S biogenesis in tumor versus non-malignant cells underlies the Fe-dependent cell growth demand of cancer cells to promote cell division and survival by promoting genomic stability via Fe-S containing DNA metabolic enzymes. In this review, we outline the complex Fe-S biogenesis process and its potential upregulation in cancer. We also discuss three therapeutic strategies to target Fe-S biogenesis: (i) redox manipulation, (ii) Fe chelation, and (iii) Fe mimicry.
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Affiliation(s)
- Michael S. Petronek
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Douglas R. Spitz
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
| | - Bryan G. Allen
- Department of Radiation Oncology, Division of Free Radical and Radiation Biology, The University of Iowa Hospitals and Clinics, Iowa City, IA 52242-1181, USA;
- Holden Comprehensive Cancer Center, Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242-1181, USA
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28
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Dietz JV, Fox JL, Khalimonchuk O. Down the Iron Path: Mitochondrial Iron Homeostasis and Beyond. Cells 2021; 10:cells10092198. [PMID: 34571846 PMCID: PMC8468894 DOI: 10.3390/cells10092198] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the processes of and components involved in mitochondrial iron trafficking and storage, as well as mitochondrial iron–sulfur cluster biogenesis and heme biosynthesis. Recent findings and the most pressing topics for future research are highlighted.
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Affiliation(s)
- Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA;
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Correspondence:
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29
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Bandyopadhyay S, Chaudhury S, Mehta D, Ramesh A. RETRACTED ARTICLE: Discovery of iron-sensing bacterial riboswitches. Nat Chem Biol 2021; 17:924. [PMID: 33020663 DOI: 10.1038/s41589-020-00665-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/29/2020] [Accepted: 08/26/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Siladitya Bandyopadhyay
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Tirumalaisamudram, Thanjavur, India
| | - Susmitnarayan Chaudhury
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Dolly Mehta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Tirumalaisamudram, Thanjavur, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India.
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30
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Hydroxyurea-The Good, the Bad and the Ugly. Genes (Basel) 2021; 12:genes12071096. [PMID: 34356112 PMCID: PMC8304116 DOI: 10.3390/genes12071096] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Hydroxyurea (HU) is mostly referred to as an inhibitor of ribonucleotide reductase (RNR) and as the agent that is commonly used to arrest cells in the S-phase of the cycle by inducing replication stress. It is a well-known and widely used drug, one which has proved to be effective in treating chronic myeloproliferative disorders and which is considered a staple agent in sickle anemia therapy and—recently—a promising factor in preventing cognitive decline in Alzheimer’s disease. The reversibility of HU-induced replication inhibition also makes it a common laboratory ingredient used to synchronize cell cycles. On the other hand, prolonged treatment or higher dosage of hydroxyurea causes cell death due to accumulation of DNA damage and oxidative stress. Hydroxyurea treatments are also still far from perfect and it has been suggested that it facilitates skin cancer progression. Also, recent studies have shown that hydroxyurea may affect a larger number of enzymes due to its less specific interaction mechanism, which may contribute to further as-yet unspecified factors affecting cell response. In this review, we examine the actual state of knowledge about hydroxyurea and the mechanisms behind its cytotoxic effects. The practical applications of the recent findings may prove to enhance the already existing use of the drug in new and promising ways.
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31
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Xu L, Chen S, Wen B, Shi H, Chi C, Liu C, Wang K, Tao X, Wang M, Lv J, Yan L, Ling L, Zhu G. Identification of a Novel Class of Photolyases as Possible Ancestors of Their Family. Mol Biol Evol 2021; 38:4505-4519. [PMID: 34175934 PMCID: PMC8476157 DOI: 10.1093/molbev/msab191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
UV irradiation induces the formation of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts in DNA. These two types of lesions can be directly photorepaired by CPD photolyases and 6-4 photolyases, respectively. Recently, a new class of 6-4 photolyases named iron–sulfur bacterial cryptochromes and photolyases (FeS-BCPs) were found, which were considered as the ancestors of all photolyases and their homologs—cryptochromes. However, a controversy exists regarding 6-4 photoproducts only constituting ∼10–30% of the total UV-induced lesions that primordial organisms would hardly survive without a CPD repair enzyme. By extensive phylogenetic analyses, we identified a novel class of proteins, all from eubacteria. They have relatively high similarity to class I/III CPD photolyases, especially in the putative substrate-binding and FAD-binding regions. However, these proteins are shorter, and they lack the “N-terminal α/β domain” of normal photolyases. Therefore, we named them short photolyase-like. Nevertheless, similar to FeS-BCPs, some of short photolyase-likes also contain four conserved cysteines, which may also coordinate an iron–sulfur cluster as FeS-BCPs. A member from Rhodococcus fascians was cloned and expressed. It was demonstrated that the protein contains a FAD cofactor and an iron–sulfur cluster, and has CPD repair activity. It was speculated that this novel class of photolyases may be the real ancestors of the cryptochrome/photolyase family.
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Affiliation(s)
- Lei Xu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Simeng Chen
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Bin Wen
- Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Hao Shi
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Changbiao Chi
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Chenxi Liu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Kangyu Wang
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Xianglin Tao
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Ming Wang
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Jun Lv
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Liang Yan
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Liefeng Ling
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Guoping Zhu
- Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, 241000, China
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32
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Structural study of the N-terminal domain of human MCM8/9 complex. Structure 2021; 29:1171-1181.e4. [PMID: 34043945 DOI: 10.1016/j.str.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/26/2021] [Accepted: 05/07/2021] [Indexed: 11/20/2022]
Abstract
MCM8/9 is a complex involved in homologous recombination (HR) repair pathway. MCM8/9 dysfunction can cause genome instability and result in primary ovarian insufficiency (POI). However, the mechanism underlying these effects is largely unknown. Here, we report crystal structures of the N-terminal domains (NTDs) of MCM8 and MCM9, and build a ring-shaped NTD structure based on a 6.6 Å resolution cryoelectron microscopy map. This shows that the MCM8/9 complex forms a 3:3 heterohexamer in an alternating pattern. A positively charged DNA binding channel and a putative ssDNA exit pathway for fork DNA unwinding are revealed. Based on the atomic model, the potential effects of the clinical POI mutants are interpreted. Surprisingly, the zinc-finger motifs are found to be capable of binding an iron atom as well. Overall, our results provide a model for the formation of the MCM8/9 complex and provide a path for further studies.
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33
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Hodáková Z, Nans A, Kunzelmann S, Mehmood S, Taylor I, Uhlmann F, Cherepanov P, Singleton MR. Structural characterisation of the Chaetomium thermophilum Chl1 helicase. PLoS One 2021; 16:e0251261. [PMID: 33970942 PMCID: PMC8109800 DOI: 10.1371/journal.pone.0251261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/22/2021] [Indexed: 11/19/2022] Open
Abstract
Chl1 is a member of the XPD family of 5'-3' DNA helicases, which perform a variety of roles in genome maintenance and transmission. They possess a variety of unique structural features, including the presence of a highly variable, partially-ordered insertion in the helicase domain 1. Chl1 has been shown to be required for chromosome segregation in yeast due to its role in the formation of persistent chromosome cohesion during S-phase. Here we present structural and biochemical data to show that Chl1 has the same overall domain organisation as other members of the XPD family, but with some conformational alterations. We also present data suggesting the insert domain in Chl1 regulates its DNA binding.
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Affiliation(s)
- Zuzana Hodáková
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Shahid Mehmood
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Ian Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
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34
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Milanese C, Gabriels S, Barnhoorn S, Cerri S, Ulusoy A, Gornati SV, Wallace DF, Blandini F, Di Monte DA, Subramaniam VN, Mastroberardino PG. Gender biased neuroprotective effect of Transferrin Receptor 2 deletion in multiple models of Parkinson's disease. Cell Death Differ 2021; 28:1720-1732. [PMID: 33323945 PMCID: PMC8166951 DOI: 10.1038/s41418-020-00698-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 01/28/2023] Open
Abstract
Alterations in the metabolism of iron and its accumulation in the substantia nigra pars compacta accompany the pathogenesis of Parkinson's disease (PD). Changes in iron homeostasis also occur during aging, which constitutes a PD major risk factor. As such, mitigation of iron overload via chelation strategies has been considered a plausible disease modifying approach. Iron chelation, however, is imperfect because of general undesired side effects and lack of specificity; more effective approaches would rely on targeting distinctive pathways responsible for iron overload in brain regions relevant to PD and, in particular, the substantia nigra. We have previously demonstrated that the Transferrin/Transferrin Receptor 2 (TfR2) iron import mechanism functions in nigral dopaminergic neurons, is perturbed in PD models and patients, and therefore constitutes a potential therapeutic target to halt iron accumulation. To validate this hypothesis, we generated mice with targeted deletion of TfR2 in dopaminergic neurons. In these animals, we modeled PD with multiple approaches, based either on neurotoxin exposure or alpha-synuclein proteotoxic mechanisms. We found that TfR2 deletion can provide neuroprotection against dopaminergic degeneration, and against PD- and aging-related iron overload. The effects, however, were significantly more pronounced in females rather than in males. Our data indicate that the TfR2 iron import pathway represents an amenable strategy to hamper PD progression. Data also suggest, however, that therapeutic strategies targeting TfR2 should consider a potential sexual dimorphism in neuroprotective response.
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Affiliation(s)
- Chiara Milanese
- Department of Molecular Genetics, Rotterdam, the Netherlands ,grid.7678.e0000 0004 1757 7797IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Sylvia Gabriels
- Department of Molecular Genetics, Rotterdam, the Netherlands
| | | | | | - Ayse Ulusoy
- grid.424247.30000 0004 0438 0426German Centre for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - S. V. Gornati
- grid.5645.2000000040459992XDepartment of Neuroscience Erasmus MC, Rotterdam, the Netherlands
| | - Daniel F. Wallace
- grid.1024.70000000089150953School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Brisbane, QLD Australia
| | - Fabio Blandini
- IRCCS Mondino Foundation, 27100 Pavia, Italy ,grid.8982.b0000 0004 1762 5736Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Donato A. Di Monte
- grid.424247.30000 0004 0438 0426German Centre for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - V. Nathan Subramaniam
- grid.1024.70000000089150953School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Brisbane, QLD Australia
| | - Pier G. Mastroberardino
- Department of Molecular Genetics, Rotterdam, the Netherlands ,grid.7678.e0000 0004 1757 7797IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy ,grid.158820.60000 0004 1757 2611Department of Life, Health, and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
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35
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Przybyla-Toscano J, Boussardon C, Law SR, Rouhier N, Keech O. Gene atlas of iron-containing proteins in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:258-274. [PMID: 33423341 DOI: 10.1111/tpj.15154] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 05/27/2023]
Abstract
Iron (Fe) is an essential element for the development and physiology of plants, owing to its presence in numerous proteins involved in central biological processes. Here, we established an exhaustive, manually curated inventory of genes encoding Fe-containing proteins in Arabidopsis thaliana, and summarized their subcellular localization, spatiotemporal expression and evolutionary age. We have currently identified 1068 genes encoding potential Fe-containing proteins, including 204 iron-sulfur (Fe-S) proteins, 446 haem proteins and 330 non-Fe-S/non-haem Fe proteins (updates of this atlas are available at https://conf.arabidopsis.org/display/COM/Atlas+of+Fe+containing+proteins). A fourth class, containing 88 genes for which iron binding is uncertain, is indexed as 'unclear'. The proteins are distributed in diverse subcellular compartments with strong differences per category. Interestingly, analysis of the gene age index showed that most genes were acquired early in plant evolutionary history and have progressively gained regulatory elements, to support the complex organ-specific and development-specific functions necessitated by the emergence of terrestrial plants. With this gene atlas, we provide a valuable and updateable tool for the research community that supports the characterization of the molecular actors and mechanisms important for Fe metabolism in plants. This will also help in selecting relevant targets for breeding or biotechnological approaches aiming at Fe biofortification in crops.
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Affiliation(s)
| | - Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-90187, Sweden
| | - Simon R Law
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-90187, Sweden
| | | | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-90187, Sweden
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Calvo JA, Fritchman B, Hernandez D, Persky NS, Johannessen CM, Piccioni F, Kelch BA, Cantor SB. Comprehensive Mutational Analysis of the BRCA1-Associated DNA Helicase and Tumor-Suppressor FANCJ/BACH1/BRIP1. Mol Cancer Res 2021; 19:1015-1025. [PMID: 33619228 DOI: 10.1158/1541-7786.mcr-20-0828] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
FANCJ (BRIP1/BACH1) is a hereditary breast and ovarian cancer (HBOC) gene encoding a DNA helicase. Similar to HBOC genes, BRCA1 and BRCA2, FANCJ is critical for processing DNA inter-strand crosslinks (ICL) induced by chemotherapeutics, such as cisplatin. Consequently, cells deficient in FANCJ or its catalytic activity are sensitive to ICL-inducing agents. Unfortunately, the majority of FANCJ clinical mutations remain uncharacterized, limiting therapeutic opportunities to effectively use cisplatin to treat tumors with mutated FANCJ. Here, we sought to perform a comprehensive screen to identify FANCJ loss-of-function (LOF) mutations. We developed a FANCJ lentivirus mutation library representing approximately 450 patient-derived FANCJ nonsense and missense mutations to introduce FANCJ mutants into FANCJ knockout (K/O) HeLa cells. We performed a high-throughput screen to identify FANCJ LOF mutants that, as compared with wild-type FANCJ, fail to robustly restore resistance to ICL-inducing agents, cisplatin or mitomycin C (MMC). On the basis of the failure to confer resistance to either cisplatin or MMC, we identified 26 missense and 25 nonsense LOF mutations. Nonsense mutations elucidated a relationship between location of truncation and ICL sensitivity, as the majority of nonsense mutations before amino acid 860 confer ICL sensitivity. Further validation of a subset of LOF mutations confirmed the ability of the screen to identify FANCJ mutations unable to confer ICL resistance. Finally, mapping the location of LOF mutations to a new homology model provides additional functional information. IMPLICATIONS: We identify 51 FANCJ LOF mutations, providing important classification of FANCJ mutations that will afford additional therapeutic strategies for affected patients.
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Affiliation(s)
- Jennifer A Calvo
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Briana Fritchman
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Nicole S Persky
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Sharon B Cantor
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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Tifoun N, De las Heras JM, Guillaume A, Bouleau S, Mignotte B, Le Floch N. Insights into the Roles of the Sideroflexins/SLC56 Family in Iron Homeostasis and Iron-Sulfur Biogenesis. Biomedicines 2021; 9:103. [PMID: 33494450 PMCID: PMC7911444 DOI: 10.3390/biomedicines9020103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/25/2023] Open
Abstract
Sideroflexins (SLC56 family) are highly conserved multi-spanning transmembrane proteins inserted in the inner mitochondrial membrane in eukaryotes. Few data are available on their molecular function, but since their first description, they were thought to be metabolite transporters probably required for iron utilization inside the mitochondrion. Such as numerous mitochondrial transporters, sideroflexins remain poorly characterized. The prototypic member SFXN1 has been recently identified as the previously unknown mitochondrial transporter of serine. Nevertheless, pending questions on the molecular function of sideroflexins remain unsolved, especially their link with iron metabolism. Here, we review the current knowledge on sideroflexins, their presumed mitochondrial functions and the sparse-but growing-evidence linking sideroflexins to iron homeostasis and iron-sulfur cluster biogenesis. Since an imbalance in iron homeostasis can be detrimental at the cellular and organismal levels, we also investigate the relationship between sideroflexins, iron and physiological disorders. Investigating Sideroflexins' functions constitutes an emerging research field of great interest and will certainly lead to the main discoveries of mitochondrial physio-pathology.
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Affiliation(s)
- Nesrine Tifoun
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - José M. De las Heras
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Arnaud Guillaume
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Sylvina Bouleau
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Bernard Mignotte
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
- École Pratique des Hautes Études, PSL University, 75014 Paris, France
| | - Nathalie Le Floch
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
- GCGP Department, IUT de Vélizy/Rambouillet, UVSQ, Université Paris-Saclay, 78120 Rambouillet, France
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Lehrke MJ, Shapiro MJ, Rajcula MJ, Kennedy MM, McCue SA, Medina KL, Shapiro VS. The mitochondrial iron transporter ABCB7 is required for B cell development, proliferation, and class switch recombination in mice. eLife 2021; 10:69621. [PMID: 34762046 PMCID: PMC8585479 DOI: 10.7554/elife.69621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are cofactors essential for the activity of numerous enzymes including DNA polymerases, helicases, and glycosylases. They are synthesized in the mitochondria as Fe-S intermediates and are exported to the cytoplasm for maturation by the mitochondrial transporter ABCB7. Here, we demonstrate that ABCB7 is required for bone marrow B cell development, proliferation, and class switch recombination, but is dispensable for peripheral B cell homeostasis in mice. Conditional deletion of ABCB7 using Mb1-cre resulted in a severe block in bone marrow B cell development at the pro-B cell stage. The loss of ABCB7 did not alter expression of transcription factors required for B cell specification or commitment. While increased intracellular iron was observed in ABCB7-deficient pro-B cells, this did not lead to increased cellular or mitochondrial reactive oxygen species, ferroptosis, or apoptosis. Interestingly, loss of ABCB7 led to replication-induced DNA damage in pro-B cells, independent of VDJ recombination, and these cells had evidence of slowed DNA replication. Stimulated ABCB7-deficient splenic B cells from CD23-cre mice also had a striking loss of proliferation and a defect in class switching. Thus, ABCB7 is essential for early B cell development, proliferation, and class switch recombination.
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Affiliation(s)
| | | | | | | | | | - Kay L Medina
- Department of Immunology, Mayo ClinicRochesterUnited States
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40
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Hershkovitz T, Kurolap A, Tal G, Paperna T, Mory A, Staples J, Brigatti KW, Gonzaga-Jauregui C, Dumin E, Saada A, Mandel H, Baris Feldman H. A recurring NFS1 pathogenic variant causes a mitochondrial disorder with variable intra-familial patient outcomes. Mol Genet Metab Rep 2020; 26:100699. [PMID: 33457206 PMCID: PMC7797929 DOI: 10.1016/j.ymgmr.2020.100699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 12/20/2020] [Indexed: 02/09/2023] Open
Abstract
Iron‑sulfur clusters (FeSCs) are vital components of a variety of essential proteins, most prominently within mitochondrial respiratory chain complexes I-III; Fe-S assembly and distribution is performed via multi-step pathways. Variants affecting several proteins in these pathways have been described in genetic disorders, including severe mitochondrial disease. Here we describe a Christian Arab kindred with two infants that died due to mitochondrial disorder involving Fe-S containing respiratory chain complexes and a third sibling who survived the initial crisis. A homozygous missense variant in NFS1: c.215G>A; p.Arg72Gln was detected by whole exome sequencing. The NFS1 gene encodes a cysteine desulfurase, which, in complex with ISD11 and ACP, initiates the first step of Fe-S formation. Arginine at position 72 plays a role in NFS1-ISD11 complex formation; therefore, its substitution with glutamine is expected to affect complex stability and function. Interestingly, this is the only pathogenic variant ever reported in the NFS1 gene, previously described once in an Old Order Mennonite family presenting a similar phenotype with intra-familial variability in patient outcomes. Analysis of datasets from both populations did not show a common haplotype, suggesting this variant is a recurrent de novo variant. Our report of the second case of NFS1-related mitochondrial disease corroborates the pathogenicity of this recurring variant and implicates it as a hot-spot variant. While the genetic resolution allows for prenatal diagnosis for the family, it also raises critical clinical questions regarding follow-up and possible treatment options of severely affected and healthy homozygous individuals with mitochondrial co-factor therapy or cysteine supplementation.
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Affiliation(s)
- Tova Hershkovitz
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alina Kurolap
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Galit Tal
- Metabolic Unit, Ruth Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | | | | | | | | | - Elena Dumin
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.,Department of Clinical Biochemistry, Rambam Health Care Campus, Haifa, Israel
| | - Ann Saada
- Department of Genetics, Hadassah Medical Center and The Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Hanna Mandel
- Metabolic Unit, Ruth Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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41
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Behmoaras J. The versatile biochemistry of iron in macrophage effector functions. FEBS J 2020; 288:6972-6989. [PMID: 33354925 DOI: 10.1111/febs.15682] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023]
Abstract
Macrophages are mononuclear phagocytes with remarkable polarization ability that allow them to have tissue-specific functions during development, homeostasis, inflammatory and infectious disease. One particular trophic factor in the tissue environment is iron, which is intimately linked to macrophage effector functions. Macrophages have a well-described role in the control of systemic iron levels, but their activation state is also depending on iron-containing proteins/enzymes. Haemoproteins, dioxygenases and iron-sulphur (Fe-S) enzymes are iron-binding proteins that have bactericidal, metabolic and epigenetic-related functions, essential to shape the context-dependent macrophage polarization. In this review, I describe mainly pro-inflammatory macrophage polarization focussing on the role of iron biochemistry in selected haemoproteins and Fe-S enzymes. I show how iron, as part of haem or Fe-S clusters, participates in the cellular control of pro-inflammatory redox reactions in parallel with its role as enzymatic cofactor. I highlight a possible coordinated regulation of haemoproteins and Fe-S enzymes during classical macrophage activation. Finally, I describe tryptophan and α-ketoglutarate metabolism as two essential effector pathways in macrophages that use diverse iron biochemistry at different enzymatic steps. Through these pathways, I show how iron participates in the regulation of essential metabolites that shape macrophage function.
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42
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Gao J, Zhou Q, Wu D, Chen L. Mitochondrial iron metabolism and its role in diseases. Clin Chim Acta 2020; 513:6-12. [PMID: 33309797 DOI: 10.1016/j.cca.2020.12.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022]
Abstract
Iron is one of the most important elements for life, but excess iron is toxic. Intracellularly, mitochondria are the center of iron utilization requiring sufficient amounts to maintain normal physiologic function. Accordingly, disruption of iron homeostasis could seriously impact mitochondrial function leading to impaired energy state and potential disease development. In this review, we discuss mechanisms of iron metabolism including transport, processing, heme synthesis, iron-sulfur cluster biogenesis and storage. We highlight the vital role of mitochondrial iron in pathologic states including neurodegenerative disorders and sideroblastic anemia.
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Affiliation(s)
- Jiayin Gao
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang 421001, China
| | - Qionglin Zhou
- Department of Pharmacy, The First People's Hospital of Shaoguan, Shaoguan Hospital of Southern Medical University, Shaoguan 512000, China
| | - Di Wu
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang 421001, China.
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang 421001, China.
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43
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K JCB, Kapoor BS, Mandal K, Ghosh S, Mokhamatam RB, Manna SK, Mukhopadhyay SS. Loss of Mitochondrial Localization of Human FANCG Causes Defective FANCJ Helicase. Mol Cell Biol 2020; 40:e00306-20. [PMID: 32989015 PMCID: PMC7652403 DOI: 10.1128/mcb.00306-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/11/2020] [Accepted: 09/17/2020] [Indexed: 11/20/2022] Open
Abstract
Fanconi anemia (FA) is a unique DNA damage repair pathway. To date, 22 genes have been identified that are associated with the FA pathway. A defect in any of those genes causes genomic instability, and the patients bearing the mutation become susceptible to cancer. In our earlier work, we identified that Fanconi anemia protein G (FANCG) protects the mitochondria from oxidative stress. In this report, we have identified eight patients having a mutation (C.65G>C), which converts arginine at position 22 to proline (p.Arg22Pro) in the N terminus of FANCG. The mutant protein, hFANCGR22P, is able to repair the DNA and able to retain the monoubiquitination of FANCD2 in the FANCGR22P/FGR22P cell. However, it lost mitochondrial localization and failed to protect mitochondria from oxidative stress. Mitochondrial instability in the FANCGR22P cell causes the transcriptional downregulation of mitochondrial iron-sulfur cluster biogenesis protein frataxin (FXN) and the resulting iron deficiency of FA protein FANCJ, an iron-sulfur-containing helicase involved in DNA repair.
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Affiliation(s)
- Jagadeesh Chandra Bose K
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Bishwajit Singh Kapoor
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Kamal Mandal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Shubhrima Ghosh
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | | | - Sunil K Manna
- Center for DNA Finger Printing and Diagnostics, Hyderabad, India
| | - Sudit S Mukhopadhyay
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
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Awate S, Sommers JA, Datta A, Nayak S, Bellani MA, Yang O, Dunn CA, Nicolae CM, Moldovan GL, Seidman MM, Cantor SB, Brosh RM. FANCJ compensates for RAP80 deficiency and suppresses genomic instability induced by interstrand cross-links. Nucleic Acids Res 2020; 48:9161-9180. [PMID: 32797166 DOI: 10.1093/nar/gkaa660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
FANCJ, a DNA helicase and interacting partner of the tumor suppressor BRCA1, is crucial for the repair of DNA interstrand crosslinks (ICL), a highly toxic lesion that leads to chromosomal instability and perturbs normal transcription. In diploid cells, FANCJ is believed to operate in homologous recombination (HR) repair of DNA double-strand breaks (DSB); however, its precise role and molecular mechanism is poorly understood. Moreover, compensatory mechanisms of ICL resistance when FANCJ is deficient have not been explored. In this work, we conducted a siRNA screen to identify genes of the DNA damage response/DNA repair regime that when acutely depleted sensitize FANCJ CRISPR knockout cells to a low concentration of the DNA cross-linking agent mitomycin C (MMC). One of the top hits from the screen was RAP80, a protein that recruits repair machinery to broken DNA ends and regulates DNA end-processing. Concomitant loss of FANCJ and RAP80 not only accentuates DNA damage levels in human cells but also adversely affects the cell cycle checkpoint, resulting in profound chromosomal instability. Genetic complementation experiments demonstrated that both FANCJ's catalytic activity and interaction with BRCA1 are important for ICL resistance when RAP80 is deficient. The elevated RPA and RAD51 foci in cells co-deficient of FANCJ and RAP80 exposed to MMC are attributed to single-stranded DNA created by Mre11 and CtIP nucleases. Altogether, our cell-based findings together with biochemical studies suggest a critical function of FANCJ to suppress incompletely processed and toxic joint DNA molecules during repair of ICL-induced DNA damage.
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Affiliation(s)
- Sanket Awate
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Sumeet Nayak
- Department of Cancer Biology, University of Massachusetts Medical School - UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher A Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Sharon B Cantor
- Department of Cancer Biology, University of Massachusetts Medical School - UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
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Kamal L, Pierce SB, Canavati C, Rayyan AA, Jaraysa T, Lobel O, Lolas S, Norquist BM, Rabie G, Zahdeh F, Levy-Lahad E, King MC, Kanaan MN. Helicase-inactivating BRIP1 mutation yields Fanconi anemia with microcephaly and other congenital abnormalities. Cold Spring Harb Mol Case Stud 2020; 6:a005652. [PMID: 33028645 PMCID: PMC7552932 DOI: 10.1101/mcs.a005652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Fanconi anemia is a genetically and phenotypically heterogeneous disorder characterized by congenital anomalies, bone marrow failure, cancer, and sensitivity of chromosomes to DNA cross-linking agents. One of the 22 genes responsible for Fanconi anemia is BRIP1, in which biallelic truncating mutations lead to Fanconi anemia group J and monoallelic truncating mutations predispose to certain cancers. However, of the more than 1000 reported missense mutations in BRIP1, very few have been functionally characterized. We evaluated the functional consequence of BRIP1 p.R848H (c.2543G > A), which was homozygous in two cousins with low birth weight, microcephaly, upper limb abnormalities, and imperforate anus and for whom chromosome breakage analysis of patient cells revealed increased mitomycin C sensitivity. BRIP1 p.R848H alters a highly conserved residue in the catalytic DNA helicase domain. We show that BRIP1 p.R848H leads to a defect in helicase activity. Heterozygosity at this missense has been reported in multiple cancer patients but, in the absence of functional studies, classified as of unknown significance. Our results support that this mutation is pathogenic for Fanconi anemia in homozygotes and for increased cancer susceptibility in heterozygous carriers.
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Affiliation(s)
- Lara Kamal
- Molecular Genetics Laboratory, Istishari Arab Hospital, Ramallah, Palestine
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Sarah B Pierce
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Christina Canavati
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Amal Abu Rayyan
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Tamara Jaraysa
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Orit Lobel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Suhair Lolas
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Barbara M Norquist
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington 98195, USA
| | - Grace Rabie
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Fouad Zahdeh
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Mary-Claire King
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Moien N Kanaan
- Molecular Genetics Laboratory, Istishari Arab Hospital, Ramallah, Palestine
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
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Pereira M, Chen TD, Buang N, Olona A, Ko JH, Prendecki M, Costa ASH, Nikitopoulou E, Tronci L, Pusey CD, Cook HT, McAdoo SP, Frezza C, Behmoaras J. Acute Iron Deprivation Reprograms Human Macrophage Metabolism and Reduces Inflammation In Vivo. Cell Rep 2020; 28:498-511.e5. [PMID: 31291584 PMCID: PMC6635384 DOI: 10.1016/j.celrep.2019.06.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/29/2019] [Accepted: 06/07/2019] [Indexed: 12/23/2022] Open
Abstract
Iron is an essential metal that fine-tunes the innate immune response by regulating macrophage function, but an integrative view of transcriptional and metabolic responses to iron perturbation in macrophages is lacking. Here, we induced acute iron chelation in primary human macrophages and measured their transcriptional and metabolic responses. Acute iron deprivation causes an anti-proliferative Warburg transcriptome, characterized by an ATF4-dependent signature. Iron-deprived human macrophages show an inhibition of oxidative phosphorylation and a concomitant increase in glycolysis, a large increase in glucose-derived citrate pools associated with lipid droplet accumulation, and modest levels of itaconate production. LPS polarization increases the itaconate:succinate ratio and decreases pro-inflammatory cytokine production. In rats, acute iron deprivation reduces the severity of macrophage-dependent crescentic glomerulonephritis by limiting glomerular cell proliferation and inducing lipid accumulation in the renal cortex. These results suggest that acute iron deprivation has in vivo protective effects mediated by an anti-inflammatory immunometabolic switch in macrophages.
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Affiliation(s)
- Marie Pereira
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Tai-Di Chen
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK; Department of Anatomic Pathology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Norzawani Buang
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Antoni Olona
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Jeong-Hun Ko
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Maria Prendecki
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Ana S H Costa
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Efterpi Nikitopoulou
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Laura Tronci
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Charles D Pusey
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - H Terence Cook
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Stephen P McAdoo
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK.
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Liu H, Perumal N, Manicam C, Mercieca K, Prokosch V. Proteomics Reveals the Potential Protective Mechanism of Hydrogen Sulfide on Retinal Ganglion Cells in an Ischemia/Reperfusion Injury Animal Model. Pharmaceuticals (Basel) 2020; 13:ph13090213. [PMID: 32867129 PMCID: PMC7557839 DOI: 10.3390/ph13090213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Glaucoma is the leading cause of irreversible blindness and is characterized by progressive retinal ganglion cell (RGC) degeneration. Hydrogen sulfide (H2S) is a potent neurotransmitter and has been proven to protect RGCs against glaucomatous injury in vitro and in vivo. This study is to provide an overall insight of H2S’s role in glaucoma pathophysiology. Ischemia-reperfusion injury (I/R) was induced in Sprague-Dawley rats (n = 12) by elevating intraocular pressure to 55 mmHg for 60 min. Six of the animals received intravitreal injection of H2S precursor prior to the procedure and the retina was harvested 24 h later. Contralateral eyes were assigned as control. RGCs were quantified and compared within the groups. Retinal proteins were analyzed via label-free mass spectrometry based quantitative proteomics approach. The pathways of the differentially expressed proteins were identified by ingenuity pathway analysis (IPA). H2S significantly improved RGC survival against I/R in vivo (p < 0.001). In total 1115 proteins were identified, 18 key proteins were significantly differentially expressed due to I/R and restored by H2S. Another 11 proteins were differentially expressed following H2S. IPA revealed a significant H2S-mediated activation of pathways related to mitochondrial function, iron homeostasis and vasodilation. This study provides first evidence of the complex role that H2S plays in protecting RGC against I/R.
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Affiliation(s)
- Hanhan Liu
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Caroline Manicam
- Experimental and Translational Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (H.L.); (N.P.); (C.M.)
| | - Karl Mercieca
- Royal Eye Hospital, School of Medicine, University of Manchester, Manchester M13 9WH, UK;
| | - Verena Prokosch
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Correspondence: ; Tel.: +49-1703862250
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48
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Structural insights into Fe–S protein biogenesis by the CIA targeting complex. Nat Struct Mol Biol 2020; 27:735-742. [DOI: 10.1038/s41594-020-0454-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/19/2020] [Indexed: 12/11/2022]
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49
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Silva RMB, Grodick MA, Barton JK. UvrC Coordinates an O 2-Sensitive [4Fe4S] Cofactor. J Am Chem Soc 2020; 142:10964-10977. [PMID: 32470300 DOI: 10.1021/jacs.0c01671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV-visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60-70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC.
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Affiliation(s)
- Rebekah M B Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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50
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Mariotti L, Wild S, Brunoldi G, Piceni A, Ceppi I, Kummer S, Lutz RE, Cejka P, Gari K. The iron-sulphur cluster in human DNA2 is required for all biochemical activities of DNA2. Commun Biol 2020; 3:322. [PMID: 32576938 PMCID: PMC7311471 DOI: 10.1038/s42003-020-1048-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/03/2020] [Indexed: 11/25/2022] Open
Abstract
The nuclease/helicase DNA2 plays important roles in DNA replication, repair and processing of stalled replication forks. DNA2 contains an iron-sulphur (FeS) cluster, conserved in eukaryotes and in a related bacterial nuclease. FeS clusters in DNA maintenance proteins are required for structural integrity and/or act as redox-sensors. Here, we demonstrate that loss of the FeS cluster affects binding of human DNA2 to specific DNA substrates, likely through a conformational change that distorts the central DNA binding tunnel. Moreover, we show that the FeS cluster is required for DNA2’s nuclease, helicase and ATPase activities. Our data also establish that oxidation of DNA2 impairs DNA binding in vitro, an effect that is reversible upon reduction. Unexpectedly, though, this redox-regulation is independent of the presence of the FeS cluster. Together, our study establishes an important structural role for the FeS cluster in human DNA2 and discovers a redox-regulatory mechanism to control DNA binding. Mariotti et al. show that the iron-sulphur cluster in human DNA2 is required for its nuclease, helicase and ATPase activities. This study highlights the structural importance of the iron-sulphur cluster in human DNA2 and presents a separate redox-regulatory mechanism that controls DNA binding.
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Affiliation(s)
- Laura Mariotti
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland.
| | - Sebastian Wild
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Giulia Brunoldi
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Alessandra Piceni
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6500, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zurich, 8092, Zurich, Switzerland
| | - Sandra Kummer
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Richard E Lutz
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6500, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zurich, 8092, Zurich, Switzerland
| | - Kerstin Gari
- Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland.
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