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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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Barua D, Płecha M, Muszewska A. A minimal Fanconi Anemia complex in early diverging fungi. Sci Rep 2024; 14:9922. [PMID: 38688950 PMCID: PMC11061109 DOI: 10.1038/s41598-024-60318-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fanconi Anemia (FA) pathway resolves DNA interstrand cross links (ICL). The FA pathway was initially recognized in vertebrates, but was later confirmed in other animals and speculated in fungi. FA proteins FANCM, FANCL and FANCJ are present in Saccharomyces cerevisiae but, their mechanism of interaction to resolve ICL is still unclear. Unlike Dikarya, early diverging fungi (EDF) possess more traits shared with animals. We traced the evolutionary history of the FA pathway across Opisthokonta. We scanned complete proteomes for FA-related homologs to establish their taxonomic distribution and analyzed their phylogenetic trees. We checked transcription profiles of FA genes to test if they respond to environmental conditions and their genomic localizations for potential co-localization. We identified fungal homologs of the activation and ID complexes, 5 out of 8 core proteins, all of the endonucleases, and deubiquitination proteins. All fungi lack FANCC, FANCF and FANCG proteins responsible for post-replication repair and chromosome stability in animals. The observed taxonomic distribution can be attributed to a gradual degradation of the FA pathway from EDF to Dikarya. One of the key differences is that EDF have the ID complex recruiting endonucleases to the site of ICL. Moreover, 21 out of 32 identified FA genes are upregulated in response to different growth conditions. Several FA genes are co-localized in fungal genomes which also could facilitate co-expression. Our results indicate that a minimal FA pathway might still be functional in Mucoromycota with a gradual loss of components in Dikarya ancestors.
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Affiliation(s)
- Drishtee Barua
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Magdalena Płecha
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
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Athar F, Templeman NM. C. elegans as a model organism to study female reproductive health. Comp Biochem Physiol A Mol Integr Physiol 2022; 266:111152. [PMID: 35032657 DOI: 10.1016/j.cbpa.2022.111152] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 12/17/2022]
Abstract
Female reproductive health has been historically understudied and underfunded. Here, we present the advantages of using a free-living nematode, Caenorhabditis elegans, as an animal system to study fundamental aspects of female reproductive health. C. elegans is a powerful high-throughput model organism that shares key genetic and physiological similarities with humans. In this review, we highlight areas of pressing medical and biological importance in the 21st century within the context of female reproductive health. These include the decline in female reproductive capacity with increasing chronological age, reproductive dysfunction arising from toxic environmental insults, and cancers of the reproductive system. C. elegans has been instrumental in uncovering mechanistic insights underlying these processes, and has been valuable for developing and testing therapeutics to combat them. Adopting a convenient model organism such as C. elegans for studying reproductive health will encourage further research into this field, and broaden opportunities for making advancements into evolutionarily conserved mechanisms that control reproductive function.
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Affiliation(s)
- Faria Athar
- Department of Biology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Nicole M Templeman
- Department of Biology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada.
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Oh S, Bae W, Alfhili MA, Lee MH. Nucleotide Excision Repair, XPA-1, and the Translesion Synthesis Complex, POLZ-1 and REV-1, Are Critical for Interstrand Cross-Link Repair in Caenorhabditis elegans Germ Cells. Biochemistry 2020; 59:3554-3561. [PMID: 32945661 DOI: 10.1021/acs.biochem.0c00719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interstrand cross-links (ICLs) are adducts of covalently linked nucleotides in opposing DNA strands that obstruct replication and prime cells for malignant transformation or premature cell death. ICLs may be caused by alkylating agents or ultraviolet (UV) irradiation. These toxic lesions are removed by diverse repair mechanisms such as the Fanconi anemia (FA) pathway, nucleotide excision repair (NER), translesion synthesis (TLS), and homologous recombination (HR). In mammals, the xeroderma pigmentosum group F (XP-F) protein participates in both the FA pathway and NER, while DNA polymerase ζ (POLZ-1) and REV-1 mediate TLS. Nevertheless, little is known regarding the genetic determinants of these pathways in ICL repair and damage tolerance in germ cells. In this study, we examined the sensitivity of Caenorhabditis elegans germ cells to ICLs generated by trimethylpsoralen/ultraviolet A (TMP/UV-A) combination, and embryonic mortality was employed as a surrogate for DNA damage in germ cells. Our results show that XPA-1, POLZ-1, and REV-1 were more critical than FA pathway mediators in preserving genomic stability in C. elegans germ cells. Notably, mutant worms lacking both XPA-1 and POLZ-1 (or REV-1) were more sensitive to ICLs compared to either single mutant alone. Moreover, knockdown of XPA-1 and REV-1 leads to the retarded disappearance of RPA-1 and RAD-51 foci upon ICL damage. Since DNA repair mechanisms are broadly conserved, our findings may have ramifications for prospective therapeutic interventions in humans.
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Affiliation(s)
- Sinae Oh
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, 03772 Seoul, South Korea
| | - Woori Bae
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, 03772 Seoul, South Korea
| | - Mohammad A Alfhili
- Chair of Medical and Molecular Genetics Research, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Myon Hee Lee
- Department of Internal Medicine, Hematology/Oncology Division, Brody School of Medicine at East Carolina University, Greenville, North Carolina 27834, United States
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Bharti SK, Khan I, Banerjee T, Sommers JA, Wu Y, Brosh RM. Molecular functions and cellular roles of the ChlR1 (DDX11) helicase defective in the rare cohesinopathy Warsaw breakage syndrome. Cell Mol Life Sci 2014; 71:2625-39. [PMID: 24487782 PMCID: PMC4537069 DOI: 10.1007/s00018-014-1569-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/07/2014] [Accepted: 01/16/2014] [Indexed: 02/08/2023]
Abstract
In 2010, a new recessive cohesinopathy disorder, designated Warsaw breakage syndrome (WABS), was described. The individual with WABS displayed microcephaly, pre- and postnatal growth retardation, and abnormal skin pigmentation. Cytogenetic analysis revealed mitomycin C (MMC)-induced chromosomal breakage; however, an additional sister chromatid cohesion defect was also observed. WABS is genetically linked to bi-allelic mutations in the ChlR1/DDX11 gene which encodes a protein of the conserved family of Iron-Sulfur (Fe-S) cluster DNA helicases. Mutations in the budding yeast ortholog of ChlR1, known as Chl1, were known to cause sister chromatid cohesion defects, indicating a conserved function of the gene. In 2012, three affected siblings were identified with similar symptoms to the original WABS case, and found to have a homozygous mutation in the conserved Fe-S domain of ChlR1, confirming the genetic linkage. Significantly, the clinically relevant mutations perturbed ChlR1 DNA unwinding activity. In addition to its genetic importance in human disease, ChlR1 is implicated in papillomavirus genome maintenance and cancer. Although its precise functions in genome homeostasis are still not well understood, ongoing molecular studies of ChlR1 suggest the helicase plays a critically important role in cellular replication and/or DNA repair.
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Affiliation(s)
- Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224 USA
| | - Irfan Khan
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224 USA
| | - Taraswi Banerjee
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224 USA
| | - Joshua A. Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224 USA
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Robert M. Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224 USA
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Lee H, Alpi AF, Park MS, Rose A, Koo HS. C. elegans ring finger protein RNF-113 is involved in interstrand DNA crosslink repair and interacts with a RAD51C homolog. PLoS One 2013; 8:e60071. [PMID: 23555887 PMCID: PMC3610817 DOI: 10.1371/journal.pone.0060071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/21/2013] [Indexed: 12/27/2022] Open
Abstract
The Fanconi anemia (FA) pathway recognizes interstrand DNA crosslinks (ICLs) and contributes to their conversion into double-strand DNA breaks, which can be repaired by homologous recombination. Seven orthologs of the 15 proteins associated with Fanconi anemia are functionally conserved in the model organism C. elegans. Here we report that RNF-113, a ubiquitin ligase, is required for RAD-51 focus formation after inducing ICLs in C. elegans. However, the formation of foci of RPA-1 or FCD-2/FANCD2 in the FA pathway was not affected by depletion of RNF-113. Nevertheless, the RPA-1 foci formed did not disappear with time in the depleted worms, implying serious defects in ICL repair. As a result, RNF-113 depletion increased embryonic lethality after ICL treatment in wild-type worms, but it did not increase the ICL-induced lethality of rfs-1/rad51C mutants. In addition, the persistence of RPA-1 foci was suppressed in doubly-deficient rnf-113;rfs-1 worms, suggesting that there is an epistatic interaction between the two genes. These results lead us to suggest that RNF-113 and RFS-1 interact to promote the displacement of RPA-1 by RAD-51 on single-stranded DNA derived from ICLs.
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Affiliation(s)
- Hyojin Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Arno F. Alpi
- Scottish Institute for Cell Signaling, University of Dundee, Dundee, United Kingdom
| | - Mi So Park
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Ann Rose
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Hyeon-Sook Koo
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, Republic of Korea
- * E-mail:
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