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Wojtaszek JL, Williams RS. From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks. DNA Repair (Amst) 2024; 142:103751. [PMID: 39180935 PMCID: PMC11404304 DOI: 10.1016/j.dnarep.2024.103751] [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: 04/22/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Since the report of "DNA untwisting" activity in 1972, ∼50 years of research has revealed seven topoisomerases in humans (TOP1, TOP1mt, TOP2α, TOP2β, TOP3α, TOP3β and Spo11). These conserved regulators of DNA topology catalyze controlled breakage to the DNA backbone to relieve the torsional stress that accumulates during essential DNA transactions including DNA replication, transcription, and DNA repair. Each topoisomerase-catalyzed reaction involves the formation of a topoisomerase cleavage complex (TOPcc), a covalent protein-DNA reaction intermediate formed between the DNA phosphodiester backbone and a topoisomerase catalytic tyrosine residue. A variety of perturbations to topoisomerase reaction cycles can trigger failure of the enzyme to re-ligate the broken DNA strand(s), thereby generating topoisomerase DNA-protein crosslinks (TOP-DPC). TOP-DPCs pose unique threats to genomic integrity. These complex lesions are comprised of structurally diverse protein components covalently linked to genomic DNA, which are bulky DNA adducts that can directly impact progression of the transcription and DNA replication apparatus. A variety of genome maintenance pathways have evolved to recognize and resolve TOP-DPCs. Eukaryotic cells harbor tyrosyl DNA phosphodiesterases (TDPs) that directly reverse 3'-phosphotyrosyl (TDP1) and 5'-phoshotyrosyl (TDP2) protein-DNA linkages. The broad specificity Mre11-Rad50-Nbs1 and APE2 nucleases are also critical for mitigating topoisomerase-generated DNA damage. These DNA-protein crosslink metabolizing enzymes are further enabled by proteolytic degradation, with the proteasome, Spartan, GCNA, Ddi2, and FAM111A proteases implicated thus far. Strategies to target, unfold, and degrade the protein component of TOP-DPCs have evolved as well. Here we survey mechanisms for addressing Topoisomerase 1 (TOP1) and Topoisomerase 2 (TOP2) DPCs, highlighting systems for which molecular structure information has illuminated function of these critical DNA damage response pathways.
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Affiliation(s)
- Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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2
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Blouin T, Saini N. Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis. Front Oncol 2024; 14:1478373. [PMID: 39328207 PMCID: PMC11424613 DOI: 10.3389/fonc.2024.1478373] [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: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Aldehyde exposure has been shown to lead to the formation of DNA damage comprising of DNA-protein crosslinks (DPCs), base adducts and interstrand or intrastrand crosslinks. DPCs have recently drawn more attention because of recent advances in detection and quantification of these adducts. DPCs are highly deleterious to genome stability and have been shown to block replication forks, leading to wide-spread mutagenesis. Cellular mechanisms to prevent DPC-induced damage include excision repair pathways, homologous recombination, and specialized proteases involved in cleaving the covalently bound proteins from DNA. These pathways were first discovered in formaldehyde-treated cells, however, since then, various other aldehydes have been shown to induce formation of DPCs in cells. Defects in DPC repair or aldehyde clearance mechanisms lead to various diseases including Ruijs-Aalfs syndrome and AMeD syndrome in humans. Here, we discuss recent developments in understanding how aldehydes form DPCs, how they are repaired, and the consequences of defects in these repair pathways.
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Affiliation(s)
- Thomas Blouin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
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3
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Yang SH, Zeng YZ, Jia XZ, Gu YW, Wood C, Yang RS, Yang JS, Yang WJ. Activated dormant stem cells recover spermatogenesis in chemoradiotherapy-induced infertility. Cell Rep 2024; 43:114582. [PMID: 39096488 DOI: 10.1016/j.celrep.2024.114582] [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: 09/12/2023] [Revised: 03/23/2024] [Accepted: 07/18/2024] [Indexed: 08/05/2024] Open
Abstract
Male infertility is a recognized side effect of chemoradiotherapy. Extant spermatogonial stem cells (SSCs) may act as originators for any subsequent recovery. However, which type of SSCs, the mechanism by which they survive and resist toxicity, and how they act to restart spermatogenesis remain largely unknown. Here, we identify a small population of Set domain-containing protein 4 (Setd4)-expressing SSCs that occur in a relatively dormant state in the mouse seminiferous tubule. Extant beyond high-dose chemoradiotherapy, these cells then activate to recover spermatogenesis. Recovery fails when Setd4+ SSCs are deleted. Confirmed to be of fetal origin, these Setd4+ SSCs are shown to facilitate early testicular development and also contribute to steady-state spermatogenesis in adulthood. Upon activation, chromatin remodeling increases their genome-wide accessibility, enabling Notch1 and Aurora activation with corresponding silencing of p21 and p53. Here, Setd4+ SSCs are presented as the originators of both testicular development and spermatogenesis recovery in chemoradiotherapy-induced infertility.
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Affiliation(s)
- Shu-Hua Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi-Zhe Zeng
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xi-Zheng Jia
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Gu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Christopher Wood
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ri-Sheng Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin-Shu Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei-Jun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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4
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Pamula MC, Lehmann R. How germ granules promote germ cell fate. Nat Rev Genet 2024:10.1038/s41576-024-00744-8. [PMID: 38890558 DOI: 10.1038/s41576-024-00744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation.
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Affiliation(s)
| | - Ruth Lehmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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5
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [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: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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6
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Brand CL, Oliver GT, Farkas IZ, Buszczak M, Levine MT. Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol 2024; 41:msae113. [PMID: 38865490 PMCID: PMC11210505 DOI: 10.1093/molbev/msae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Genevieve T Oliver
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabella Z Farkas
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Buszczak
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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7
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Ma JY, Xia TJ, Li S, Yin S, Luo SM, Li G. Germline cell de novo mutations and potential effects of inflammation on germline cell genome stability. Semin Cell Dev Biol 2024; 154:316-327. [PMID: 36376195 DOI: 10.1016/j.semcdb.2022.11.003] [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: 07/14/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
Uncontrolled pathogenic genome mutations in germline cells might impair adult fertility, lead to birth defects or even affect the adaptability of a species. Understanding the sources of DNA damage, as well as the features of damage response in germline cells are the overarching tasks to reduce the mutations in germline cells. With the accumulation of human genome data and genetic reports, genome variants formed in germline cells are being extensively explored. However, the sources of DNA damage, the damage repair mechanisms, and the effects of DNA damage or mutations on the development of germline cells are still unclear. Besides exogenous triggers of DNA damage such as irradiation and genotoxic chemicals, endogenous exposure to inflammation may also contribute to the genome instability of germline cells. In this review, we summarized the features of de novo mutations and the specific DNA damage responses in germline cells and explored the possible roles of inflammation on the genome stability of germline cells.
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Affiliation(s)
- Jun-Yu Ma
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Tian-Jin Xia
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China; College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shuai Li
- Center for Clinical Epidemiology and Methodology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Shen Yin
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Shi-Ming Luo
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Guowei Li
- Center for Clinical Epidemiology and Methodology, Guangdong Second Provincial General Hospital, Guangzhou, China.
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8
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Ribeiro J, Crossan GP. GCNA is a histone binding protein required for spermatogonial stem cell maintenance. Nucleic Acids Res 2023; 51:4791-4813. [PMID: 36919611 PMCID: PMC10250205 DOI: 10.1093/nar/gkad168] [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: 06/29/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Recycling and de-novo deposition of histones during DNA replication is a critical challenge faced by eukaryotic cells and is coordinated by histone chaperones. Spermatogenesis is highly regulated sophisticated process necessitating not only histone modification but loading of testis specific histone variants. Here, we show that Germ Cell Nuclear Acidic protein (GCNA), a germ cell specific protein in adult mice, can bind histones and purified GCNA exhibits histone chaperone activity. GCNA associates with the DNA replication machinery and supports progression through S-phase in murine undifferentiated spermatogonia (USGs). Whilst GCNA is dispensable for embryonic germ cell development, it is required for the maintenance of the USG pool and for long-term production of sperm. Our work describes the role of a germ cell specific histone chaperone in USGs maintenance in mice. These findings provide a mechanistic basis for the male infertility observed in patients carrying GCNA mutations.
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9
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Reh B, Wang X, Feng Y, Bhandari RK. Potassium perchlorate effects on primordial germ cells of developing medaka larvae. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 251:106283. [PMID: 36063761 DOI: 10.1016/j.aquatox.2022.106283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Perchlorate is a chemical compound commonly used in military artillery and equipment. It has been detected in drinking water, air, soil, and breast milk. Exposure of humans to perchlorate can occur in the theater of war and areas adjacent to military training grounds. A high concentration of perchlorate has been found to affect reproduction in vertebrates, including fish. However, whether environmental concentrations of perchlorate can affect primordial germ cells (PGCs), the founders of sperm and eggs, is not clearly understood. In the present study, we examined the effects of 0, 10, 100, and 1000 μg/L potassium perchlorate exposure on the embryonic development of medaka and their PGCs. Perchlorate exposure delayed hatching time, reduced heartbeat, inhibited migration of PGCs, and increased developmental deformities in the larvae. The 10 and 20 mg/L concentrations of perchlorate were lethal to embryos, whereas vitamin C co-treatment (1 mg/L) completely blocked perchlorate-induced mortality. RNA-seq analysis of isolated PGCs showed a non-linear pattern in expression profiles of differentially altered genes. Significantly upregulated genes were found in PGCs from the 10 and 1000 μg/L groups, whereas the 100 μg/L groups showed the highest number of significantly downregulated genes. Gene ontology analysis predicted differentially expressed genes to be involved in proteolysis, metabolic processes, peptides activity, hydrolase activity, and hormone activity. Among the cellular components, extracellular, intracellular, sarcoplasmic, and 6-phosphofructokinase and membrane-bounded processes were affected. Ingenuity Pathway Analysis of PGC transcriptomes revealed thyroid hormone signaling to be affected by all concentrations of perchlorate. The present results suggested that perchlorate affected the development of medaka larvae and vitamin C was able to ameliorate perchlorate-induced embryo mortality. Additionally, perchlorate altered the global transcriptional network in PGCs in a non-linear fashion suggesting its potential effects on developing germ cells and fertility.
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Affiliation(s)
- Beh Reh
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
| | - Xuegeng Wang
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA; Institute of Modern Aquaculture Science and Engineering, College of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Yashi Feng
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
| | - Ramji K Bhandari
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA.
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10
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Peart NJ, Johnson TA, Lee S, Sears MJ, Yang F, Quesnel-Vallières M, Feng H, Recinos Y, Barash Y, Zhang C, Hermann BP, Wang PJ, Geyer CB, Carstens RP. The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice. PLoS Genet 2022; 18:e1010416. [PMID: 36129965 PMCID: PMC9529142 DOI: 10.1371/journal.pgen.1010416] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/03/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Control over gene expression is exerted, in multiple stages of spermatogenesis, at the post-transcriptional level by RNA binding proteins (RBPs). We identify here an essential role in mammalian spermatogenesis and male fertility for 'RNA binding protein 46' (RBM46). A highly evolutionarily conserved gene, Rbm46 is also essential for fertility in both flies and fish. We found Rbm46 expression was restricted to the mouse germline, detectable in males in the cytoplasm of premeiotic spermatogonia and meiotic spermatocytes. To define its requirement for spermatogenesis, we generated Rbm46 knockout (KO, Rbm46-/-) mice; although male Rbm46-/- mice were viable and appeared grossly normal, they were infertile. Testes from adult Rbm46-/- mice were small, with seminiferous tubules containing only Sertoli cells and few undifferentiated spermatogonia. Using genome-wide unbiased high throughput assays RNA-seq and 'enhanced crosslinking immunoprecipitation' coupled with RNA-seq (eCLIP-seq), we discovered RBM46 could bind, via a U-rich conserved consensus sequence, to a cohort of mRNAs encoding proteins required for completion of differentiation and subsequent meiotic initiation. In summary, our studies support an essential role for RBM46 in regulating target mRNAs during spermatogonia differentiation prior to the commitment to meiosis in mice.
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Affiliation(s)
- Natoya J. Peart
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Taylor A. Johnson
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Sungkyoung Lee
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew J. Sears
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Fang Yang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Huijuan Feng
- Department of Systems Biology and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Yocelyn Recinos
- Department of Systems Biology and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Chaolin Zhang
- Department of Systems Biology and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Brian P. Hermann
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christopher B. Geyer
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- East Carolina Diabetes and Obesity Institute at East Carolina University, Greenville, North Carolina, United States of America
| | - Russ P. Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
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11
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Li P, Tang J, Yu Z, Jin C, Wang Z, Li M, Zou D, Mang X, Liu J, Lu Y, Miao S, Wang L, Li K, Song W. CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice. Biol Reprod 2022; 107:1331-1344. [PMID: 35980806 DOI: 10.1093/biolre/ioac162] [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: 02/17/2022] [Revised: 06/18/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Spermatogenesis is sustained by homeostatic balance between the self-renewal and differentiation of spermatogonial stem cells (SSCs), which is dependent on the strict regulation of transcription factor and chromatin modulator gene expression. Chromodomain helicase DNA-binding protein 4 (CHD4) is highly expressed in SSCs but roles in mouse spermatogenesis are not fully understood. Here, we report that the germ-cell-specific deletion of Chd4 resulted in complete infertility in male mice, with rapid loss of SSCs and excessive germ cell apoptosis. Chd4-knockdown in cultured SSCs also promoted the expression of apoptosis-related genes and thereby activated the tumor necrosis factor signaling pathway. Mechanistically, CHD4 occupies the genomic regulatory region of key apoptosis-related genes including Jun and Nfkb1. Together, our findings reveal the determinant role of CHD4 in SSCs survival in vivo, which will offer insight into the pathogenesis of male sterility and potential novel therapeutic targets.
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Affiliation(s)
- Pengyu Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Jielin Tang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Zhixin Yu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Cheng Jin
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Zhipeng Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Mengzhen Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Dingfeng Zou
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Xinyu Mang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Jun Liu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Linfang Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College; Beijing 100005, China
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12
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Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
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13
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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14
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Woodman MF, Ozcan MCH, Gura MA, De La Cruz P, Gadson AK, Grive KJ. The Requirement of Ubiquitin C-Terminal Hydrolase L1 (UCHL1) in Mouse Ovarian Development and Fertility †. Biol Reprod 2022; 107:500-513. [PMID: 35512140 PMCID: PMC9382372 DOI: 10.1093/biolre/ioac086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 11/14/2022] Open
Abstract
Ubiquitin C-Terminal Hydrolase L1 (UCHL1) is a de-ubiquitinating enzyme enriched in neuronal and gonadal tissues known to regulate the cellular stores of mono-ubiquitin and protein turnover. While its function in maintaining proper motor neuron function is well-established, investigation into its role in the health and function of reproductive processes is only just beginning to be studied. Single-cell-sequencing analysis of all ovarian cells from the murine perinatal period revealed that Uchl1 is very highly expressed in the developing oocyte population, an observation which was corroborated by high levels of oocyte-enriched UCHL1 protein expression in oocytes of all stages throughout the mouse reproductive lifespan. To better understand the role UCHL1 may be playing in oocytes, we utilized a UCHL1-deficient mouse line, finding reduced number of litters, reduced litter sizes, altered folliculogenesis, morphologically abnormal oocytes, disrupted estrous cyclicity and apparent endocrine dysfunction in these animals compared to their wild-type and heterozygous littermates. These data reveal a novel role of UCHL1 in female fertility as well as overall ovarian function, and suggest a potentially essential role for the ubiquitin proteasome pathway in mediating reproductive health. Summary sentence: Ubiquitin C-Terminal Hydrolase L1 (UCHL1) is required for proper ovarian folliculogenesis, estrous cyclicity, and fertility in the female mouse.
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Affiliation(s)
- Morgan F Woodman
- Women and Infants Hospital of Rhode Island, Department of Obstetrics and Gynecology, Program in Women's Oncology, Providence, RI 02905
| | - Meghan C H Ozcan
- Women and Infants Hospital of Rhode Island, Department of Obstetrics and Gynecology, Reproductive Endocrinology and Infertility Fellowship Program, Providence, RI 02905.,Warren Alpert Medical School of Brown University, Department of Obstetrics and Gynecology, Providence, RI 02905
| | - Megan A Gura
- Brown University, MCB Graduate Program and Department of Molecular Biology, Cell Biology, and Biochemistry, Providence, RI, 02906
| | - Payton De La Cruz
- Women and Infants Hospital of Rhode Island, Department of Obstetrics and Gynecology, Program in Women's Oncology, Providence, RI 02905.,Brown University, Pathobiology Graduate Program, Providence, RI, 02906
| | - Alexis K Gadson
- Women and Infants Hospital of Rhode Island, Department of Obstetrics and Gynecology, Reproductive Endocrinology and Infertility Fellowship Program, Providence, RI 02905.,Warren Alpert Medical School of Brown University, Department of Obstetrics and Gynecology, Providence, RI 02905
| | - Kathryn J Grive
- Women and Infants Hospital of Rhode Island, Department of Obstetrics and Gynecology, Program in Women's Oncology, Providence, RI 02905.,Women and Infants Hospital of Rhode Island, Department of Obstetrics and Gynecology, Reproductive Endocrinology and Infertility Fellowship Program, Providence, RI 02905
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15
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McFadden WM, Yanowitz JL. idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R. PLoS One 2022; 17:e0266929. [PMID: 35436286 PMCID: PMC9015136 DOI: 10.1371/journal.pone.0266929] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/29/2022] [Indexed: 12/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are proteins or protein-domains that do not have a single native structure, rather, they are a class of flexible peptides that can rapidly adopt multiple conformations. IDPs are quite abundant, and their dynamic characteristics provide unique advantages for various biological processes. The field of “unstructured biology” has emerged, in part, because of numerous computational studies that had identified the unique characteristics of IDPs and IDRs. The package ‘idpr’, short for Intrinsically Disordered Proteins in R, implements several R functions that match the established characteristics of IDPs to protein sequences of interest. This includes calculations of residue composition, charge-hydropathy relationships, and predictions of intrinsic disorder. Additionally, idpr integrates several amino acid substitution matrices and calculators to supplement IDP-based workflows. Overall, idpr aims to integrate tools for the computational analysis of IDPs within R, facilitating the analysis of these important, yet under-characterized, proteins. The idpr package can be downloaded from Bioconductor (https://bioconductor.org/packages/idpr/).
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Affiliation(s)
| | - Judith L. Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- * E-mail:
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16
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Abstract
Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
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17
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Pereira C, Arroyo-Martinez GA, Guo MZ, Downey MS, Kelly ER, Grive KJ, Mahadevaiah SK, Sims JR, Faca VM, Tsai C, Schiltz CJ, Wit N, Jacobs H, Clark NL, Freire R, Turner J, Lyndaker AM, Brieno-Enriquez MA, Cohen PE, Smolka MB, Weiss RS. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis. eLife 2022; 11:68677. [PMID: 35133274 PMCID: PMC8824475 DOI: 10.7554/elife.68677] [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: 03/23/2021] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage response mechanisms have meiotic roles that ensure successful gamete formation. While completion of meiotic double-strand break (DSB) repair requires the canonical RAD9A-RAD1-HUS1 (9A-1-1) complex, mammalian meiocytes also express RAD9A and HUS1 paralogs, RAD9B and HUS1B, predicted to form alternative 9-1-1 complexes. The RAD1 subunit is shared by all predicted 9-1-1 complexes and localizes to meiotic chromosomes even in the absence of HUS1 and RAD9A. Here, we report that testis-specific disruption of RAD1 in mice resulted in impaired DSB repair, germ cell depletion, and infertility. Unlike Hus1 or Rad9a disruption, Rad1 loss in meiocytes also caused severe defects in homolog synapsis, impaired phosphorylation of ATR targets such as H2AX, CHK1, and HORMAD2, and compromised meiotic sex chromosome inactivation. Together, these results establish critical roles for both canonical and alternative 9-1-1 complexes in meiotic ATR activation and successful prophase I completion.
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Affiliation(s)
| | | | - Matthew Z Guo
- Department of Biomedical Sciences, Cornell University
| | | | - Emma R Kelly
- Division of Mathematics and Natural Sciences, Elmira College
| | | | | | - Jennie R Sims
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University
| | - Vitor M Faca
- Department of Biochemistry and Immunology, FMRP, University of São Paulo
| | - Charlton Tsai
- Department of Biomedical Sciences, Cornell University
| | | | - Niek Wit
- Division of Immunology, The Netherlands Cancer Institute
| | - Heinz Jacobs
- Division of Immunology, The Netherlands Cancer Institute
| | | | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna
- Universidad Fernando Pessoa Canarias
| | - James Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute
| | - Amy M Lyndaker
- Division of Mathematics and Natural Sciences, Elmira College
| | - Miguel A Brieno-Enriquez
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University
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18
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Chin AF, Zheng Y, Hilser VJ. Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ. Protein Sci 2022; 31:822-834. [PMID: 34984754 DOI: 10.1002/pro.4270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/05/2022]
Abstract
Intrinsically disordered proteins (IDPs) effect biological function despite their sequence-encoded lack of preference for stable three-dimensional structure. Among their many functions, IDPs form membraneless cellular compartments through liquid-liquid phase separation (LLPS), also termed biomolecular condensation. The extent to which LLPS has been evolutionarily selected remains largely unknown, as the complexities of IDP evolution hamper progress. Unlike structured proteins, rapid sequence divergence typical of IDPs confounds inference of their biophysical or biological functions from comparative sequence analyses. Here, we leverage mitosis as a universal eukaryotic feature to interrogate condensate evolutionary history. We observe that evolution has conserved the ability for six homologs of the mitotic IDP BuGZ to undergo LLPS and to serve the same mitotic function, despite low sequence conservation. We also observe that cellular context may tune LLPS. The phylogenetic correlation of LLPS and mitotic function in one protein raises the possibility of an ancient evolutionary interplay between LLPS and biological function, dating back at least 1.6 billion years to the last common ancestor of plants and animals. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yixian Zheng
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, Maryland, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland, USA
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19
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Kiyozumi D, Ikawa M. Proteolysis in Reproduction: Lessons From Gene-Modified Organism Studies. Front Endocrinol (Lausanne) 2022; 13:876370. [PMID: 35600599 PMCID: PMC9114714 DOI: 10.3389/fendo.2022.876370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022] Open
Abstract
The physiological roles of proteolysis are not limited to degrading unnecessary proteins. Proteolysis plays pivotal roles in various biological processes through cleaving peptide bonds to activate and inactivate proteins including enzymes, transcription factors, and receptors. As a wide range of cellular processes is regulated by proteolysis, abnormalities or dysregulation of such proteolytic processes therefore often cause diseases. Recent genetic studies have clarified the inclusion of proteases and protease inhibitors in various reproductive processes such as development of gonads, generation and activation of gametes, and physical interaction between gametes in various species including yeast, animals, and plants. Such studies not only clarify proteolysis-related factors but the biological processes regulated by proteolysis for successful reproduction. Here the physiological roles of proteases and proteolysis in reproduction will be reviewed based on findings using gene-modified organisms.
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Affiliation(s)
- Daiji Kiyozumi
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
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20
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Xu C, Cao Y, Bao J. Building RNA-protein germ granules: insights from the multifaceted functions of DEAD-box helicase Vasa/Ddx4 in germline development. Cell Mol Life Sci 2021; 79:4. [PMID: 34921622 PMCID: PMC11072811 DOI: 10.1007/s00018-021-04069-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
The segregation and maintenance of a dedicated germline in multicellular organisms is essential for species propagation in the sexually reproducing metazoan kingdom. The germline is distinct from somatic cells in that it is ultimately dedicated to acquiring the "totipotency" and to regenerating the offspring after fertilization. The most striking feature of germ cells lies in the presence of characteristic membraneless germ granules that have recently proven to behave like liquid droplets resulting from liquid-liquid phase separation (LLPS). Vasa/Ddx4, a faithful DEAD-box family germline marker highly conserved across metazoan species, harbors canonical DEAD-box motifs and typical intrinsically disordered sequences at both the N-terminus and C-terminus. This feature enables it to serve as a primary driving force behind germ granule formation and helicase-mediated RNA metabolism (e.g., piRNA biogenesis). Genetic ablation of Vasa/Ddx4 or the catalytic-dead mutations abolishing its helicase activity led to sexually dimorphic germline defects resulting in either male or female sterility among diverse species. While recent efforts have discovered pivotal functions of Vasa/Ddx4 in somatic cells, especially in multipotent stem cells, we herein summarize the helicase-dependent and -independent functions of Vasa/Ddx4 in the germline, and discuss recent findings of Vasa/Ddx4-mediated phase separation, germ granule formation and piRNA-dependent retrotransposon control essential for germline development.
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Affiliation(s)
- Caoling Xu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China
| | - Yuzhu Cao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China
| | - Jianqiang Bao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China.
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21
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Pathogenic variations in Germ Cell Nuclear Acidic Peptidase (GCNA) are associated with human male infertility. Eur J Hum Genet 2021; 29:1781-1788. [PMID: 34413498 PMCID: PMC8632907 DOI: 10.1038/s41431-021-00946-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/29/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023] Open
Abstract
Infertility affects one in six couples, half of which are caused by a male factor. Male infertility can be caused by both, qualitative and quantitative defects, leading to Oligo- astheno-terato-zoospermia (OAT; impairment in ejaculate sperm cell concentration, motility and morphology). Azoospermia defined as complete absence of sperm cells in the ejaculation. While hundreds of genes are involved in spermatogenesis the genetic etiology of men's infertility remains incomplete.We identified a hemizygous stop gain pathogenic variation (PV) in the X-linked Germ Cell Nuclear Acidic Peptidase (GCNA), in an Azoospermic patient by exome sequencing. Assessment of the prevalence of pathogenic variations in this gene in infertile males by exome sequence data of 11 additional unrelated patients identified a probable hemizygous causative missense PV in GCNA in a severe OAT patient. Expression of GCNA in the patients' testes biopsies and the stage of spermatogonial developmental arrest were determined by immunofluorescence and immunohistochemistry. The Azoospermic patient presented spermatogenic maturation arrest with an almost complete absence of early and late primary spermatocytes and thus the complete absence of sperm. GCNA is critical for genome integrity and its loss results in genomic instability and infertility in Drosophila, C. elegans, zebrafish, and mouse. PVs in GCNA appear to be incompatible with male fertility in humans as well: A stop-gain PV caused Azoospermia and a missense PV caused severe OAT with very low fertilization rates and no pregnancy in numerous IVF treatments.
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22
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Hansen CL, Pelegri F. Primordial Germ Cell Specification in Vertebrate Embryos: Phylogenetic Distribution and Conserved Molecular Features of Preformation and Induction. Front Cell Dev Biol 2021; 9:730332. [PMID: 34604230 PMCID: PMC8481613 DOI: 10.3389/fcell.2021.730332] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022] Open
Abstract
The differentiation of primordial germ cells (PGCs) occurs during early embryonic development and is critical for the survival and fitness of sexually reproducing species. Here, we review the two main mechanisms of PGC specification, induction, and preformation, in the context of four model vertebrate species: mouse, axolotl, Xenopus frogs, and zebrafish. We additionally discuss some notable molecular characteristics shared across PGC specification pathways, including the shared expression of products from three conserved germline gene families, DAZ (Deleted in Azoospermia) genes, nanos-related genes, and DEAD-box RNA helicases. Then, we summarize the current state of knowledge of the distribution of germ cell determination systems across kingdom Animalia, with particular attention to vertebrate species, but include several categories of invertebrates - ranging from the "proto-vertebrate" cephalochordates to arthropods, cnidarians, and ctenophores. We also briefly highlight ongoing investigations and potential lines of inquiry that aim to understand the evolutionary relationships between these modes of specification.
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Affiliation(s)
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
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23
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Liu JCY, Kühbacher U, Larsen NB, Borgermann N, Garvanska DH, Hendriks IA, Ackermann L, Haahr P, Gallina I, Guérillon C, Branigan E, Hay RT, Azuma Y, Nielsen ML, Duxin JP, Mailand N. Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO-RNF4 pathway. EMBO J 2021; 40:e107413. [PMID: 34346517 PMCID: PMC8441304 DOI: 10.15252/embj.2020107413] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 07/03/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
DNA-protein crosslinks (DPCs) obstruct essential DNA transactions, posing a serious threat to genome stability and functionality. DPCs are proteolytically processed in a ubiquitin- and DNA replication-dependent manner by SPRTN and the proteasome but can also be resolved via targeted SUMOylation. However, the mechanistic basis of SUMO-mediated DPC resolution and its interplay with replication-coupled DPC repair remain unclear. Here, we show that the SUMO-targeted ubiquitin ligase RNF4 defines a major pathway for ubiquitylation and proteasomal clearance of SUMOylated DPCs in the absence of DNA replication. Importantly, SUMO modifications of DPCs neither stimulate nor inhibit their rapid DNA replication-coupled proteolysis. Instead, DPC SUMOylation provides a critical salvage mechanism to remove DPCs formed after DNA replication, as DPCs on duplex DNA do not activate interphase DNA damage checkpoints. Consequently, in the absence of the SUMO-RNF4 pathway cells are able to enter mitosis with a high load of unresolved DPCs, leading to defective chromosome segregation and cell death. Collectively, these findings provide mechanistic insights into SUMO-driven pathways underlying replication-independent DPC resolution and highlight their critical importance in maintaining chromosome stability and cellular fitness.
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Affiliation(s)
- Julio C Y Liu
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Ulrike Kühbacher
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Nicolai B Larsen
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Nikoline Borgermann
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Dimitriya H Garvanska
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Ivo A Hendriks
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Leena Ackermann
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Peter Haahr
- Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Irene Gallina
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Claire Guérillon
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Emma Branigan
- Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Ronald T Hay
- Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Yoshiaki Azuma
- Department of Molecular BiosciencesUniversity of KansasLawrenceKSUSA
| | - Michael Lund Nielsen
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Julien P Duxin
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Protein Signaling ProgramNovo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
- Center for Chromosome StabilityDepartment of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
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24
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Fukuda E, Tanaka H, Yamaguchi K, Takasaka M, Kawamura Y, Okuda H, Isotani A, Ikawa M, Shapiro VS, Tsuchida J, Okada Y, Tsujimura A, Miyagawa Y, Fukuhara S, Kawakami Y, Wada M, Nishimune Y, Goshima N. Identification and characterization of the antigen recognized by the germ cell mAb TRA98 using a human comprehensive wet protein array. Genes Cells 2021; 26:180-189. [PMID: 33527666 DOI: 10.1111/gtc.12832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022]
Abstract
TRA98 is a rat monoclonal antibody (mAb) which recognizes a specific antigen in the nuclei of germ cells. mAb TRA98 has been used to understand the mechanism of germ cell development and differentiation in many studies. In mice, the antigen recognized by mAb TRA98 or GCNA1 has been reported to be a GCNA gene product, but despite the demonstration of the immunoreactivity of this mAb in human testis and sperm in 1997, the antigen in humans remains unknown, as of date. To identify the human antigen recognized by mAb TRA98, a human comprehensive wet protein array was developed containing 19,446 proteins derived from human cDNAs. Using this array, it was found that the antigen of mAb TRA98 is not a GCNA gene product, but nuclear factor-κB activating protein (NKAP). In mice, mAb TRA98 recognized both the GCNA gene product and NKAP. Furthermore, conditional knockout of Nkap in mice revealed a phenotype of Sertoli cell-only syndrome. Although NKAP is a ubiquitously expressed protein, NKAP recognized by mAb TRA98 in mouse testis was SUMOylated. These results suggest that NKAP undergoes modifications, such as SUMOylation in the testis, and plays an important role in spermatogenesis.
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Affiliation(s)
- Eriko Fukuda
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hiromitsu Tanaka
- Molecular Biology Division, Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
| | - Kei Yamaguchi
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Mieko Takasaka
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | | | - Hidenobu Okuda
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ayako Isotani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Junji Tsuchida
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Disease, Osaka University, Osaka, Japan
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | - Akira Tsujimura
- Department of Urology, Juntendo University Urayasu Hospital, Urayasu, Chiba, Japan
| | - Yasushi Miyagawa
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinichiro Fukuhara
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Kawakami
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Morimasa Wada
- Molecular Biology Division, Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
| | - Yoshitake Nishimune
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Disease, Osaka University, Osaka, Japan
| | - Naoki Goshima
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.,Department of Human Sciences, Faculty of Human Sciences, Musasino University, Tokyo, Japan
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25
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Schmidt H, Putnam A, Rasoloson D, Seydoux G. Protein-based condensation mechanisms drive the assembly of RNA-rich P granules. eLife 2021; 10:63698. [PMID: 34106046 PMCID: PMC8238508 DOI: 10.7554/elife.63698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Germ granules are protein-RNA condensates that segregate with the embryonic germline. In Caenorhabditis elegans embryos, germ (P) granule assembly requires MEG-3, an intrinsically disordered protein that forms RNA-rich condensates on the surface of PGL condensates at the core of P granules. MEG-3 is related to the GCNA family and contains an N-terminal disordered region (IDR) and a predicted ordered C-terminus featuring an HMG-like motif (HMGL). We find that MEG-3 is a modular protein that uses its IDR to bind RNA and its C-terminus to drive condensation. The HMGL motif mediates binding to PGL-3 and is required for co-assembly of MEG-3 and PGL-3 condensates in vivo. Mutations in HMGL cause MEG-3 and PGL-3 to form separate condensates that no longer co-segregate to the germline or recruit RNA. Our findings highlight the importance of protein-based condensation mechanisms and condensate-condensate interactions in the assembly of RNA-rich germ granules.
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Affiliation(s)
- Helen Schmidt
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Andrea Putnam
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Dominique Rasoloson
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
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Variants in GCNA, X-linked germ-cell genome integrity gene, identified in men with primary spermatogenic failure. Hum Genet 2021; 140:1169-1182. [PMID: 33963445 DOI: 10.1007/s00439-021-02287-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/23/2021] [Indexed: 01/25/2023]
Abstract
Male infertility impacts millions of couples yet, the etiology of primary infertility remains largely unknown. A critical element of successful spermatogenesis is maintenance of genome integrity. Here, we present a genomic study of spermatogenic failure (SPGF). Our initial analysis (n = 176) did not reveal known gene-candidates but identified a potentially significant single-nucleotide variant (SNV) in X-linked germ-cell nuclear antigen (GCNA). Together with a larger follow-up study (n = 2049), 7 likely clinically relevant GCNA variants were identified. GCNA is critical for genome integrity in male meiosis and knockout models exhibit impaired spermatogenesis and infertility. Single-cell RNA-seq and immunohistochemistry confirm human GCNA expression from spermatogonia to elongated spermatids. Five identified SNVs were located in key functional regions, including N-terminal SUMO-interacting motif and C-terminal Spartan-like protease domain. Notably, variant p.Ala115ProfsTer7 results in an early frameshift, while Spartan-like domain missense variants p.Ser659Trp and p.Arg664Cys change conserved residues, likely affecting 3D structure. For variants within GCNA's intrinsically disordered region, we performed computational modeling for consensus motifs. Two SNVs were predicted to impact the structure of these consensus motifs. All identified variants have an extremely low minor allele frequency in the general population and 6 of 7 were not detected in > 5000 biological fathers. Considering evidence from animal models, germ-cell-specific expression, 3D modeling, and computational predictions for SNVs, we propose that identified GCNA variants disrupt structure and function of the respective protein domains, ultimately arresting germ-cell division. To our knowledge, this is the first study implicating GCNA, a key genome integrity factor, in human male infertility.
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27
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Nicholls PK, Page DC. Germ cell determination and the developmental origin of germ cell tumors. Development 2021; 148:239824. [PMID: 33913479 DOI: 10.1242/dev.198150] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In each generation, the germline is tasked with producing somatic lineages that form the body, and segregating a population of cells for gametogenesis. During animal development, when do cells of the germline irreversibly commit to producing gametes? Integrating findings from diverse species, we conclude that the final commitment of the germline to gametogenesis - the process of germ cell determination - occurs after primordial germ cells (PGCs) colonize the gonads. Combining this understanding with medical findings, we present a model whereby germ cell tumors arise from cells that failed to undertake germ cell determination, regardless of their having colonized the gonads. We propose that the diversity of cell types present in these tumors reflects the broad developmental potential of migratory PGCs.
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Affiliation(s)
- Peter K Nicholls
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.,Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
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28
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Pachva MC, Kisselev AF, Matkarimov BT, Saparbaev M, Groisman R. DNA-Histone Cross-Links: Formation and Repair. Front Cell Dev Biol 2021; 8:607045. [PMID: 33409281 PMCID: PMC7779557 DOI: 10.3389/fcell.2020.607045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/30/2020] [Indexed: 12/25/2022] Open
Abstract
The nucleosome is a stretch of DNA wrapped around a histone octamer. Electrostatic interactions and hydrogen bonds between histones and DNA are vital for the stable organization of nucleosome core particles, and for the folding of chromatin into more compact structures, which regulate gene expression via controlled access to DNA. As a drawback of tight association, under genotoxic stress, DNA can accidentally cross-link to histone in a covalent manner, generating a highly toxic DNA-histone cross-link (DHC). DHC is a bulky lesion that can impede DNA transcription, replication, and repair, often with lethal consequences. The chemotherapeutic agent cisplatin, as well as ionizing and ultraviolet irradiations and endogenously occurring reactive aldehydes, generate DHCs by forming either stable or transient covalent bonds between DNA and side-chain amino groups of histone lysine residues. The mechanisms of DHC repair start to unravel, and certain common principles of DNA-protein cross-link (DPC) repair mechanisms that participate in the removal of cross-linked histones from DNA have been described. In general, DPC is removed via a two-step repair mechanism. First, cross-linked proteins are degraded by specific DPC proteases or by the proteasome, relieving steric hindrance. Second, the remaining DNA-peptide cross-links are eliminated in various DNA repair pathways. Delineating the molecular mechanisms of DHC repair would help target specific DNA repair proteins for therapeutic intervention to combat tumor resistance to chemotherapy and radiotherapy.
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Affiliation(s)
- Manideep C Pachva
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Alexei F Kisselev
- Department Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | | | - Murat Saparbaev
- Groupe "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Regina Groisman
- Groupe "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
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29
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Abstract
Proteins covalently attached to DNA, also known as DNA-protein crosslinks (DPCs), are common and bulky DNA lesions that interfere with DNA replication, repair, transcription and recombination. Research in the past several years indicates that cells possess dedicated enzymes, known as DPC proteases, which digest the protein component of a DPC. Interestingly, DPC proteases also play a role in proteolysis beside DPC repair, such as in degrading excess histones during DNA replication or controlling DNA replication checkpoints. Here, we discuss the importance of DPC proteases in DNA replication, genome stability and their direct link to human diseases and cancer therapy.
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Affiliation(s)
- Annamaria Ruggiano
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, OX3 7DQ, Oxford, UK
| | - Kristijan Ramadan
- Medical Research Council (MRC) Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, OX3 7DQ, Oxford, UK.
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30
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Sun Y, Saha LK, Saha S, Jo U, Pommier Y. Debulking of topoisomerase DNA-protein crosslinks (TOP-DPC) by the proteasome, non-proteasomal and non-proteolytic pathways. DNA Repair (Amst) 2020; 94:102926. [DOI: 10.1016/j.dnarep.2020.102926] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023]
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31
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Kühbacher U, Duxin JP. How to fix DNA-protein crosslinks. DNA Repair (Amst) 2020; 94:102924. [PMID: 32683310 PMCID: PMC7511601 DOI: 10.1016/j.dnarep.2020.102924] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/18/2022]
Abstract
Proteins that act on DNA, or are in close proximity to it, can become inadvertently crosslinked to DNA and form highly toxic lesions, known as DNA-protein crosslinks (DPCs). DPCs are generated by different chemotherapeutics, environmental or endogenous sources of crosslinking agents, or by lesions on DNA that stall the catalytic cycle of certain DNA processing enzymes. These bulky adducts impair processes on DNA such as DNA replication or transcription, and therefore pose a serious threat to genome integrity. The large diversity of DPCs suggests that there is more than one canonical mechanism to repair them. Indeed, many different enzymes have been shown to act on DPCs by either processing the protein, the DNA or the crosslink itself. In addition, the cell cycle stage or cell type are likely to dictate pathway choice. In recent years, a detailed understanding of DPC repair during S phase has started to emerge. Here, we review the current knowledge on the mechanisms of replication-coupled DPC repair, and describe and also speculate on possible pathways that remove DPCs outside of S phase. Moreover, we highlight a recent paradigm shifting finding that indicates that DPCs are not always detrimental, but can also play a protective role, preserving the genome from more deleterious forms of DNA damage.
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Affiliation(s)
- Ulrike Kühbacher
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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32
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Vaz B, El Mansouri F, Liu X, Taketo T. Premature ovarian insufficiency in the XO female mouse on the C57BL/6J genetic background. Mol Hum Reprod 2020; 26:678-688. [PMID: 32634219 PMCID: PMC7473787 DOI: 10.1093/molehr/gaaa049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
In humans, all but 1% of monosomy 45.X embryos die in utero and those who reach term suffer from congenital abnormalities and infertility termed Turner's syndrome (TS). By contrast, XO female mice on various genetic backgrounds show much milder physical defects and normal fertility, diminishing their value as an animal model for studying the infertility of TS patients. In this article, we report that XO mice on the C57BL/6J (B6) genetic background showed early oocyte loss, infertility or subfertility and high embryonic lethality, suggesting that the effect of monosomy X in the female germline may be shared between mice and humans. First, we generated XO mice on either a mixed N2(C3H.B6) or B6 genetic background and compared the number of oocytes in neonatal ovaries; N2.XO females retained 45% of the number of oocytes in N2.XX females, whereas B6.XO females retained only 15% of that in B6.XX females. Second, while N2.XO females were as fertile as N2.XX females, both the frequency of delivery and the total number of pups delivered by B6.XO females were significantly lower than those by B6.XX females. Third, after mating with B6 males, both N2.XO and B6.XO females rarely produced XO pups carrying paternal X chromosomes, although a larger percentage of embryos was found to be XO before implantation. Furthermore, B6.XO females delivered 20% XO pups among female progeny after mating with C3H males. We conclude that the impact of monosomy X on female mouse fertility depends on the genetic background.
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Affiliation(s)
- B Vaz
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - F El Mansouri
- Department of Surgery, McGill University, Montreal, QC H4A3J1, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A3J1, Canada
| | - X Liu
- Department of Surgery, McGill University, Montreal, QC H4A3J1, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A3J1, Canada
| | - T Taketo
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
- Department of Surgery, McGill University, Montreal, QC H4A3J1, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A3J1, Canada
- Department of Obstetrics & Gynecology, McGill University, Montreal, QC H4A3J1, Canada
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33
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Nicol B, Rodriguez K, Yao HHC. Aberrant and constitutive expression of FOXL2 impairs ovarian development and functions in mice. Biol Reprod 2020; 103:966-977. [PMID: 32945847 DOI: 10.1093/biolre/ioaa146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/05/2023] Open
Abstract
Development and functions of the ovary rely on appropriate signaling and communication between various ovarian cell types. FOXL2, a transcription factor that plays a key role at different stages of ovarian development, is associated with primary ovarian insufficiency and ovarian cancer as a result of its loss-of-function or mutations. In this study, we investigated the impact of aberrant, constitutive expression of FOXL2 in somatic cells of the ovary. Overexpression of FOXL2 that started during fetal life resulted in defects in nest breakdown and consequent formation of polyovular follicles. Granulosa cell differentiation was impaired and recruitment and differentiation of steroidogenic theca cells was compromised. As a consequence, adult ovaries overexpressing FOXL2 exhibited defects in compartmentalization of granulosa and theca cells, significant decreased steroidogenesis and lack of ovulation. These findings demonstrate that fine-tuned expression of FOXL2 is required for proper folliculogenesis and fertility.
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Affiliation(s)
- Barbara Nicol
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Karina Rodriguez
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Humphrey H-C Yao
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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34
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p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nat Chem Biol 2020; 16:1078-1086. [DOI: 10.1038/s41589-020-0600-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
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35
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Yamashita YM. When the Family Treasure Is a Doormat. Dev Cell 2020; 52:3-4. [PMID: 31951554 DOI: 10.1016/j.devcel.2019.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Germ cells carry genetic information to the next generation, necessitating special attention to their genome maintenance. Two new studies in this issue of Developmental Cell (Bhargava et al., 2020; Dokshin et al., 2020) reveal an essential function of germ cell-specific protein GCNA in the genome maintenance of germ cells.
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Affiliation(s)
- Yukiko M Yamashita
- Life Sciences Institute, University of Michigan Ann Arbor, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute.
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36
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Vernet N, Condrea D, Mayere C, Féret B, Klopfenstein M, Magnant W, Alunni V, Teletin M, Souali-Crespo S, Nef S, Mark M, Ghyselinck NB. Meiosis occurs normally in the fetal ovary of mice lacking all retinoic acid receptors. SCIENCE ADVANCES 2020; 6:eaaz1139. [PMID: 32917583 PMCID: PMC7244263 DOI: 10.1126/sciadv.aaz1139] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/13/2020] [Indexed: 05/27/2023]
Abstract
Gametes are generated through a specialized cell differentiation process, meiosis, which, in ovaries of most mammals, is initiated during fetal life. All-trans retinoic acid (ATRA) is considered as the molecular signal triggering meiosis initiation. In the present study, we analyzed female fetuses ubiquitously lacking all ATRA nuclear receptors (RAR), obtained through a tamoxifen-inducible cre recombinase-mediated gene targeting approach. Unexpectedly, mutant oocytes robustly expressed meiotic genes, including the meiotic gatekeeper STRA8. In addition, ovaries from mutant fetuses grafted into adult recipient females yielded offspring bearing null alleles for all Rar genes. Thus, our results show that RAR are fully dispensable for meiotic initiation, as well as for the production of functional oocytes. Assuming that the effects of ATRA all rely on RAR, our study goes against the current model according to which meiosis is triggered by endogenous ATRA in the developing ovary. It therefore revives the search for the meiosis-inducing substance.
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Affiliation(s)
- Nadège Vernet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Diana Condrea
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Chloé Mayere
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Betty Féret
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Muriel Klopfenstein
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - William Magnant
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Violaine Alunni
- GenomEast platform, France Génomique consortium, IGBMC, 1 rue Laurent Fries, F-67404 Illkirch Cedex, France
| | - Marius Teletin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), France
| | - Sirine Souali-Crespo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Manuel Mark
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), France
| | - Norbert B Ghyselinck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France.
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37
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Lai X, Chahtane H, Martin-Arevalillo R, Zubieta C, Parcy F. Contrasted evolutionary trajectories of plant transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:101-107. [PMID: 32417720 DOI: 10.1016/j.pbi.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.
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Affiliation(s)
- Xuelei Lai
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et de Développement des Plantes, INRAE, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France.
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38
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Reinking HK, Hofmann K, Stingele J. Function and evolution of the DNA-protein crosslink proteases Wss1 and SPRTN. DNA Repair (Amst) 2020; 88:102822. [PMID: 32058279 DOI: 10.1016/j.dnarep.2020.102822] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022]
Abstract
Covalent DNA-protein crosslinks (DPCs) are highly toxic DNA adducts, which interfere with faithful DNA replication. The proteases Wss1 and SPRTN degrade DPCs and have emerged as crucially important DNA repair enzymes. Their protective role has been described in various model systems ranging from yeasts, plants, worms and flies to mice and humans. Loss of DPC proteases results in genome instability, cellular arrest, premature ageing and cancer predisposition. Here we discuss recent insights into the function and molecular mechanism of these enzymes. Furthermore, we present an in-depth phylogenetic analysis of the Wss1/SPRTN protease continuum. Remarkably flexible domain architectures and constantly changing protein-protein interaction motifs indicate ongoing evolutionary dynamics. Finally, we discuss recent data, which suggest that further partially-overlapping proteolytic systems targeting DPCs exist in eukaryotes. These new developments raise interesting questions regarding the division of labour between different DPC proteases and the mechanisms and principles of repair pathway choice.
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Affiliation(s)
- Hannah K Reinking
- Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Germany
| | - Julian Stingele
- Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany.
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39
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Dokshin GA, Davis GM, Sawle AD, Eldridge MD, Nicholls PK, Gourley TE, Romer KA, Molesworth LW, Tatnell HR, Ozturk AR, de Rooij DG, Hannon GJ, Page DC, Mello CC, Carmell MA. GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability. Dev Cell 2020; 52:53-68.e6. [PMID: 31839538 PMCID: PMC7227305 DOI: 10.1016/j.devcel.2019.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/14/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs.
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Affiliation(s)
- Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory M Davis
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ashley D Sawle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Taylin E Gourley
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Katherine A Romer
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Luke W Molesworth
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Hannah R Tatnell
- School of Health and Life Sciences, Federation University, VIC 3841, Australia
| | - Ahmet R Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dirk G de Rooij
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, the Netherlands; Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam 1105, the Netherlands
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David C Page
- Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Michelle A Carmell
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Whitehead Institute, 455 Main Street, Cambridge, MA 02142, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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40
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Nicholls PK, Schorle H, Naqvi S, Hu YC, Fan Y, Carmell MA, Dobrinski I, Watson AL, Carlson DF, Fahrenkrug SC, Page DC. Mammalian germ cells are determined after PGC colonization of the nascent gonad. Proc Natl Acad Sci U S A 2019; 116:25677-25687. [PMID: 31754036 PMCID: PMC6925976 DOI: 10.1073/pnas.1910733116] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mammalian primordial germ cells (PGCs) are induced in the embryonic epiblast, before migrating to the nascent gonads. In fish, frogs, and birds, the germline segregates even earlier, through the action of maternally inherited germ plasm. Across vertebrates, migrating PGCs retain a broad developmental potential, regardless of whether they were induced or maternally segregated. In mammals, this potential is indicated by expression of pluripotency factors, and the ability to generate teratomas and pluripotent cell lines. How the germline loses this developmental potential remains unknown. Our genome-wide analyses of embryonic human and mouse germlines reveal a conserved transcriptional program, initiated in PGCs after gonadal colonization, that differentiates germ cells from their germline precursors and from somatic lineages. Through genetic studies in mice and pigs, we demonstrate that one such gonad-induced factor, the RNA-binding protein DAZL, is necessary in vivo to restrict the developmental potential of the germline; DAZL's absence prolongs expression of a Nanog pluripotency reporter, facilitates derivation of pluripotent cell lines, and causes spontaneous gonadal teratomas. Based on these observations in humans, mice, and pigs, we propose that germ cells are determined after gonadal colonization in mammals. We suggest that germ cell determination was induced late in embryogenesis-after organogenesis has begun-in the common ancestor of all vertebrates, as in modern mammals, where this transition is induced by somatic cells of the gonad. We suggest that failure of this process of germ cell determination likely accounts for the origin of human testis cancer.
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Affiliation(s)
| | - Hubert Schorle
- Whitehead Institute, Cambridge, MA 02142
- Department of Developmental Pathology, Institute of Pathology, University of Bonn Medical School, 53127 Bonn, Germany
| | - Sahin Naqvi
- Whitehead Institute, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Yueh-Chiang Hu
- Whitehead Institute, Cambridge, MA 02142
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Yuting Fan
- Whitehead Institute, Cambridge, MA 02142
- Reproductive Medicine Center, Sixth Affiliated Hospital, Sun Yat-sen University, 510655 Guangzhou, China
| | | | - Ina Dobrinski
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | | | | | - David C Page
- Whitehead Institute, Cambridge, MA 02142;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142
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41
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Bhargava V, Goldstein CD, Russell L, Xu L, Ahmed M, Li W, Casey A, Servage K, Kollipara R, Picciarelli Z, Kittler R, Yatsenko A, Carmell M, Orth K, Amatruda JF, Yanowitz JL, Buszczak M. GCNA Preserves Genome Integrity and Fertility Across Species. Dev Cell 2019; 52:38-52.e10. [PMID: 31839537 DOI: 10.1016/j.devcel.2019.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/07/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
Abstract
The propagation of species depends on the ability of germ cells to protect their genome from numerous exogenous and endogenous threats. While these cells employ ubiquitous repair pathways, specialized mechanisms that ensure high-fidelity replication, chromosome segregation, and repair of germ cell genomes remain incompletely understood. We identified Germ Cell Nuclear Acidic Peptidase (GCNA) as a conserved regulator of genome stability in flies, worms, zebrafish, and human germ cell tumors. GCNA contains an acidic intrinsically disordered region (IDR) and a protease-like SprT domain. In addition to chromosomal instability and replication stress, Gcna mutants accumulate DNA-protein crosslinks (DPCs). GCNA acts in parallel with the SprT domain protein Spartan. Structural analysis reveals that while the SprT domain is needed to limit DNA damage, the IDR imparts significant function. This work shows that GCNA protects germ cells from various sources of damage, providing insights into conserved mechanisms that promote genome integrity across generations.
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Affiliation(s)
- Varsha Bhargava
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Courtney D Goldstein
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Logan Russell
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Murtaza Ahmed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Li
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA; Tsinghua University MD Program, School of Medicine, Tsinghua University, Haidian District, Beijing 100084, PR China
| | - Amanda Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kelly Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, TX 75235, USA
| | - Rahul Kollipara
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zachary Picciarelli
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alexander Yatsenko
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Michelle Carmell
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, TX 75235, USA
| | - James F Amatruda
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Judith L Yanowitz
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA.
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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42
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Interplay between Caspase 9 and X-linked Inhibitor of Apoptosis Protein (XIAP) in the oocyte elimination during fetal mouse development. Cell Death Dis 2019; 10:790. [PMID: 31624230 PMCID: PMC6797809 DOI: 10.1038/s41419-019-2019-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/07/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022]
Abstract
Mammalian female fertility is limited by the number and quality of oocytes in the ovarian reserve. The number of oocytes is finite since all germ cells cease proliferation to become oocytes in fetal life. Moreover, 70-80% of the initial oocyte population is eliminated during fetal and neonatal development, restricting the ovarian reserve. Why so many oocytes are lost during normal development remains an enigma. In Meiotic Prophase I (MPI), oocytes go through homologous chromosome synapsis and recombination, dependent on formation and subsequent repair of DNA double strand breaks (DSBs). The oocytes that have failed in DSB repair or synapsis get eliminated mainly in neonatal ovaries. However, a large oocyte population is eliminated before birth, and the cause or mechanism of this early oocyte loss is not well understood. In the current paper, we show that the oocyte loss in fetal ovaries was prevented by a deficiency of Caspase 9 (CASP9), which is the hub of the mitochondrial apoptotic pathway. Furthermore, CASP9 and its downstream effector Caspase 3 were counteracted by endogenous X-linked Inhibitor of Apoptosis (XIAP) to regulate the oocyte population; while XIAP overexpression mimicked CASP9 deficiency, XIAP deficiency accelerated oocyte loss. In the CASP9 deficiency, more oocytes were accumulated at the pachytene stage with multiple γH2AFX foci and high LINE1 expression levels, but with normal levels of synapsis and overall DSB repair. We conclude that the oocytes with LINE1 overexpression were preferentially eliminated by CASP9-dependent apoptosis in balance with XIAP during fetal ovarian development. When such oocytes were retained, however, they get eliminated by a CASP9-independent mechanism during neonatal development. Thus, the oocyte is equipped with multiple surveillance mechanisms during MPI progression to safe-guard the quality of oocytes in the ovarian reserve.
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43
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Zhou H, Zeng Z, Koentgen F, Khan M, Mombaerts P. The testicular soma of Tsc22d3 knockout mice supports spermatogenesis and germline transmission from spermatogonial stem cell lines upon transplantation. Genesis 2019; 57:e23295. [PMID: 31001916 PMCID: PMC6617806 DOI: 10.1002/dvg.23295] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/19/2019] [Accepted: 03/22/2019] [Indexed: 12/16/2022]
Abstract
Spermatogonial stem cells (SSCs) are adult stem cells that are slowly cycling and self-renewing. The pool of SSCs generates very large numbers of male gametes throughout the life of the individual. SSCs can be cultured in vitro for long periods of time, and established SSC lines can be manipulated genetically. Upon transplantation into the testes of infertile mice, long-term cultured mouse SSCs can differentiate into fertile spermatozoa, which can give rise to live offspring. Here, we show that the testicular soma of mice with a conditional knockout (conKO) in the X-linked gene Tsc22d3 supports spermatogenesis and germline transmission from cultured mouse SSCs upon transplantation. Infertile males were produced by crossing homozygous Tsc22d3 floxed females with homozygous ROSA26-Cre males. We obtained 96 live offspring from six long-term cultured SSC lines with the aid of intracytoplasmic sperm injection. We advocate the further optimization of Tsc22d3-conKO males as recipients for testis transplantation of SSC lines.
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Affiliation(s)
- Hai Zhou
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Zhen Zeng
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | | | - Mona Khan
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
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44
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Marnik EA, Updike DL. Membraneless organelles: P granules in Caenorhabditis elegans. Traffic 2019; 20:373-379. [PMID: 30924287 DOI: 10.1111/tra.12644] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/22/2022]
Abstract
Membraneless organelles are distinct compartments within a cell that are not enclosed by a traditional lipid membrane and instead form through a process called liquid-liquid phase separation. Examples of these non-membrane-bound organelles include nucleoli, stress granules, P bodies, pericentriolar material and germ granules. Many recent studies have used Caenorhabditis elegans germ granules, known as P granules, to expand our understanding of the formation of these unique cellular compartments. From this work, we know that proteins with intrinsically disordered regions (IDRs) play a critical role in the process of phase separation. IDR phase separation is further tuned through their interactions with RNA and through protein modifications such as phosphorylation and methylation. These findings from C elegans, combined with work done in other model organisms, continue to provide insight into the formation of membraneless organelles and the important role they play in compartmentalizing cellular processes.
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Affiliation(s)
- Elisabeth A Marnik
- Center for Regenerative Biology and Medicine, The Mount Desert Island Biological Laboratory, Bar Harbor, Maine
| | - Dustin L Updike
- Center for Regenerative Biology and Medicine, The Mount Desert Island Biological Laboratory, Bar Harbor, Maine
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45
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Borgermann N, Ackermann L, Schwertman P, Hendriks IA, Thijssen K, Liu JC, Lans H, Nielsen ML, Mailand N. SUMOylation promotes protective responses to DNA-protein crosslinks. EMBO J 2019; 38:embj.2019101496. [PMID: 30914427 PMCID: PMC6463212 DOI: 10.15252/embj.2019101496] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/20/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022] Open
Abstract
DNA‐protein crosslinks (DPCs) are highly cytotoxic lesions that obstruct essential DNA transactions and whose resolution is critical for cell and organismal fitness. However, the mechanisms by which cells respond to and overcome DPCs remain incompletely understood. Recent studies unveiled a dedicated DPC repair pathway in higher eukaryotes involving the SprT‐type metalloprotease SPRTN/DVC1, which proteolytically processes DPCs during DNA replication in a ubiquitin‐regulated manner. Here, we show that chemically induced and defined enzymatic DPCs trigger potent chromatin SUMOylation responses targeting the crosslinked proteins and associated factors. Consequently, inhibiting SUMOylation compromises DPC clearance and cellular fitness. We demonstrate that ACRC/GCNA family SprT proteases interact with SUMO and establish important physiological roles of Caenorhabditis elegans GCNA‐1 and SUMOylation in promoting germ cell and embryonic survival upon DPC formation. Our findings provide first global insights into signaling responses to DPCs and reveal an evolutionarily conserved function of SUMOylation in facilitating responses to these lesions in metazoans that may complement replication‐coupled DPC resolution processes.
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Affiliation(s)
- Nikoline Borgermann
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leena Ackermann
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Petra Schwertman
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Karen Thijssen
- Department of Molecular Genetics, Oncode Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Julio Cy Liu
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark .,Center for Chromosome Stability, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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46
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Kojima ML, de Rooij DG, Page DC. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. eLife 2019; 8:43738. [PMID: 30810530 PMCID: PMC6392498 DOI: 10.7554/elife.43738] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 02/10/2019] [Indexed: 12/22/2022] Open
Abstract
The germ line provides the cellular link between generations of multicellular organisms, its cells entering the meiotic cell cycle only once each generation. However, the mechanisms governing this initiation of meiosis remain poorly understood. Here, we examined cells undergoing meiotic initiation in mice, and we found that initiation involves the dramatic upregulation of a transcriptional network of thousands of genes whose expression is not limited to meiosis. This broad gene expression program is directly upregulated by STRA8, encoded by a germ cell-specific gene required for meiotic initiation. STRA8 binds its own promoter and those of thousands of other genes, including meiotic prophase genes, factors mediating DNA replication and the G1-S cell-cycle transition, and genes that promote the lengthy prophase unique to meiosis I. We conclude that, in mice, the robust amplification of this extraordinarily broad transcription program by a common factor triggers initiation of meiosis.
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Affiliation(s)
- Mina L Kojima
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | | | - David C Page
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, United States
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47
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Maezawa S, Alavattam KG, Tatara M, Nagai R, Barski A, Namekawa SH. A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†. Biol Reprod 2019; 100:409-419. [PMID: 30137219 DOI: 10.1093/biolre/ioy181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/20/2018] [Accepted: 08/16/2018] [Indexed: 11/14/2022] Open
Abstract
Genes involved in sexual reproduction diverge rapidly as a result of reproductive fitness. Here, we identify a novel protein domain in the germline-specific Polycomb protein SCML2 that is required for the establishment of unique gene expression programs after the mitosis-to-meiosis transition in spermatogenesis. We term this novel domain, which is comprised of rapidly evolved, DNA-binding repeat units of 28 amino acids, the SCML2 DNA-binding (SDB) repeats. These repeats are acquired in a specific subgroup of the rodent lineage, having been subjected to positive selection in the course of evolution. Mouse SCML2 has two DNA-binding domains: one is the SDB repeats and the other is an RNA-binding region, which is conserved in human SCML2. For the recruitment of SCML2 to target loci, the SDB repeats cooperate with the other functional domains of SCML2 to bind chromatin. The cooperative action of these domains enables SCML2 to sense DNA hypomethylation in an in vivo chromatin environment, thereby enabling SCML2 to bind to hypomethylated chromatin. We propose that the rapid evolution of SCML2 is due to reproductive adaptation, which has promoted species-specific gene expression programs in spermatogenesis.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mayu Tatara
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Rika Nagai
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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48
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Kulkarni P, Uversky VN. Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome. Proteomics 2018; 18:e1800061. [DOI: 10.1002/pmic.201800061] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/07/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research; City of Hope National Medical Center; Duarte CA 91010 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa FL 33612 USA
- Laboratory of New methods in Biology; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region 142290 Russia
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49
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Abstract
DNA-protein crosslinks (DPCs) are a specific type of DNA lesion consisting of a protein covalently and irreversibly bound to DNA, which arise after exposure to physical and chemical crosslinking agents. DPCs can be bulky and thereby pose a barrier to DNA replication and transcription. The persistence of DPCs during S phase causes DNA replication stress and genome instability. The toxicity of DPCs is exploited in cancer therapy: many common chemotherapeutics kill cancer cells by inducing DPC formation. Recent work from several laboratories discovered a specialized repair pathway for DPCs, namely DPC proteolysis (DPCP) repair. DPCP repair is carried out by replication-coupled DNA-dependent metalloproteases: Wss1 in yeast and SPRTN in metazoans. Mutations in SPRTN cause premature ageing and liver cancer in humans and mice; thus, defective DPC repair has great clinical ramifications. In the present review, we will revise the current knowledge on the mechanisms of DPCP repair and on the regulation of DPC protease activity, while highlighting the most significant unresolved questions in the field. Finally, we will discuss the impact of faulty DPC repair on disease and cancer therapy.
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50
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Seydoux G. The P Granules of C. elegans: A Genetic Model for the Study of RNA-Protein Condensates. J Mol Biol 2018; 430:4702-4710. [PMID: 30096346 DOI: 10.1016/j.jmb.2018.08.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 01/25/2023]
Abstract
P granules are RNA/protein condensates in the germline of Caenorhabditis elegans. Genetic analyses have begun to identify the proteins that regulate P granule assembly in the cytoplasm of zygotes. Among them, the RGG-domain protein PGL-3, the intrinsically disordered protein MEG-3, and the RNA helicase LAF-1 all bind and phase separate with RNA in vitro. We discuss how RNA-induced phase separation, competition with other RNA-binding proteins, and reversible phosphorylation contribute to the asymmetric localization of P granules in the cytoplasm of newly fertilized embryos. P granules contain RNA silencing complexes that monitor the germline transcriptome and may provide an RNA memory of germline gene expression across generations.
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Affiliation(s)
- Geraldine Seydoux
- Department of Molecular Biology and Genetics, HHMI, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.
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