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Chatterjee T, Tiwari A, Gupta R, Shukla H, Varshney A, Mishra S, Habib S. A Plasmodium apicoplast-targeted unique exonuclease/FEN exhibits interspecies functional differences attributable to an insertion that alters DNA-binding. Nucleic Acids Res 2024; 52:7843-7862. [PMID: 38888125 PMCID: PMC11260460 DOI: 10.1093/nar/gkae512] [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: 07/25/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
The human malaria parasite Plasmodium falciparum genome is among the most A + T rich, with low complexity regions (LCRs) inserted in coding sequences including those for proteins targeted to its essential relict plastid (apicoplast). Replication of the apicoplast genome (plDNA), mediated by the atypical multifunctional DNA polymerase PfPrex, would require additional enzymatic functions for lagging strand processing. We identified an apicoplast-targeted, [4Fe-4S]-containing, FEN/Exo (PfExo) with a long LCR insertion and detected its interaction with PfPrex. Distinct from other known exonucleases across organisms, PfExo recognized a wide substrate range; it hydrolyzed 5'-flaps, processed dsDNA as a 5'-3' exonuclease, and was a bipolar nuclease on ssDNA and RNA-DNA hybrids. Comparison with the rodent P. berghei ortholog PbExo, which lacked the insertion and [4Fe-4S], revealed interspecies functional differences. The insertion-deleted PfExoΔins behaved like PbExo with a limited substrate repertoire because of compromised DNA binding. Introduction of the PfExo insertion into PbExo led to gain of activities that the latter initially lacked. Knockout of PbExo indicated essentiality of the enzyme for survival. Our results demonstrate the presence of a novel apicoplast exonuclease with a functional LCR that diversifies substrate recognition, and identify it as the candidate flap-endonuclease and RNaseH required for plDNA replication and maintenance.
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Affiliation(s)
- Tribeni Chatterjee
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Anupama Tiwari
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ritika Gupta
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Aastha Varshney
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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2
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Petrykey K, Lippé S, Sultan S, Robaey P, Drouin S, Affret-Bertout L, Beaulieu P, St-Onge P, Baedke JL, Yasui Y, Hudson MM, Laverdière C, Sinnett D, Krajinovic M. Genetic Factors and Long-term Treatment-Related Neurocognitive Deficits, Anxiety, and Depression in Childhood Leukemia Survivors: An Exome-Wide Association Study. Cancer Epidemiol Biomarkers Prev 2024; 33:234-243. [PMID: 38051303 PMCID: PMC10903523 DOI: 10.1158/1055-9965.epi-23-0634] [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: 06/13/2023] [Revised: 09/23/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND An increased risk of neurocognitive deficits, anxiety, and depression has been reported in childhood cancer survivors. METHODS We analyzed associations of neurocognitive deficits, as well as anxiety and depression, with common and rare genetic variants derived from whole-exome sequencing data of acute lymphoblastic leukemia (ALL) survivors from the PETALE cohort. In addition, significant associations were assessed using stratified and multivariable analyses. Next, top-ranking common associations were analyzed in an independent SJLIFE replication cohort of ALL survivors. RESULTS Significant associations were identified in the entire discovery cohort (N = 229) between the AK8 gene and changes in neurocognitive function, whereas PTPRZ1, MUC16, TNRC6C-AS1 were associated with anxiety. Following stratification according to sex, the ZNF382 gene was linked to a neurocognitive deficit in males, whereas APOL2 and C6orf165 were associated with anxiety and EXO5 with depression. Following stratification according to prognostic risk groups, the modulatory effect of rare variants on depression was additionally found in the CYP2W1 and PCMTD1 genes. In the replication SJLIFE cohort (N = 688), the male-specific association in the ZNF382 gene was not significant; however, a P value<0.05 was observed when the entire SJLIFE cohort was analyzed. ZNF382 was significant in males in the combined cohorts as shown by meta-analyses as well as the depression-associated gene EXO5. CONCLUSIONS Further research is needed to confirm whether the current findings, along with other known risk factors, may be valuable in identifying patients at increased risk of these long-term complications. IMPACT Our results suggest that specific genes may be related to increased neuropsychological consequences.
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Affiliation(s)
- Kateryna Petrykey
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Department of Pharmacology and Physiology, Université de Montréal (Quebec), Canada
| | - Sarah Lippé
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Department of Psychology, Université de Montréal (Quebec), Canada
| | - Serge Sultan
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Department of Psychology, Université de Montréal (Quebec), Canada
| | - Philippe Robaey
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Children’s Hospital of Eastern Ontario, Ottawa (Ontario), Canada
- Department of Psychiatry, Université de Montréal (Quebec), Canada
- Department of Psychiatry, University of Ottawa (Ontario), Canada
| | - Simon Drouin
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
| | | | - Patrick Beaulieu
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
| | - Pascal St-Onge
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
| | - Jessica L. Baedke
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis (TN), USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis (TN), USA
| | - Melissa M. Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis (TN), USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis (TN), USA
| | - Caroline Laverdière
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Department of Pediatrics, Université de Montréal (Quebec), Canada
| | - Daniel Sinnett
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Department of Pediatrics, Université de Montréal (Quebec), Canada
| | - Maja Krajinovic
- Sainte-Justine University Health Center (SJUHC), Montreal (Quebec), Canada
- Department of Pharmacology and Physiology, Université de Montréal (Quebec), Canada
- Department of Pediatrics, Université de Montréal (Quebec), Canada
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3
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Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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4
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Dusi DMA, Alves ER, Cabral GB, Mello LV, Rigden DJ, Silveira ÉD, Alves-Ferreira M, Guimarães LA, Gomes ACMM, Rodrigues JCM, Carneiro VTC. An exonuclease V homologue is expressed predominantly during early megasporogenesis in apomictic Brachiaria brizantha. PLANTA 2023; 258:5. [PMID: 37219749 DOI: 10.1007/s00425-023-04162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
MAIN CONCLUSION An exonuclease V homologue from apomictic Brachiaria brizantha is expressed and localized in nucellar cells at key moments when these cells differentiate to give rise to unreduced gametophytes. Brachiaria is a genus of forage grasses with economical and agricultural importance to Brazil. Brachiaria reproduces by aposporic apomixis, in which unreduced embryo sacs, derived from nucellar cells, other than the megaspore mother cell (MMC), are formed. The unreduced embryo sacs produce an embryo without fertilization resulting in clones of the mother plant. Comparative gene expression analysis in ovaries of sexual and apomictic Brachiaria spp. revealed a sequence from B. brizantha that showed a distinct pattern of expression in ovaries of sexual and apomictic plants. In this work, we describe a gene named BbrizExoV with strong identity to exonuclease V (Exo V) genes from other grasses. Sequence analysis in signal prediction tools showed that BbrizExoV might have dual localization, depending on the translation point. A longer form to the nucleus and a shorter form which would be directed to the chloroplast. This is also the case for monocot sequences analyzed from other species. The long form of BbrizExoV protein localizes to the nucleus of onion epidermal cells. Analysis of ExoV proteins from dicot species, with exception of Arabidopsis thaliana ExoVL protein, showed only one localization. Using a template-based AlphaFold 2 modelling approach the structure of BbrizExoV in complex with metal and ssDNA was predicted based on the holo structure of the human counterpart. Features predicted to define ssDNA binding but a lack of sequence specificity are shared between the human enzyme and BbrizExoV. Expression analyses indicated the precise site and timing of transcript accumulation during ovule development, which coincides with the differentiation of nucelar cells to form the typical aposporic four-celled unreduced gametophyte. A putative function for this protein is proposed based on its homology and expression pattern.
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Affiliation(s)
- Diva M A Dusi
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil
| | - Elizângela R Alves
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil
- Department of Celular Biology, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Gláucia B Cabral
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil
| | - Luciane V Mello
- School of Life Sciences, University of Liverpool, Crown St, Liverpool, L69 7ZB, UK
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool, L69 7ZB, UK
| | - Érica D Silveira
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil
- Department of Genetics, Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n Prédio do CCS Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Márcio Alves-Ferreira
- Department of Genetics, Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n Prédio do CCS Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Larissa A Guimarães
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil
- Department of Celular Biology, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Ana Cristina M M Gomes
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil
| | - Júlio C M Rodrigues
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil.
| | - Vera T C Carneiro
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Genetic Resources and Biotechnology, Cx. Postal 02372, Brasilia, DF, 70770-917, Brazil.
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5
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Huang Y, Chen J, Dong C, Sosa D, Xia S, Ouyang Y, Fan C, Li D, Mortola E, Long M, Bergelson J. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. THE PLANT CELL 2022; 34:802-817. [PMID: 34875081 PMCID: PMC8824575 DOI: 10.1093/plcell/koab291] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/25/2021] [Indexed: 05/04/2023]
Abstract
Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-sequencing analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.
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Affiliation(s)
- Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jiahui Chen
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chuan Dong
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Dezhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Emily Mortola
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
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6
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Tsutakawa SE, Bacolla A, Katsonis P, Bralić A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Front Mol Biosci 2021; 8:791792. [PMID: 34966786 PMCID: PMC8710748 DOI: 10.3389/fmolb.2021.791792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.
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Affiliation(s)
- Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.,Department of Cancer Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
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7
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So M, Stiban J, Ciesielski GL, Hovde SL, Kaguni LS. Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase. Front Genet 2021; 12:790521. [PMID: 34950192 PMCID: PMC8688847 DOI: 10.3389/fgene.2021.790521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Recent evidence suggests that iron-sulfur clusters (ISCs) in DNA replicative proteins sense DNA-mediated charge transfer to modulate nuclear DNA replication. In the mitochondrial DNA replisome, only the replicative DNA helicase (mtDNA helicase) from Drosophila melanogaster (Dm) has been shown to contain an ISC in its N-terminal, primase-like domain (NTD). In this report, we confirm the presence of the ISC and demonstrate the importance of a metal cofactor in the structural stability of the Dm mtDNA helicase. Further, we show that the NTD also serves a role in membrane binding. We demonstrate that the NTD binds to asolectin liposomes, which mimic phospholipid membranes, through electrostatic interactions. Notably, membrane binding is more specific with increasing cardiolipin content, which is characteristically high in the mitochondrial inner membrane (MIM). We suggest that the N-terminal domain of the mtDNA helicase interacts with the MIM to recruit mtDNA and initiate mtDNA replication. Furthermore, Dm NUBPL, the known ISC donor for respiratory complex I and a putative donor for Dm mtDNA helicase, was identified as a peripheral membrane protein that is likely to execute membrane-mediated ISC delivery to its target proteins.
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Affiliation(s)
- Minyoung So
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland.,Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States
| | - Stacy L Hovde
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
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8
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Stupp D, Sharon E, Bloch I, Zitnik M, Zuk O, Tabach Y. Co-evolution based machine-learning for predicting functional interactions between human genes. Nat Commun 2021; 12:6454. [PMID: 34753957 PMCID: PMC8578642 DOI: 10.1038/s41467-021-26792-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/09/2021] [Indexed: 12/20/2022] Open
Abstract
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary questions. Here, we develop a machine-learning approach for utilizing phylogenetic profiles across 1154 eukaryotic species. This method integrates co-evolution across eukaryotic clades to predict functional interactions between human genes and the context for these interactions. We benchmark our approach showing a 14% performance increase (auROC) compared to previous methods. Using this approach, we predict functional annotations for less studied genes. We focus on DNA repair and verify that 9 of the top 50 predicted genes have been identified elsewhere, with others previously prioritized by high-throughput screens. Overall, our approach enables better annotation of function and functional interactions and facilitates the understanding of evolutionary processes underlying co-evolution. The manuscript is accompanied by a webserver available at: https://mlpp.cs.huji.ac.il. With the rise in number of eukaryotic species being fully sequenced, large scale phylogenetic profiling can give insights on gene function, Here, the authors describe a machine-learning approach that integrates co-evolution across eukaryotic clades to predict gene function and functional interactions among human genes.
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Affiliation(s)
- Doron Stupp
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
| | - Elad Sharon
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard University, Boston, MA, 02115, USA
| | - Or Zuk
- Department of Statistics and Data Science, The Hebrew University of Jerusalem, Jerusalem, 9190501, Israel.
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, 9112001, Jerusalem, Israel.
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9
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Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, Tainer JA. EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart. Mol Cell 2021; 81:2989-3006.e9. [PMID: 34197737 PMCID: PMC8720176 DOI: 10.1016/j.molcel.2021.05.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/09/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Stalled DNA replication fork restart after stress as orchestrated by ATR kinase, BLM helicase, and structure-specific nucleases enables replication, cell survival, and genome stability. Here we unveil human exonuclease V (EXO5) as an ATR-regulated DNA structure-specific nuclease and BLM partner for replication fork restart. We find that elevated EXO5 in tumors correlates with increased mutation loads and poor patient survival, suggesting that EXO5 upregulation has oncogenic potential. Structural, mechanistic, and mutational analyses of EXO5 and EXO5-DNA complexes reveal a single-stranded DNA binding channel with an adjacent ATR phosphorylation motif (T88Q89) that regulates EXO5 nuclease activity and BLM binding identified by mass spectrometric analysis. EXO5 phospho-mimetic mutant rescues the restart defect from EXO5 depletion that decreases fork progression, DNA damage repair, and cell survival. EXO5 depletion furthermore rescues survival of FANCA-deficient cells and indicates EXO5 functions epistatically with SMARCAL1 and BLM. Thus, an EXO5 axis connects ATR and BLM in directing replication fork restart.
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Affiliation(s)
- Shashank Hambarde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurosurgery, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Raj K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vijay Charaka
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vashino Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Oliver Limbo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Remy Le Meur
- Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul Russell
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Schlacher
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurosurgery, The Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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10
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Zaman Q, Khan R, Hameed U, Shah W, Waqas A, Zubair M, Dil S, Zafar T, Ali A, Unar A, Shi Q. Exonuclease 5 is dispensable for meiotic progression and male fertility in mouse. Gene 2020; 769:145254. [PMID: 33164760 DOI: 10.1016/j.gene.2020.145254] [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: 07/09/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 11/15/2022]
Abstract
Exonuclease 5 (Exo5) belongs to a class of bi-directional, ssDNA-specific exonucleases that mainly involved in the DNA repair pathways. Exo5 has been reported to be crucial for DNA- DNA mismatch repair (MMR) in several human cell lines. However, its in vivo function in mammals still needs to be explored. Thus, to study the in vivo role of Exo5 in spermatogenesis, Exo5 knockout mice were generated using CRISPR/Cas9 technology. Unexpectedly, we found that the knockout mice are fertile despite a slight decrease in sperm count. Furthermore, Exo5-/- mice showed no detectable developmental anomalies, exhibited no remarkable differences in the epididymal histology and testis/body weight ratio. Moreover, cytological investigations on meiocytes revealed non-significant differences in chromosomal synapsis, recombination, and meiotic progression of prophase I, further demonstrating that Exo5 has no essential role in spermatogenesis in mice under normal breeding conditions. Collectively, these data indicate that Exo5 is dispensable for meiotic progression and fertility in mice.
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Affiliation(s)
- Qumar Zaman
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ranjha Khan
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Uzma Hameed
- Institute of Industrial Biotechnology, Government College University Lahore, Pakistan
| | - Wasim Shah
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education Lahore, Multan Campus, Multan, Pakistan
| | - Muhammad Zubair
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Sobia Dil
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Tuba Zafar
- Institute of Industrial Biotechnology, Government College University Lahore, Pakistan
| | - Asim Ali
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ahsanullah Unar
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Qinghua Shi
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China.
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11
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Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol 2020; 55:482-507. [PMID: 32856505 PMCID: PMC7821911 DOI: 10.1080/10409238.2020.1813070] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023]
Abstract
The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.
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Affiliation(s)
- Colleen C. Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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12
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Ali S, Zhang Y, Zhou M, Li H, Jin W, Zheng L, Yu X, Stark JM, Weitzel JN, Shen B. Functional deficiency of DNA repair gene EXO5 results in androgen-induced genomic instability and prostate tumorigenesis. Oncogene 2019; 39:1246-1259. [PMID: 31616062 DOI: 10.1038/s41388-019-1061-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/16/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Germline mutations of DNA double-strand break (DSB) response and repair genes that drive tumorigenesis could be a major cause of prostate cancer (PCa) heritability. In this study, we demonstrated the role of novel exonuclease 5 (EXO5) gene in androgen-induced double strand breaks repair via homology-directed repair pathway and prostate tumorigenesis. Using whole-exome sequencing of samples from 20 PCa families, with three or more siblings diagnosed with metastatic PCa, we identified mutations in 31 genes involved in DSB response and repair. Among them, the L151P mutation in the exonuclease 5 (EXO5) gene was present in all affected siblings in three PCa families. We found two other EXO5 SNPs significantly associated with risk of PCa in cases-controls study from databases of genotype and phenotype (dbGaP), which are in linkage disequilibrium (D' = 1) with Exo5 L151P found in PCa family. The L151 residue is conserved across diverse species and its mutation is deleterious for protein functions, as demonstrated by our bioinformatics analyses. The L151P mutation impairs the DNA repair function of EXO5 due to loss of nuclease activity, as well as failure of nuclear localization. CRISPR elimination of EXO5 in a PCa cell line impaired homology-directed recombination repair (HDR) and caused androgen-induced genomic instability, as indicated by frequent occurrence of the oncogenic fusion transcript TMPRSS2-ERG. Genetic and functional validation of the EXO5 mutations indicated that EXO5 is a risk gene for prostate tumorigenesis, likely due to its functions in HDR.
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Affiliation(s)
- Shafat Ali
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Yilan Zhang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, USA
| | - Weiwei Jin
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA
| | - Jeffrey N Weitzel
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, USA.
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13
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The roles of fission yeast exonuclease 5 in nuclear and mitochondrial genome stability. DNA Repair (Amst) 2019; 83:102720. [PMID: 31563844 DOI: 10.1016/j.dnarep.2019.102720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/04/2019] [Accepted: 09/19/2019] [Indexed: 11/22/2022]
Abstract
The Exo5 family consists of bi-directional, single-stranded DNA-specific exonucleases that contain an iron-sulfur cluster as a structural motif and have multiple roles in DNA metabolism. S. cerevisiae Exo5 is essential for mitochondrial genome maintenance, while the human ortholog is important for nuclear genome stability and DNA repair. Here, we identify the Exo5 ortholog in Schizosaccharomyes pombe (spExo5). The activity of spExo5 is highly similar to that of the human enzyme. When the single-stranded DNA is coated with single-stranded DNA binding protein RPA, spExo5 become a 5'-specific exonuclease. Exo5Δ mutants are sensitive to various DNA damaging agents, particularly interstrand crosslinking agents. An epistasis analysis places exo5+ in the Fanconi pathway for interstrand crosslink repair. Exo5+ is in a redundant pathway with rad2+, which encodes the flap endonuclease FEN1, for mitochondrial genome maintenance. Deletion of both genes lead to severe depletion of the mitochondrial genome, and defects in respiration, indicating that either spExo5 or spFEN1 is necessary for mitochondrial DNA metabolism.
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14
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Wei T, Wang F, Zhang Z, Qiang J, Lv J, Chen T, Li J, Chen X. Recent Progress in the Development of Fluorometric Chemosensors to Detect Enzymatic Activity. Curr Med Chem 2019; 26:3923-3957. [DOI: 10.2174/0929867325666180214105552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/10/2017] [Accepted: 12/27/2017] [Indexed: 12/16/2022]
Abstract
Enzymes are a class of macromolecules that function as highly efficient and specific
biological catalysts requiring only mild reaction conditions. Enzymes are essential to
maintaining life activities, including promoting metabolism and homeostasis, and participating
in a variety of physiological functions. Accordingly, enzymatic levels and activity are
closely related to the health of the organism, where enzymatic dysfunctions often lead to corresponding
diseases in the host. Due to this, diagnosis of certain diseases is based on the levels
and activity of certain enzymes. Therefore, rapid real-time and accurate detection of enzymes
in situ are important for diagnosis, monitoring, clinical treatment and pathological
studies of disease. Fluorescent probes have unique advantages in terms of detecting enzymes,
including being simple to use in highly sensitive and selective real-time rapid in-situ noninvasive
and highly spatial resolution visual imaging. However, fluorescent probes are most
commonly used to detect oxidoreductases, transferases and hydrolases due to the processes
and types of enzyme reactions. This paper summarizes the application of fluorescent probes to
detect these three types of enzymes over the past five years. In addition, we introduce the
mechanisms underlying detection of these enzymes by their corresponding probes.
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Affiliation(s)
- Tingwen Wei
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Fang Wang
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Zhijie Zhang
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Jiang Qiang
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Jing Lv
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Tiantian Chen
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Jia Li
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
| | - Xiaoqiang Chen
- State Key laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 210009, China
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15
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Paumard‐Hernández B, Calvete O, Inglada Pérez L, Tejero H, Al‐Shahrour F, Pita G, Barroso A, Carlos Triviño J, Urioste M, Valverde C, González Billalabeitia E, Quiroga V, Francisco Rodríguez Moreno J, Fernández Aramburo A, López C, Maroto P, Sastre J, José Juan Fita M, Duran I, Lorenzo‐Lorenzo I, Iranzo P, García del Muro X, Ros S, Zambrana F, María Autran A, Benítez J. Whole exome sequencing identifies
PLEC
,
EXO5
and
DNAH7
as novel susceptibility genes in testicular cancer. Int J Cancer 2018; 143:1954-1962. [DOI: 10.1002/ijc.31604] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/27/2022]
Affiliation(s)
| | - Oriol Calvete
- Human Genetics Group, Spanish National Cancer Research Center (CNIO)Madrid Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER)Madrid Spain
| | - Lucia Inglada Pérez
- Center for Biomedical Network Research on Rare Diseases (CIBERER)Madrid Spain
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO)Madrid Spain
| | - Héctor Tejero
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO)Madrid Spain
| | - Fátima Al‐Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO)Madrid Spain
| | - Guillermo Pita
- Human Genotyping‐CEGEN Unit, Human Cancer Genetic Program, Spanish National Cancer Research Centre (CNIO)Madrid Spain
| | - Alicia Barroso
- Human Genetics Group, Spanish National Cancer Research Center (CNIO)Madrid Spain
| | - Juan Carlos Triviño
- Bioinformatic Unit, Sistemas Genómicos, Valencia Spain, Spanish National Cancer Research Centre (CNIO)Madrid Spain
| | - Miguel Urioste
- Center for Biomedical Network Research on Rare Diseases (CIBERER)Madrid Spain
- Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO)Madrid Spain
| | - Claudia Valverde
- Department of Medical OncologyVall d'Hebron Institute of Oncology, Vall d'Hebron University HospitalBarcelona Spain
- Spanish Germ Cell Group (SGCCG)
| | - Enrique González Billalabeitia
- Spanish Germ Cell Group (SGCCG)
- Medical Oncology‐Haematology DepartmentHospital Universitario Morales MeseguerMurcia Spain
| | - Vanesa Quiroga
- Spanish Germ Cell Group (SGCCG)
- Medical Oncology DepartmentHospital Universitari Germans Trias i Pujol, Institut Català d'Oncologia‐BadalonaBarcelona Spain
| | | | - Antonio Fernández Aramburo
- Spanish Germ Cell Group (SGCCG)
- Department of OncologyComplejo Hospitalario Universitario AlbaceteAlbacete Spain
| | - Cristina López
- Spanish Germ Cell Group (SGCCG)
- Medical Oncology DepartmentInstituto de Investigación Sanitaria Gregorio MarañónMadrid Spain
| | - Pablo Maroto
- Spanish Germ Cell Group (SGCCG)
- Medical Oncology and Biochemistry DepartmentsHospital de la Santa Creu i Sant PauBarcelona Spain
| | - Javier Sastre
- Spanish Germ Cell Group (SGCCG)
- Department of Medical OncologyHospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC)Madrid Spain
| | - María José Juan Fita
- Spanish Germ Cell Group (SGCCG)
- Medical OncologyFundación Instituto Valenciano de OncologíaValencia Spain
| | - Ignacio Duran
- Spanish Germ Cell Group (SGCCG)
- Department of Medical OncologyInstituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilla Spain
| | | | - Patricia Iranzo
- Spanish Germ Cell Group (SGCCG)
- Department of Medical OncologyHospital Clinico Universitario Lozano BlesaZaragoza Spain
| | - Xavier García del Muro
- Spanish Germ Cell Group (SGCCG)
- Sarcoma Multidisciplinary Unit and Medical Oncology DepartmentInstitut Català d'Oncologia Hospitalet, IDIBELLBarcelona Spain
| | - Silverio Ros
- Department of Clinical OncologyHospital Universitario Virgen ArrixacaMurcia Spain
| | - Francisco Zambrana
- Spanish Germ Cell Group (SGCCG)
- Medical Oncology DepartmentHospital Universitario Infanta Sofía, San Sebastián De Los Reyes Spain
| | - Ana María Autran
- Spanish Germ Cell Group (SGCCG)
- Medical Urology departmentFundación Jiménez DíazMadrid Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO)Madrid Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER)Madrid Spain
- Human Genotyping‐CEGEN Unit, Human Cancer Genetic Program, Spanish National Cancer Research Centre (CNIO)Madrid Spain
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16
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Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 2018; 23:239-254.e6. [PMID: 29617664 PMCID: PMC5961503 DOI: 10.1016/j.celrep.2018.03.076] [Citation(s) in RCA: 696] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.
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Affiliation(s)
| | - Linghua Wang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA; Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Feng
- TESARO Inc., Waltham, MA 02451, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase Miller
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Haoran Chen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Pora Kim
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Denise Wolf
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer, Houston, TX 77030, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Raymond J Monnat
- Departments of Pathology & Genome Sciences, University of Washington, Seattle, WA 98195-7705, USA.
| | | | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA; Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
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17
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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Maréchal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res 2014; 25:9-23. [PMID: 25403473 DOI: 10.1038/cr.2014.147] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- 1] Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA [2] Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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He HZ, Chan WI, Mak TY, Liu LJ, Wang M, Chan DSH, Ma DL, Leung CH. Detection of 3′→5′ exonuclease activity using a metal-based luminescent switch-on probe. Methods 2013; 64:218-23. [DOI: 10.1016/j.ymeth.2013.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/02/2013] [Accepted: 08/07/2013] [Indexed: 12/22/2022] Open
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A proteome-wide visual screen identifies fission yeast proteins localizing to DNA double-strand breaks. DNA Repair (Amst) 2013; 12:433-43. [PMID: 23628481 DOI: 10.1016/j.dnarep.2013.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 03/18/2013] [Accepted: 04/03/2013] [Indexed: 11/23/2022]
Abstract
DNA double-strand breaks (DSBs) are a major threat to genome integrity. Proteins involved in DNA damage checkpoint signaling and DSB repair often relocalize and concentrate at DSBs. Here, we used an ORFeome library of the fission yeast Schizosaccharomyces pombe to systematically identify proteins targeted to DSBs. We found 51 proteins that, when expressed from a strong exogenous promoter on the ORFeome plasmids, were able to form a distinct nuclear focus at an HO endonuclease-induced DSB. The majority of these proteins have known connections to DNA damage response, but few have been visualized at a specific DSB before. Among the screen hits, 37 can be detected at DSBs when expressed from native promoters. We classified them according to the focus emergence timing of the endogenously tagged proteins. Eight of these 37 proteins are yet unnamed. We named these eight proteins DNA-break-localizing proteins (Dbls) and performed preliminary functional analysis on two of them, Dbl1 (SPCC2H8.05c) and Dbl2 (SPCC553.01c). We found that Dbl1 and Dbl2 contribute to the normal DSB targeting of checkpoint protein Rad26 (homolog of human ATRIP) and DNA repair helicase Fml1 (homolog of human FANCM), respectively. As the first proteome-wide inventory of DSB-localizing proteins, our screen result will be a useful resource for understanding the mechanisms of eukaryotic DSB response.
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