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Sakthivel D, Brown-Suedel AN, Lopez KE, Salgar S, Coutinho LE, Keane F, Huang S, Sherry KM, Charendoff CI, Dunne KP, Robichaux DJ, Vargas-Hernández A, Le B, Shin CS, Carisey AF, Poreba M, Flanagan JM, Bouchier-Hayes L. Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia. SCIENCE ADVANCES 2024; 10:eadj3145. [PMID: 39093977 PMCID: PMC11296348 DOI: 10.1126/sciadv.adj3145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/28/2024] [Indexed: 08/04/2024]
Abstract
Mutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm (NPM1c+). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a proapoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm and DNA damage-induced apoptosis is caspase-2 dependent in NPM1c+ but not in NPM1wt AML cells. Strikingly, in NPM1c+ cells, caspase-2 loss results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment of the AKT/mTORC1 pathways, and inhibition of Rictor cleavage. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile of NPM1wt cells lacking caspase-2. Our results show that caspase-2 is essential for proliferation and self-renewal of AML cells expressing mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function.
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Affiliation(s)
- Dharaniya Sakthivel
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexandra N. Brown-Suedel
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Karla E. Lopez
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Suruchi Salgar
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Luiza E. Coutinho
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Francesca Keane
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shixia Huang
- Advanced Technology Cores, Department of Molecular and Cellular Biology, Huffington Department of Education, Innovation & Technology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kenneth Mc Sherry
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chloé I. Charendoff
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin P. Dunne
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dexter J. Robichaux
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Vargas-Hernández
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - BaoChau Le
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Crystal S. Shin
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexandre F. Carisey
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marcin Poreba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50370, Poland
| | - Jonathan M. Flanagan
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
| | - Lisa Bouchier-Hayes
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital William T. Shearer Center for Human Immunobiology, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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2
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Fu L, Wu Q, Fu J. Exploring the biological roles of DHX36, a DNA/RNA G-quadruplex helicase, highlights functions in male infertility: A comprehensive review. Int J Biol Macromol 2024; 268:131811. [PMID: 38677694 DOI: 10.1016/j.ijbiomac.2024.131811] [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: 01/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024]
Abstract
It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.
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Affiliation(s)
- Li Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Junjiang Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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3
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Lu Z, Xie S, Su H, Han S, Huang H, Zhou X. Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase. Nucleic Acids Res 2024; 52:e37. [PMID: 38452210 PMCID: PMC11040147 DOI: 10.1093/nar/gkae126] [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: 09/19/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 03/09/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures pivotal to cellular processes and disease pathways. Deciphering G4-interacting proteins is imperative for unraveling G4's biological significance. In this study, we developed a G4-targeting biotin ligase named G4PID, meticulously assessing its binding affinity and specificity both in vitro and in vivo. Capitalizing on G4PID, we devised a tailored approach termed G-quadruplex-interacting proteins specific biotin-ligation procedure (PLGPB) to precisely profile G4-interacting proteins. Implementing this innovative strategy in live cells, we unveiled a cohort of 149 potential G4-interacting proteins, which exhibiting multifaceted functionalities. We then substantiate the directly binding affinity of 7 candidate G4-interacting-proteins (SF3B4, FBL, PP1G, BCL7C, NDUV1, ILF3, GAR1) in vitro. Remarkably, we verified that splicing factor 3B subunit 4 (SF3B4) binds preferentially to the G4-rich 3' splice site and the corresponding splicing sites are modulated by the G4 stabilizer PDS, indicating the regulating role of G4s in mRNA splicing procedure. The PLGPB strategy could biotinylate multiple proteins simultaneously, which providing an opportunity to map G4-interacting proteins network in living cells.
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Affiliation(s)
- Ziang Lu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Shengjie Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Haomiao Su
- Department of Chemistry, Yale University, 600 West Campus Drive West Haven, West Haven, CT 06516, USA
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Haiyan Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
- Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
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4
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Fukute J, Maki K, Adachi T. The nucleolar shell provides anchoring sites for DNA untwisting. Commun Biol 2024; 7:83. [PMID: 38263258 PMCID: PMC10805735 DOI: 10.1038/s42003-023-05750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024] Open
Abstract
DNA underwinding (untwisting) is a crucial step in transcriptional activation. DNA underwinding occurs between the site where torque is generated by RNA polymerase (RNAP) and the site where the axial rotation of DNA is constrained. However, what constrains DNA axial rotation in the nucleus is yet unknown. Here, we show that the anchorage to the nuclear protein condensates constrains DNA axial rotation for DNA underwinding in the nucleolus. In situ super-resolution imaging of underwound DNA reveal that underwound DNA accumulates in the nucleolus, a nuclear condensate with a core-shell structure. Specifically, underwound DNA is distributed in the nucleolar core owing to RNA polymerase I (RNAPI) activities. Furthermore, underwound DNA in the core decreases when nucleolar shell components are prevented from binding to their recognition structure, G-quadruplex (G4). Taken together, these results suggest that the nucleolar shell provides anchoring sites that constrain DNA axial rotation for RNAPI-driven DNA underwinding in the core. Our findings will contribute to understanding how nuclear protein condensates make up constraints for the site-specific regulation of DNA underwinding and transcription.
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Affiliation(s)
- Jumpei Fukute
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan
| | - Koichiro Maki
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan.
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan.
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Sakyo, Kyoto, Japan.
- Department of Medicine and Medical Science, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan.
| | - Taiji Adachi
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Sakyo, Kyoto, Japan
- Department of Medicine and Medical Science, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
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5
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Okuwaki M, Ozawa SI, Ebine S, Juichi M, Umeki T, Niioka K, Kikuchi T, Tanaka N. The stability of NPM1 oligomers regulated by acidic disordered regions controls the quality of liquid droplets. J Biochem 2023; 174:461-476. [PMID: 37540843 DOI: 10.1093/jb/mvad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023] Open
Abstract
The nucleolus is a membrane-less nuclear body that typically forms through the process of liquid-liquid phase separation (LLPS) involving its components. NPM1 drives LLPS within the nucleolus and its oligomer formation and inter-oligomer interactions play a cooperative role in inducing LLPS. However, the molecular mechanism underlaying the regulation of liquid droplet quality formed by NPM1 remains poorly understood. In this study, we demonstrate that the N-terminal and central acidic residues within the intrinsically disordered regions (IDR) of NPM1 contribute to attenuating oligomer stability, although differences in the oligomer stability were observed only under stringent conditions. Furthermore, the impact of the IDRs is augmented by an increase in net negative charges resulting from phosphorylation within the IDRs. Significantly, we observed an increase in fluidity of liquid droplets formed by NPM1 with decreased oligomer stability. These results indicate that the difference in oligomer stability only observed biochemically under stringent conditions has a significant impact on liquid droplet quality formed by NPM1. Our findings provide new mechanistic insights into the regulation of nucleolar dynamics during the cell cycle.
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Affiliation(s)
- Mitsuru Okuwaki
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Shin-Ichiro Ozawa
- Laboratory of Physical Chemistry for Drug Design, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Shuhei Ebine
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Motoki Juichi
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Tadanobu Umeki
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Kazuki Niioka
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Taiyo Kikuchi
- Laboratory of Biochemistry, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
| | - Nobutada Tanaka
- Laboratory of Physical Chemistry for Drug Design, School of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-Ku, 108-8641 Tokyo, Japan
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6
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Sharma T, Kundu N, Kaur S, Shankaraswamy J, Saxena S. Why to target G-quadruplexes using peptides: Next-generation G4-interacting ligands. J Pept Sci 2023; 29:e3491. [PMID: 37009771 DOI: 10.1002/psc.3491] [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: 11/18/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
Guanine-rich oligonucleotides existing in both DNA and RNA are able to fold into four-stranded DNA secondary structures via Hoogsteen type hydrogen-bonding, where four guanines self-assemble into a square planar arrangement, which, when stacked upon each other, results in the formation of higher-order structures called G-quadruplexes. Their distribution is not random; they are more frequently present at telomeres, proto-oncogenic promoters, introns, 5'- and 3'-untranslated regions, stem cell markers, ribosome binding sites and so forth and are associated with various biological functions, all of which play a pivotal role in various incurable diseases like cancer and cellular ageing. Several studies have suggested that G-quadruplexes could not regulate biological processes by themselves; instead, various proteins take part in this regulation and can be important therapeutic targets. There are certain limitations in using whole G4-protein for therapeutics purpose because of its high manufacturing cost, laborious structure prediction, dynamic nature, unavailability for oral administration due to its degradation in the gut and inefficient penetration to reach the target site because of the large size. Hence, biologically active peptides can be the potential candidates for therapeutic intervention instead of the whole G4-protein complex. In this review, we aimed to clarify the biological roles of G4s, how we can identify them throughout the genome via bioinformatics, the proteins interacting with G4s and how G4-interacting peptide molecules may be the potential next-generation ligands for targeting the G4 motifs located in biologically important regions.
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Affiliation(s)
- Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Mojerla, Sri Konda Laxman Telangana State Horticultural University, Budwel, Telangana, India
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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Jia Q, Deng H, Wu Y, He Y, Tang F. Carcinogen-induced super-enhancer RNA promotes nasopharyngeal carcinoma metastasis through NPM1/c-Myc/NDRG1 axis. Am J Cancer Res 2023; 13:3781-3798. [PMID: 37693164 PMCID: PMC10492133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/06/2023] [Indexed: 09/12/2023] Open
Abstract
Chemical carcinogen is one etiology of nasopharyngeal carcinoma (NPC) occurrence, N,N'-Dinitrosopiperazine (DNP) has been verified to cause NPC cell metastasis and generate induced pluripotent stem cells (iPSCs). To investigate the oncogenic mechanism of DNP, NPC cells were exposed to DNP, and subjected to RNA-seq, GRO-seq, ChIP-seq, and data analysis. The results showed that the super-enhancer RNA (seRNA) participates in DNP-mediated NPC metastasis through regulating N-myc downstream regulated gene 1 (NDRG1). Mechanistically, DNP exposure upregulates the levels of NPC metastatic seRNA (seRNA-NPCm), seRNA-NPCm interacted with a special super-enhancer (SE) upstream of NDRG1 gene and bound to nucleophosmin (NPM1)/c-Myc complex at the NDRG1 promoter, resulting in an increase of NDRG1 transcription. Functional studies showed that DNP significantly increased the metastatic capability of NPC cells in vitro and in vivo. Knockdown of seRNA-NPCm in NPC cells impaired the capability of metastasis. Furthermore, stably overexpressing seRNA-NPCm significantly increased the metastatic ability of NPC cells, while restoration of NDRG1 levels in these cells restored their metastatic capacity. Finally, the immunohistochemistry and in situ hybridization analyses revealed that the expression of seRNA-NPCm in NPC patients is positively correlated with NDRG1, and the NDRG1 level independently predicts poor prognosis of NPC patients. Collectively, DNP induces seRNA-NPCm, and seRNA-NPCm promotes NPC metastasis through NPM1/c-Myc/NDRG1 axis.
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Affiliation(s)
- Qunying Jia
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory of Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Hongyu Deng
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory of Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Yao Wu
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory of Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Hunan University of Chinese MedicineChangsha 410208, Hunan, China
| | - Yingchun He
- Hunan University of Chinese MedicineChangsha 410208, Hunan, China
| | - Faqin Tang
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory of Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
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8
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Sakthivel D, Brown-Suedel AN, Keane F, Huang S, Sherry KM, Charendoff CI, Dunne KP, Robichaux DJ, Le B, Shin CS, Carisey AF, Flanagan JM, Bouchier-Hayes L. Caspase-2 is essential for proliferation and self-renewal of nucleophosmin-mutated acute myeloid leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542723. [PMID: 37398413 PMCID: PMC10312440 DOI: 10.1101/2023.05.29.542723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mutation in nucleophosmin (NPM1) causes relocalization of this normally nucleolar protein to the cytoplasm ( NPM1c+ ). Despite NPM1 mutation being the most common driver mutation in cytogenetically normal adult acute myeloid leukemia (AML), the mechanisms of NPM1c+-induced leukemogenesis remain unclear. Caspase-2 is a pro-apoptotic protein activated by NPM1 in the nucleolus. Here, we show that caspase-2 is also activated by NPM1c+ in the cytoplasm, and DNA damage-induced apoptosis is caspase-2-dependent in NPM1c+ AML but not in NPM1wt cells. Strikingly, in NPM1c+ cells, loss of caspase-2 results in profound cell cycle arrest, differentiation, and down-regulation of stem cell pathways that regulate pluripotency including impairment in the AKT/mTORC1 and Wnt signaling pathways. In contrast, there were minimal differences in proliferation, differentiation, or the transcriptional profile of NPM1wt cells with and without caspase-2. Together, these results show that caspase-2 is essential for proliferation and self-renewal of AML cells that have mutated NPM1. This study demonstrates that caspase-2 is a major effector of NPM1c+ function and may even be a druggable target to treat NPM1c+ AML and prevent relapse.
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9
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Pavlova I, Iudin M, Surdina A, Severov V, Varizhuk A. G-Quadruplexes in Nuclear Biomolecular Condensates. Genes (Basel) 2023; 14:genes14051076. [PMID: 37239436 DOI: 10.3390/genes14051076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates.
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Affiliation(s)
- Iuliia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Mikhail Iudin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anastasiya Surdina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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10
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G4-interacting proteins endangering genomic stability at G4 DNA-forming sites. Biochem Soc Trans 2023; 51:403-413. [PMID: 36629511 PMCID: PMC10018705 DOI: 10.1042/bst20221018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
In guanine-rich DNA strands, base-base interactions among guanines allow the conformational shift from the B-form DNA to the non-canonical quadruplex or G4 structure. The functional significance of G4 DNA in vivo is largely dependent on the interaction with protein factors, many of which contain the arginine-glycine-glycine or RGG repeat and other consensus G4-binding motifs. These G4-interacting proteins can significantly modulate the effect of G4 DNA structure on genome maintenance, either preventing or aggravating G4-assoicated genome instability. While the role of helicases in resolving G4 DNA structure has been extensively discussed, identification and characterization of protein factors contributing to elevation in G4-associated genome instability has been relatively sparse. In this minireview, we will particularly highlight recent discoveries regarding how interaction between certain G4-binding proteins and G4 DNA could exacerbate genome instability potentiated by G4 DNA-forming sequences.
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11
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Saluri M, Leppert A, Gese GV, Sahin C, Lama D, Kaldmäe M, Chen G, Elofsson A, Allison TM, Arsenian-Henriksson M, Johansson J, Lane DP, Hällberg BM, Landreh M. A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1. PNAS NEXUS 2023; 2:pgac303. [PMID: 36743470 PMCID: PMC9896144 DOI: 10.1093/pnasnexus/pgac303] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant nucleolar protein that forms large oligomers and undergoes liquid-liquid phase separation by binding RNA or ribosomal proteins. It provides the scaffold for ribosome assembly but also prevents protein aggregation as part of the cellular stress response. Here, we use aggregation assays and native mass spectrometry (MS) to examine the relationship between the self-assembly and chaperone activity of NPM1. We find that oligomerization of full-length NPM1 modulates its ability to retard amyloid formation in vitro. Machine learning-based structure prediction and cryo-electron microscopy reveal fuzzy interactions between the acidic disordered region and the C-terminal nucleotide-binding domain, which cross-link NPM1 pentamers into partially disordered oligomers. The addition of basic peptides results in a tighter association within the oligomers, reducing their capacity to prevent amyloid formation. Together, our findings show that NPM1 uses a "grappling hook" mechanism to form a network-like structure that traps aggregation-prone proteins. Nucleolar proteins and RNAs simultaneously modulate the association strength and chaperone activity, suggesting a mechanism by which nucleolar composition regulates the chaperone activity of NPM1.
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Affiliation(s)
- Mihkel Saluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | | | | | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden,Structural Biology and NMR laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 57 Huddinge,, Sweden
| | - Arne Elofsson
- Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, 114 19 Stockholm, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Upper Riccarton, Christchurch 8041, New Zealand
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 57 Huddinge,, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
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12
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Jing Y, Jiang X, Lei L, Peng M, Ren J, Xiao Q, Tao Y, Tao Y, Huang J, Wang L, Tang Y, Yang Z, Yang Z, Zhang L. Mutant NPM1-regulated lncRNA HOTAIRM1 promotes leukemia cell autophagy and proliferation by targeting EGR1 and ULK3. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:312. [PMID: 34615546 PMCID: PMC8493742 DOI: 10.1186/s13046-021-02122-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022]
Abstract
Background Acute myeloid leukemia (AML) with mutated nucleophosmin (NPM1), which displays a distinct long noncoding RNA (lncRNA) expression profile, has been defined as a unique subgroup in the new classification of myeloid neoplasms. However, the biological roles of key lncRNAs in the development of NPM1-mutated AML are currently unclear. Here, we aimed to investigate the functional and mechanistic roles of the lncRNA HOTAIRM1 in NPM1-mutated AML. Methods The expression of HOTAIRM1 was analyzed with a public database and further determined by qRT-PCR in NPM1-mutated AML samples and cell lines. The cause of upregulated HOTAIRM1 expression was investigated by luciferase reporter, chromatin immunoprecipitation and ubiquitination assays. The functional role of HOTAIRM1 in autophagy and proliferation was evaluated using western blot analysis, immunofluorescence staining, a Cell Counting Kit-8 (CCK-8) assay, a 5-ethynyl-2′-deoxyuridine (EdU) incorporation assay, flow cytometric analyses and animal studies. The action mechanism of HOTAIRM1 was explored through RNA fluorescence in situ hybridization, RNA pulldown and RNA immunoprecipitation assays. Results HOTAIRM1 was highly expressed in NPM1-mutated AML. High HOTAIRM1 expression was induced in part by mutant NPM1 via KLF5-dependent transcriptional regulation. Importantly, HOTAIRM1 promoted autophagy and proliferation both in vitro and in vivo. Mechanistic investigations demonstrated that nuclear HOTAIRM1 promoted EGR1 degradation by serving as a scaffold to facilitate MDM2-EGR1 complex formation, while cytoplasmic HOTAIRM1 acted as a sponge for miR-152-3p to increase ULK3 expression. Conclusions Taken together, our findings identify two oncogenic regulatory axes in NPM1-mutated AML centered on HOTAIRM1: one involving EGR1 and MDM2 in the nucleus and the other involving the miR-152-3p/ULK3 axis in the cytoplasm. Our study indicates that HOTAIRM1 may be a promising therapeutic target for this distinct leukemia subtype. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02122-2.
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Affiliation(s)
- Yipei Jing
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Xueke Jiang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Li Lei
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Meixi Peng
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Jun Ren
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Qiaoling Xiao
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Yao Tao
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Yonghong Tao
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Junpeng Huang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Lu Wang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Yuting Tang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China
| | - Zailin Yang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zesong Yang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling Zhang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing, 400016, China.
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Herbert A. The Simple Biology of Flipons and Condensates Enhances the Evolution of Complexity. Molecules 2021; 26:molecules26164881. [PMID: 34443469 PMCID: PMC8400190 DOI: 10.3390/molecules26164881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/09/2023] Open
Abstract
The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.
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Affiliation(s)
- Alan Herbert
- Unit 3412, Discovery, InsideOutBio 42 8th Street, Charlestown, MA 02129, USA
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14
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La Manna S, Florio D, Di Natale C, Scognamiglio PL, Sibillano T, Netti PA, Giannini C, Marasco D. Type F mutation of nucleophosmin 1 Acute Myeloid Leukemia: A tale of disorder and aggregation. Int J Biol Macromol 2021; 188:207-214. [PMID: 34364939 DOI: 10.1016/j.ijbiomac.2021.08.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/15/2023]
Abstract
Protein aggregation is suggested as a reversible, wide-spread physiological process used by cells to regulate their growth and adapt to different stress conditions. Nucleophosmin 1(NPM1) protein is an abundant multifunctional nucleolar chaperone and its gene is the most frequently mutated in Acute Myeloid Leukemia (AML) patients. So far, the role of NPM1 mutations in leukemogenesis has remained largely elusive considering that they have the double effect of unfolding the C-terminal domain (CTD) and delocalizing the protein in the cytosol (NPM1c+). This mislocalization heavily impacts on cell cycle regulation. Our recent investigations unequivocally demonstrated an amyloid aggregation propensity introduced by AML mutations. Herein, employing complementary biophysical assays, we have characterized a N-terminal extended version of type F AML mutation of CTD and proved that it is able to form assemblies with amyloid character and fibrillar morphology. The present study represents an additional phase of knowledge to deepen the roles exerted by different types of cytoplasmatic NPM1c+ forms to develop in the future potential therapeutics for their selective targeting.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy
| | - Concetta Di Natale
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Pasqualina Liana Scognamiglio
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), National Research Council, 70125 Bari, Italy
| | - Paolo A Netti
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), National Research Council, 70125 Bari, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy.
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15
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Singh S, Berroyer A, Kim M, Kim N. Yeast Nucleolin Nsr1 Impedes Replication and Elevates Genome Instability at an Actively Transcribed Guanine-Rich G4 DNA-Forming Sequence. Genetics 2020; 216:1023-1037. [PMID: 33106247 PMCID: PMC7768239 DOI: 10.1534/genetics.120.303736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/21/2020] [Indexed: 12/01/2022] Open
Abstract
A significant increase in genome instability is associated with the conformational shift of a guanine-run-containing DNA strand into the four-stranded G-quadruplex (G4) DNA. The mechanism underlying the recombination and genome rearrangements following the formation of G4 DNA in vivo has been difficult to elucidate but has become better clarified by the identification and functional characterization of several key G4 DNA-binding proteins. Mammalian nucleolin (NCL) is a highly specific G4 DNA-binding protein with a well-defined role in the transcriptional regulation of genes with associated G4 DNA-forming sequence motifs at their promoters. The consequence of the in vivo interaction between G4 DNA and nucleolin in respect to the genome instability has not been previously investigated. We show here that the yeast nucleolin Nsr1 is enriched at a G4 DNA-forming sequence in vivo and is a major factor in inducing the genome instability associated with the cotranscriptionally formed G4 DNA in the yeast genome. We also show that Nsr1 results in impeding replication past such a G4 DNA-forming sequence. The G4-associated genome instability and the G4 DNA-binding in vivo require the arginine-glycine-glycine (RGG) repeats located at the C-terminus of the Nsr1 protein. Nsr1 with the deletion of RGG domain supports normal cell growth and is sufficient for its pre-rRNA processing function. However, the truncation of the RGG domain of Nsr1 significantly weakens its interaction with G4 DNA in vivo and restores unhindered replication, overall resulting in a sharp reduction in the genome instability associated with a guanine-rich G4 DNA-forming sequence. Our data suggest that the interaction between Nsr1 with the intact RGG repeats and G4 DNA impairs genome stability by precluding the access of G4-resolving proteins and impeding replication.
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Affiliation(s)
- Shivani Singh
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Alexandra Berroyer
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Minseon Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
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16
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López DJ, Rodríguez JA, Bañuelos S. Nucleophosmin, a multifunctional nucleolar organizer with a role in DNA repair. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140532. [PMID: 32853771 DOI: 10.1016/j.bbapap.2020.140532] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
Nucleophosmin (NPM1) is a mostly nucleolar protein with crucial functions in cell growth and homeostasis, including regulation of ribosome biogenesis and stress response. Such multiple activities rely on its ability to interact with nucleic acids and with hundreds of proteins, as well as on a dynamic subcellular distribution. NPM1 is thus regulated by a complex interplay between localization and interactions, further modulated by post-translational modifications. NPM1 is a homopentamer, with globular domains connected by long, intrinsically disordered linkers. This configuration allows NPM1 to engage in liquid-liquid phase separation phenomena, which could underlie a key role in nucleolar organization. Here, we will discuss NPM1 conformational and functional versatility, emphasizing its emerging, and still largely unexplored, role in DNA damage repair. Since NPM1 is altered in a subtype of acute myeloid leukaemia (AML), we will also present ongoing research on the molecular mechanisms underlying its pathogenic role and potential NPM1-targeting therapeutic strategies.
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Affiliation(s)
- David J López
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - José A Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Sonia Bañuelos
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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17
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Human MYC G-quadruplex: From discovery to a cancer therapeutic target. Biochim Biophys Acta Rev Cancer 2020; 1874:188410. [PMID: 32827579 DOI: 10.1016/j.bbcan.2020.188410] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Overexpression of the MYC oncogene is a molecular hallmark of both cancer initiation and progression. Targeting MYC is a logical and effective cancer therapeutic strategy. A special DNA secondary structure, the G-quadruplex (G4), is formed within the nuclease hypersensitivity element III1 (NHE III1) region, located upstream of the MYC gene's P1 promoter that drives the majority of its transcription. Targeting such G4 structures has been a focus of anticancer therapies in recent decades. Thus, a comprehensive review of the MYC G4 structure and its role as a potential therapeutic target is timely. In this review, we first outline the discovery of the MYC G4 structure and evidence of its formation in vitro and in cells. Then, we describe the functional role of G4 in regulating MYC gene expression. We also summarize three types of MYC G4-interacting proteins that can promote, stabilize and unwind G4 structures. Finally, we discuss G4-binding molecules and the anticancer activities of G4-stabilizing ligands, including small molecular compounds and peptides, and assess their potential as novel anticancer therapeutics.
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18
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Cela I, Di Matteo A, Federici L. Nucleophosmin in Its Interaction with Ligands. Int J Mol Sci 2020; 21:E4885. [PMID: 32664415 PMCID: PMC7402337 DOI: 10.3390/ijms21144885] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
Nucleophosmin (NPM1) is a mainly nucleolar protein that shuttles between nucleoli, nucleoplasm and cytoplasm to fulfill its many functions. It is a chaperone of both nucleic acids and proteins and plays a role in cell cycle control, centrosome duplication, ribosome maturation and export, as well as the cellular response to a variety of stress stimuli. NPM1 is a hub protein in nucleoli where it contributes to nucleolar organization through heterotypic and homotypic interactions. Furthermore, several alterations, including overexpression, chromosomal translocations and mutations are present in solid and hematological cancers. Recently, novel germline mutations that cause dyskeratosis congenita have also been described. This review focuses on NPM1 interactions and inhibition. Indeed, the list of NPM1 binding partners is ever-growing and, in recent years, many studies contributed to clarifying the structural basis for NPM1 recognition of both nucleic acids and several proteins. Intriguingly, a number of natural and synthetic ligands that interfere with NPM1 interactions have also been reported. The possible role of NPM1 inhibitors in the treatment of multiple cancers and other pathologies is emerging as a new therapeutic strategy.
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Affiliation(s)
- Ilaria Cela
- Center for Advanced Studies and Technology (CAST), University of Chieti “G. d’Annunzio”, Via Polacchi, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology (IBPM) of the CNR, c/o “Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy;
| | - Luca Federici
- Center for Advanced Studies and Technology (CAST), University of Chieti “G. d’Annunzio”, Via Polacchi, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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19
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Wu Q, Song Y, Liu R, Wang R, Mei W, Chen W, Yang H, Wang X. Synthesis, docking studies and antitumor activity of phenanthroimidazole derivatives as promising c-myc G-quadruplex DNA stabilizers. Bioorg Chem 2020; 102:104074. [PMID: 32738566 DOI: 10.1016/j.bioorg.2020.104074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/24/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022]
Abstract
Phenanthroimidazole derivatives containing phenanthroline and imidazole heterocyclic aromatic rings are effective agents to inhibit tumor cell growth. Herein, halogen element-modified imidazo[4,5f][1,10]phenanthroline derivatives 1-6 (1, 4-fluorophenyl; 2, 4-chlorophenyl; 3, 4-bromobenyl; 4, 2,3-dichlorophenyl; 5, 3,4-dichlorophenyl; and 6, 2,4-dichlorophenyl) were synthesized, and their antitumor activities were investigated. All of the compounds, especially 4, exhibited an excellent inhibitory effect against nasopharyngeal carcinoma CNE-1 cells. This effect was better than that of doxorubicin. Compound 4 also markedly blocked the proliferation of the CNE-1 cells in a zebrafish xenograft model. The antitumor mechanisms might be attributed to apoptosis induction, which triggered ROS-mediated DNA damage and generated mitochondrial dysfunction by stabilizing c-myc G-quadruplex DNA structure. Results indicated that phenanthroimidazole derivatives could act as promising anticancer agents.
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Affiliation(s)
- Qiong Wu
- The First Affiliation Hospital of Guangdong Pharmaceutical University, Guangzhou 510062, China; Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
| | - Yue Song
- The First Affiliation Hospital of Guangdong Pharmaceutical University, Guangzhou 510062, China
| | - Ruotong Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
| | - Rui Wang
- The First Affiliation Hospital of Guangdong Pharmaceutical University, Guangzhou 510062, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China; Guangzhou Key Laboratory of Construction and Application of New Drug Screening Model Systems, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Weiming Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
| | - Huanglan Yang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
| | - Xicheng Wang
- The First Affiliation Hospital of Guangdong Pharmaceutical University, Guangzhou 510062, China.
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20
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21
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White MR, Mitrea DM, Zhang P, Stanley CB, Cassidy DE, Nourse A, Phillips AH, Tolbert M, Taylor JP, Kriwacki RW. C9orf72 Poly(PR) Dipeptide Repeats Disturb Biomolecular Phase Separation and Disrupt Nucleolar Function. Mol Cell 2019; 74:713-728.e6. [PMID: 30981631 DOI: 10.1016/j.molcel.2019.03.019] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/12/2019] [Accepted: 03/18/2019] [Indexed: 12/11/2022]
Abstract
Repeat expansion in the C9orf72 gene is the most common cause of the neurodegenerative disorder amyotrophic lateral sclerosis (C9-ALS) and is linked to the unconventional translation of five dipeptide-repeat polypeptides (DPRs). The two enriched in arginine, poly(GR) and poly(PR), infiltrate liquid-like nucleoli, co-localize with the nucleolar protein nucleophosmin (NPM1), and alter the phase separation behavior of NPM1 in vitro. Here, we show that poly(PR) DPRs bind tightly to a long acidic tract within the intrinsically disordered region of NPM1, altering its phase separation with nucleolar partners to the extreme of forming large, soluble complexes that cause droplet dissolution in vitro. In cells, poly(PR) DPRs disperse NPM1 from nucleoli and entrap rRNA in static condensates in a DPR-length-dependent manner. We propose that R-rich DPR toxicity involves disrupting the role of phase separation by NPM1 in organizing ribosomal proteins and RNAs within the nucleolus.
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Affiliation(s)
- Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peipei Zhang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher B Stanley
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Devon E Cassidy
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michele Tolbert
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA.
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Jariyapong P, Pudgerd A, Cheloh N, Hirono I, Kondo H, Vanichviriyakit R, Weerachatyanukul W, Chotwiwatthanakun C. Hematopoietic tissue of Macrobrachium rosenbergii plays dual roles as a source of hemocyte hematopoiesis and as a defensive mechanism against Macrobrachium rosenbergii nodavirus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 86:756-763. [PMID: 30553890 DOI: 10.1016/j.fsi.2018.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/03/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
White tail disease caused by Macrobrachium rosenbergii nodavirus (MrNV) infection takes place only in nauplii, not adults, of M. rosenbergii prawn. Hemocyte homeostasis and immune-related functions derived from the hematopoietic tissue (Hpt) in adult prawn are presumed to play roles in resisting viral infection. To elucidate the role of the Hpt cell response to MrNV, a comparative transcriptome analysis was performed with MrNV-infected prawn at various time intervals. The results showed that there were 462 unigenes that were differentially expressed between mock and infected samples. BlastX sequence analysis revealed that two proteins, crustacean hematopoietic factor (CHF) and cell growth-regulating zinc finger protein (Lyar), are involved in hemocyte hematopoiesis and are up-regulated during MrNV infection. In fact, genes involved in cell growth regulation and immunity were highly expressed at 6 h and decreased within 24 h post-infection. Localization studies in the Hpt tissue revealed the presence of anti-lipopolysaccharide factor (ALF) and CHF mRNAs in Hpt cells. Considering these findings, we concluded that resistance to MrNV infection in adult prawn is due to an increase in humoral immune factors and the acceleration of hemocyte homeostasis by the dual roles of the Hpt organ in M. rosenbergii.
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Affiliation(s)
- Pitchanee Jariyapong
- School of Medicine, Walailak University, Thasala District, Nakhonsrithammarat, 80161, Thailand; Research Center of Excellence on Shrimp, Walailak University, Thasala District, Nakhonsrithammarat, 80161, Thailand
| | - Arnon Pudgerd
- Division of Anatomy, School of Medical Science, University of Phayao, Muang, Phayao, 56000, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Nifareesa Cheloh
- Faculty of Agriculture, Princess of Naradhiwas University, Mueang Narathiwat District, Narathiwat, 96000, Thailand
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, 108-8477, Japan
| | - Rapeepun Vanichviriyakit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Wattana Weerachatyanukul
- Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand.
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23
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Bian WX, Xie Y, Wang XN, Xu GH, Fu BS, Li S, Long G, Zhou X, Zhang XL. Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication. Nucleic Acids Res 2019; 47:56-68. [PMID: 30462330 PMCID: PMC6326805 DOI: 10.1093/nar/gky1177] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/22/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV core RNA G4 and host cellular proteins, and the roles of the HCV core RNA G4 in HCV infection and pathogenesis remain elusive. Here, we identified a cellular protein, nucleolin (NCL), which bound and stabilized the HCV core RNA G4 structure. We demonstrated the direct interaction and colocalization between NCL and wild-type core RNA G4 at both in vitro and in cell physiological conditions of the alive virus; however no significant interaction was found between NCL and G4-modified core RNA. NCL is also associated with HCV particles. HCV infection induced NCL mRNA and protein expression, while NCL suppressed wild-type viral replication and expression, but not G4-modified virus. Silencing of NCL greatly enhanced viral RNA replication. Our findings provide new insights that NCL may act as a host factor for anti-viral innate immunity, and binding of cellular NCL with the viral core RNA G4 structure is involved in suppressing HCV replication.
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Affiliation(s)
- Wen-Xiu Bian
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Yan Xie
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Xiao-Ning Wang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Hua Xu
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Bo-Shi Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Shu Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
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24
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Burra S, Marasco D, Malfatti MC, Antoniali G, Virgilio A, Esposito V, Demple B, Galeone A, Tell G. Human AP-endonuclease (Ape1) activity on telomeric G4 structures is modulated by acetylatable lysine residues in the N-terminal sequence. DNA Repair (Amst) 2018; 73:129-143. [PMID: 30509560 DOI: 10.1016/j.dnarep.2018.11.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 02/08/2023]
Abstract
Loss of telomeres stability is a hallmark of cancer cells. Exposed telomeres are prone to aberrant end-joining reactions leading to chromosomal fusions and translocations. Human telomeres contain repeated TTAGGG elements, in which the 3' exposed strand may adopt a G-quadruplex (G4) structure. The guanine-rich regions of telomeres are hotspots for oxidation forming 8-oxoguanine, a lesion that is handled by the base excision repair (BER) pathway. One key player of this pathway is Ape1, the main human endonuclease processing abasic sites. Recent evidences showed an important role for Ape1 in telomeric physiology, but the molecular details regulating Ape1 enzymatic activities on G4-telomeric sequences are lacking. Through a combination of in vitro assays, we demonstrate that Ape1 can bind and process different G4 structures and that this interaction involves specific acetylatable lysine residues (i.e. K27/31/32/35) present in the unstructured N-terminal sequence of the protein. The cleavage of an abasic site located in a G4 structure by Ape1 depends on the DNA conformation or the position of the lesion and on electrostatic interactions between the protein and the nucleic acids. Moreover, Ape1 mutants mimicking the acetylated protein display increased cleavage activity for abasic sites. We found that nucleophosmin (NPM1), which binds the N-terminal sequence of Ape1, plays a role in modulating telomere length and Ape1 activity at abasic G4 structures. Thus, the Ape1 N-terminal sequence is an important relay site for regulating the enzyme's activity on G4-telomeric sequences, and specific acetylatable lysine residues constitute key regulatory sites of Ape1 enzymatic activity dynamics at telomeres.
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Affiliation(s)
- Silvia Burra
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Bruce Demple
- Department of Pharmacological Sciences, Stony Brook University, School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Aldo Galeone
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy.
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25
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Wu Q, Liao S, Yu G, Wu J, Mei W. High-order self-assembly of G-quadruplex DNA: Nano-network formation under the guidance of arene ruthenium(II) complexes. J Inorg Biochem 2018; 189:81-90. [PMID: 30243121 DOI: 10.1016/j.jinorgbio.2018.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Qiong Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Siyan Liao
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 510180, China
| | - Gengnan Yu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jian Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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26
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Kunchala P, Kuravi S, Jensen R, McGuirk J, Balusu R. When the good go bad: Mutant NPM1 in acute myeloid leukemia. Blood Rev 2018; 32:167-183. [DOI: 10.1016/j.blre.2017.11.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/19/2017] [Accepted: 11/02/2017] [Indexed: 12/26/2022]
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27
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Chaudhary S, Kaushik M, Kukreti R, Kukreti S. Structural switch from a multistranded G-quadruplex to single strands as a consequence of point mutation in the promoter of the human GRIN1 gene. MOLECULAR BIOSYSTEMS 2018; 13:1805-1816. [PMID: 28702665 DOI: 10.1039/c7mb00360a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A huge number of G-rich sequences forming quadruplexes are found in the human genome, especially in telomeric regions, UTRs, and the promoter regions of a number of genes. One such gene is GRIN1 encoding the NR1 subunit of the N-methyl-d-aspartate receptor (NMDA). Several lines of reports have implicated that attenuated function of NMDA results in schizophrenia, a genetic disorder characterized by hallucinations, delusions, and psychosis. Involvement of the GRIN1 gene in the pathogenesis of schizophrenia has been extensively analysed. Recent reports have demonstrated that polymorphism in the promoter region of GRIN1 at position -855 (G/C) has a possible association with schizophrenia. The binding site for the NF-κB transcription factor gets altered due to this mutation, resulting in reduced gene expression as well as NMDA activity. By combining gel electrophoresis (PAGE), circular dichroism (CD) and CD melting techniques, the G → C single nucleotide polymorphism (SNP) at the G-rich sequence (d-CTTAGCCCGAGGAG[combining low line]GGGGGTCCCAAGT; GRIN1) was investigated. We report that the GRIN1 sequence can form an octameric/multistranded quadruplex structure with parallel conformation in the presence of K+ as well as Na+. CD and gel studies are in good correlation in order to detect molecularity and strand conformation. The parallel G-quadruplex species was hypothesized to be octameric in K+/Na+ salts. The mutated sequence (d-CTTAGCCCGAGGAC[combining low line]GGGGGTCCCAAGT; GRIN1M) remained single stranded under physiological conditions. CD melting studies support the formation of an interstranded G-quadruplex structure by the GRIN1 sequence. Two structural models are propounded for a multistranded parallel G-quadruplex conformation which might be responsible for regulating the gene expression normally underlying memory and learning.
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Affiliation(s)
- Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India.
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28
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Mitrea DM, Cika JA, Stanley CB, Nourse A, Onuchic PL, Banerjee PR, Phillips AH, Park CG, Deniz AA, Kriwacki RW. Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation. Nat Commun 2018; 9:842. [PMID: 29483575 PMCID: PMC5827731 DOI: 10.1038/s41467-018-03255-3] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid-liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes within NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.
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Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jaclyn A Cika
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrative Biomedical Sciences Program, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Christopher B Stanley
- Biology and Biomedical Sciences Group, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paulo L Onuchic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Physics, University of Buffalo, Buffalo, NY, 14260, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
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29
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De Santis A, La Manna S, Krauss IR, Malfitano AM, Novellino E, Federici L, De Cola A, Di Matteo A, D'Errico G, Marasco D. Nucleophosmin-1 regions associated with acute myeloid leukemia interact differently with lipid membranes. Biochim Biophys Acta Gen Subj 2018; 1862:967-978. [PMID: 29330024 DOI: 10.1016/j.bbagen.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/04/2017] [Accepted: 01/08/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Augusta De Santis
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Anna Maria Malfitano
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Sciences and CeSI-MeT, University of Chieti "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Antonella De Cola
- Department of Medical, Oral and Biotechnological Sciences and CeSI-MeT, University of Chieti "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gerardino D'Errico
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy.
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30
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Molecules that target nucleophosmin for cancer treatment: an update. Oncotarget 2018; 7:44821-44840. [PMID: 27058426 PMCID: PMC5190137 DOI: 10.18632/oncotarget.8599] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/28/2016] [Indexed: 11/25/2022] Open
Abstract
Nucleophosmin is a highly and ubiquitously expressed protein, mainly localized in nucleoli but able to shuttle between nucleus and cytoplasm. Nucleophosmin plays crucial roles in ribosome maturation and export, centrosome duplication, cell cycle progression, histone assembly and response to a variety of stress stimuli. Much interest in this protein has arisen in the past ten years, since the discovery of heterozygous mutations in the terminal exon of the NPM1 gene, which are the most frequent genetic alteration in acute myeloid leukemia. Nucleophosmin is also frequently overexpressed in solid tumours and, in many cases, its overexpression correlates with mitotic index and metastatization. Therefore it is considered as a promising target for the treatment of both haematologic and solid malignancies. NPM1 targeting molecules may suppress different functions of the protein, interfere with its subcellular localization, with its oligomerization properties or drive its degradation. In the recent years, several such molecules have been described and here we review what is currently known about them, their interaction with nucleophosmin and the mechanistic basis of their toxicity. Collectively, these molecules exemplify a number of different strategies that can be adopted to target nucleophosmin and we summarize them at the end of the review.
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31
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De Cola A, Franceschini M, Di Matteo A, Colotti G, Celani R, Clemente E, Ippoliti R, Cimini AM, Dhez AC, Vallée B, Raineri F, Cascone I, Destouches D, De Laurenzi V, Courty J, Federici L. N6L pseudopeptide interferes with nucleophosmin protein-protein interactions and sensitizes leukemic cells to chemotherapy. Cancer Lett 2017; 412:272-282. [PMID: 29111347 DOI: 10.1016/j.canlet.2017.10.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/24/2017] [Accepted: 10/24/2017] [Indexed: 12/16/2022]
Abstract
NPM1 is a multifunctional nucleolar protein implicated in several processes such as ribosome maturation and export, DNA damage response and apoptotic response to stress stimuli. The NPM1 gene is involved in human tumorigenesis and is found mutated in one third of acute myeloid leukemia patients, leading to the aberrant cytoplasmic localization of NPM1. Recent studies indicated that the N6L multivalent pseudopeptide, a synthetic ligand of cell-surface nucleolin, is also able to bind NPM1 with high affinity. N6L inhibits cell growth with different mechanisms and represents a good candidate as a novel anticancer drug for a number of malignancies of different histological origin. In this study we investigated whether N6L treatment could drive antitumor effect in acute myeloid leukemia cell lines. We found that N6L binds NPM1 at the N-terminal domain, co-localizes with cytoplasmic, mutated NPM1, and interferes with its protein-protein associations. N6L toxicity appears to be p53 dependent but interestingly, the leukemic cell line harbouring the mutated form of NPM1 is more resistant to treatment, suggesting that NPM1 cytoplasmic delocalization confers protection from p53 activation. Moreover, we show that N6L sensitizes AML cells to doxorubicin and cytarabine treatment. These studies suggest that N6L may be a promising option in combination therapies for acute myeloid leukemia treatment.
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Affiliation(s)
- A De Cola
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, CESI-MeT, Centro Scienze dell'Invecchiamento e Medicina Traslazionale, Universita' "G. d'Annunzio" Chieti-Pescara, Chieti, Italy
| | - M Franceschini
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, CESI-MeT, Centro Scienze dell'Invecchiamento e Medicina Traslazionale, Universita' "G. d'Annunzio" Chieti-Pescara, Chieti, Italy
| | - A Di Matteo
- Istituto di Biologia e Patologia Molecolari del CNR, Rome, Italy
| | - G Colotti
- Istituto di Biologia e Patologia Molecolari del CNR, Rome, Italy
| | - R Celani
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, CESI-MeT, Centro Scienze dell'Invecchiamento e Medicina Traslazionale, Universita' "G. d'Annunzio" Chieti-Pescara, Chieti, Italy
| | - E Clemente
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, CESI-MeT, Centro Scienze dell'Invecchiamento e Medicina Traslazionale, Universita' "G. d'Annunzio" Chieti-Pescara, Chieti, Italy
| | - R Ippoliti
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, Università dell'Aquila, L'Aquila, Italy
| | - A M Cimini
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, Università dell'Aquila, L'Aquila, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, USA; National Institute for Nuclear Physics (INFN), Gran Sasso National Laboratory (LNGS), Assergi, Italy
| | - A C Dhez
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, Università dell'Aquila, L'Aquila, Italy
| | - B Vallée
- Université; Paris-Est Créteil, CNRS, ERL 9215, Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Créteil, F-94000, France
| | - F Raineri
- Université; Paris-Est Créteil, CNRS, ERL 9215, Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Créteil, F-94000, France
| | - I Cascone
- Université; Paris-Est Créteil, CNRS, ERL 9215, Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Créteil, F-94000, France
| | - D Destouches
- Université; Paris-Est Créteil, CNRS, ERL 9215, Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Créteil, F-94000, France
| | - V De Laurenzi
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, CESI-MeT, Centro Scienze dell'Invecchiamento e Medicina Traslazionale, Universita' "G. d'Annunzio" Chieti-Pescara, Chieti, Italy
| | - J Courty
- Université; Paris-Est Créteil, CNRS, ERL 9215, Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), Créteil, F-94000, France
| | - L Federici
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, CESI-MeT, Centro Scienze dell'Invecchiamento e Medicina Traslazionale, Universita' "G. d'Annunzio" Chieti-Pescara, Chieti, Italy.
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Urbaneja MA, Skjærven L, Aubi O, Underhaug J, López DJ, Arregi I, Alonso-Mariño M, Cuevas A, Rodríguez JA, Martinez A, Bañuelos S. Conformational stabilization as a strategy to prevent nucleophosmin mislocalization in leukemia. Sci Rep 2017; 7:13959. [PMID: 29066752 PMCID: PMC5655693 DOI: 10.1038/s41598-017-14497-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/11/2017] [Indexed: 01/20/2023] Open
Abstract
Nucleophosmin (NPM) is a nucleolar protein involved in ribosome assembly and cell homeostasis. Mutations in the C-terminal domain of NPM that impair native folding and localization are associated with acute myeloid leukemia (AML). We have performed a high-throughput screening searching for compounds that stabilize the C-terminal domain. We identified three hit compounds which show the ability to increase the thermal stability of both the C-terminal domain as well as full-length NPM. The best hit also seemed to favor folding of an AML-like mutant. Computational pocket identification and molecular docking support a stabilization mechanism based on binding of the phenyl/benzene group of the compounds to a particular hydrophobic pocket and additional polar interactions with solvent-accessible residues. Since these results indicate a chaperoning potential of our candidate hits, we tested their effect on the subcellular localization of AML-like mutants. Two compounds partially alleviated the aggregation and restored nucleolar localization of misfolded mutants. The identified hits appear promising as pharmacological chaperones aimed at therapies for AML based on conformational stabilization of NPM.
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Affiliation(s)
- María A Urbaneja
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Oscar Aubi
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jarl Underhaug
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
| | - David J López
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Igor Arregi
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
- R&D Department, Roxall España, Bilbao, Spain
| | - Marián Alonso-Mariño
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Andoni Cuevas
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - José A Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway.
| | - Sonia Bañuelos
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Di Matteo A, Franceschini M, Paiardini A, Grottesi A, Chiarella S, Rocchio S, Di Natale C, Marasco D, Vitagliano L, Travaglini-Allocatelli C, Federici L. Structural investigation of nucleophosmin interaction with the tumor suppressor Fbw7γ. Oncogenesis 2017; 6:e379. [PMID: 28920929 PMCID: PMC5623904 DOI: 10.1038/oncsis.2017.78] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleophosmin (NPM1) is a multifunctional nucleolar protein implicated in ribogenesis, centrosome duplication, cell cycle control, regulation of DNA repair and apoptotic response to stress stimuli. The majority of these functions are played through the interactions with a variety of protein partners. NPM1 is frequently overexpressed in solid tumors of different histological origin. Furthermore NPM1 is the most frequently mutated protein in acute myeloid leukemia (AML) patients. Mutations map to the C-terminal domain and lead to the aberrant and stable localization of the protein in the cytoplasm of leukemic blasts. Among NPM1 protein partners, a pivotal role is played by the tumor suppressor Fbw7γ, an E3-ubiquitin ligase that degrades oncoproteins like c-MYC, cyclin E, Notch and c-jun. In AML with NPM1 mutations, Fbw7γ is degraded following its abnormal cytosolic delocalization by mutated NPM1. This mechanism also applies to other tumor suppressors and it has been suggested that it may play a key role in leukemogenesis. Here we analyse the interaction between NPM1 and Fbw7γ, by identifying the protein surfaces implicated in recognition and key aminoacids involved. Based on the results of computational methods, we propose a structural model for the interaction, which is substantiated by experimental findings on several site-directed mutants. We also extend the analysis to two other NPM1 partners (HIV Tat and CENP-W) and conclude that NPM1 uses the same molecular surface as a platform for recognizing different protein partners. We suggest that this region of NPM1 may be targeted for cancer treatment.
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Affiliation(s)
- A Di Matteo
- Istituto di Biologia e Patologia Molecolari - Consiglio Nazionale delle ricerche, Roma, Italy
| | - M Franceschini
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, Chieti, Italy.,CeSI-Met - Università di Chieti-Pescara 'G d'Annunzio', Chieti, Italy
| | - A Paiardini
- Dipartimento di Biologia e Biotecnologie 'C Darwin' - Sapienza Università di Roma, Roma, Italy
| | - A Grottesi
- CINECA Consorzio Interuniversitario, Sede di Roma, Roma, Italy
| | - S Chiarella
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, Chieti, Italy.,CeSI-Met - Università di Chieti-Pescara 'G d'Annunzio', Chieti, Italy
| | - S Rocchio
- Dipartimento di Scienze Biochimiche 'A Rossi Fanelli' - Sapienza Università di Roma, Roma, Italy
| | - C Di Natale
- Dipartimento di Farmacia,- Università di Napoli 'Federico II', Napoli, Italy
| | - D Marasco
- Dipartimento di Farmacia,- Università di Napoli 'Federico II', Napoli, Italy
| | - L Vitagliano
- Istituto di Biostrutture e Bioimmagini - Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - C Travaglini-Allocatelli
- Dipartimento di Scienze Biochimiche 'A Rossi Fanelli' - Sapienza Università di Roma, Roma, Italy
| | - L Federici
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, Chieti, Italy.,CeSI-Met - Università di Chieti-Pescara 'G d'Annunzio', Chieti, Italy
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34
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Satkunanathan S, Thorpe R, Zhao Y. The function of DNA binding protein nucleophosmin in AAV replication. Virology 2017; 510:46-54. [PMID: 28704696 PMCID: PMC5572047 DOI: 10.1016/j.virol.2017.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 01/11/2023]
Abstract
Adeno-associated viruses (AAV) contain minimal viral proteins necessary for their replication. During virus assembly, AAV acquire, inherently and submissively, various cellular proteins. Our previous studies identified the association of AAV vectors with the DNA binding protein nucleophosmin (NPM1). Nucleophosmin has been reported to enhance AAV infection by mobilizing AAV capsids into and out of the nucleolus, indicating the importance of NPM1 in the AAV life cycle; however the role of NPM1 in AAV production remains unknown. In this study, we systematically investigated NPM1 function on AAV production using NPM1 knockdown cells and revealing for the first time the presence of G-quadruplex DNA sequences (GQRS) in the AAV genome, the synergistic NPM1-GQRS function in AAV production and the significant enhancement of NPM1 gene knockdown on AAV vector production. Understanding the role of cellular proteins in the AAV life cycle will greatly facilitate high titre production of AAV vectors for clinical use.
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Affiliation(s)
- Stifani Satkunanathan
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Robin Thorpe
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Yuan Zhao
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
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35
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Hanley ML, Yoo TY, Sonnett M, Needleman DJ, Mitchison TJ. Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin. Mol Biol Cell 2017; 28:1444-1456. [PMID: 28404751 PMCID: PMC5449145 DOI: 10.1091/mbc.e16-12-0860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/27/2017] [Accepted: 04/04/2017] [Indexed: 01/30/2023] Open
Abstract
The chromosomal passenger complex (CPC) is a conserved, essential regulator of cell division. As such, significant anti-cancer drug development efforts have been focused on targeting it, most notably by inhibiting its AURKB kinase subunit. The CPC is activated by AURKB-catalyzed autophosphorylation on multiple subunits, but how this regulates CPC interactions with other mitotic proteins remains unclear. We investigated the hydrodynamic behavior of the CPC in Xenopus laevis egg cytosol using sucrose gradient sedimentation and in HeLa cells using fluorescence correlation spectroscopy. We found that autophosphorylation of the CPC decreases its sedimentation coefficient in egg cytosol and increases its diffusion coefficient in live cells, indicating a decrease in mass. Using immunoprecipitation coupled with mass spectrometry and immunoblots, we discovered that inactive, unphosphorylated CPC interacts with nucleophosmin/nucleoplasmin proteins, which are known to oligomerize into pentamers and decamers. Autophosphorylation of the CPC causes it to dissociate from nucleophosmin/nucleoplasmin. We propose that nucleophosmin/nucleoplasmin complexes serve as chaperones that negatively regulate the CPC and/or stabilize its inactive form, preventing CPC autophosphorylation and recruitment to chromatin and microtubules in mitosis.
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Affiliation(s)
- Mariah L Hanley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701.,Department of Chemistry, Harvard University, Cambridge, MA 02138-2902
| | - Tae Yeon Yoo
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138-2902
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
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36
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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37
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Wu Q, Zheng K, Liao S, Ding Y, Li Y, Mei W. Arene Ruthenium(II) Complexes as Low-Toxicity Inhibitor against the Proliferation, Migration, and Invasion of MDA-MB-231 Cells through Binding and Stabilizing c-myc G-Quadruplex DNA. Organometallics 2016. [DOI: 10.1021/acs.organomet.5b00820] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Qiong Wu
- Key
Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Kangdi Zheng
- School
of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Siyan Liao
- School
of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yang Ding
- School
of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yangqiu Li
- Key
Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Wenjie Mei
- School
of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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38
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Biophysical Characterization of Nucleophosmin Interactions with Human Immunodeficiency Virus Rev and Herpes Simplex Virus US11. PLoS One 2015; 10:e0143634. [PMID: 26624888 PMCID: PMC4704560 DOI: 10.1371/journal.pone.0143634] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/06/2015] [Indexed: 02/07/2023] Open
Abstract
Nucleophosmin (NPM1, also known as B23, numatrin or NO38) is a pentameric RNA-binding protein with RNA and protein chaperon functions. NPM1 has increasingly emerged as a potential cellular factor that directly associates with viral proteins; however, the significance of these interactions in each case is still not clear. In this study, we have investigated the physical interaction of NPM1 with both human immunodeficiency virus type 1 (HIV-1) Rev and Herpes Simplex virus type 1 (HSV-1) US11, two functionally homologous proteins. Both viral proteins show, in mechanistically different modes, high affinity for a binding site on the N-terminal oligomerization domain of NPM1. Rev, additionally, exhibits low-affinity for the central histone-binding domain of NPM1. We also showed that the proapoptotic cyclic peptide CIGB-300 specifically binds to NPM1 oligomerization domain and blocks its association with Rev and US11. Moreover, HIV-1 virus production was significantly reduced in the cells treated with CIGB-300. Results of this study suggest that targeting NPM1 may represent a useful approach for antiviral intervention.
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39
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Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex. Proc Natl Acad Sci U S A 2015. [PMID: 26195789 DOI: 10.1073/pnas.1422605112] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Four-stranded nucleic acid structures called G-quadruplexes have been associated with important cellular processes, which should require G-quadruplex-protein interaction. However, the structural basis for specific G-quadruplex recognition by proteins has not been understood. The DEAH (Asp-Glu-Ala-His) box RNA helicase associated with AU-rich element (RHAU) (also named DHX36 or G4R1) specifically binds to and resolves parallel-stranded G-quadruplexes. Here we identified an 18-amino acid G-quadruplex-binding domain of RHAU and determined the structure of this peptide bound to a parallel DNA G-quadruplex. Our structure explains how RHAU specifically recognizes parallel G-quadruplexes. The peptide covers a terminal guanine base tetrad (G-tetrad), and clamps the G-quadruplex using three-anchor-point electrostatic interactions between three positively charged amino acids and negatively charged phosphate groups. This binding mode is strikingly similar to that of most ligands selected for specific G-quadruplex targeting. Binding to an exposed G-tetrad represents a simple and efficient way to specifically target G-quadruplex structures.
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40
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Marasco D, Scognamiglio PL. Identification of inhibitors of biological interactions involving intrinsically disordered proteins. Int J Mol Sci 2015; 16:7394-412. [PMID: 25849651 PMCID: PMC4425024 DOI: 10.3390/ijms16047394] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 03/01/2015] [Accepted: 03/06/2015] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs) are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few "hot spots", thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs.
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Affiliation(s)
- Daniela Marasco
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy.
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy.
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41
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Dynamic conformations of nucleophosmin (NPM1) at a key monomer-monomer interface affect oligomer stability and interactions with granzyme B. PLoS One 2014; 9:e115062. [PMID: 25490769 PMCID: PMC4260957 DOI: 10.1371/journal.pone.0115062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 11/05/2014] [Indexed: 01/02/2023] Open
Abstract
Nucleophosmin (NPM1) is an abundant, nucleolar tumor antigen with important roles in cell proliferation and putative contributions to oncogenesis. Wild-type NPM1 forms pentameric oligomers through interactions at the amino-terminal core domain. A truncated form of NPM1 found in some hepatocellular carcinoma tissue formed an unusually stable oligomer and showed increased susceptibility to cleavage by granzyme B. Initiation of translation at the seventh methionine generated a protein (M7-NPM) that shared all these properties. We used deuterium exchange mass spectrometry (DXMS) to perform a detailed structural analysis of wild-type NPM1 and M7-NPM, and found dynamic conformational shifts or local “unfolding” at a specific monomer-monomer interface which included the β-hairpin “latch.” We tested the importance of interactions at the β-hairpin “latch” by replacing a conserved tyrosine in the middle of the β-hairpin loop with glutamic acid, generating Y67E-NPM. Y67E-NPM did not form stable oligomers and further, prevented wild-type NPM1 oligomerization in a dominant-negative fashion, supporting the critical role of the β-hairpin “latch” in monomer-monomer interactions. Also, we show preferential cleavage by granzyme B at one of two available aspartates (either D161 or D122) in M7-NPM and Y67E-NPM, whereas wild-type NPM1 was cleaved at both sites. Thus, we observed a correlation between the propensity to form oligomers and granzyme B cleavage site selection in nucleophosmin proteins, suggesting that a small change at an important monomer-monomer interface can affect conformational shifts and impact protein-protein interactions.
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42
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DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
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43
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Arcovito A, Chiarella S, Della Longa S, Di Matteo A, Lo Sterzo C, Scaglione GL, Federici L. Synergic role of nucleophosmin three-helix bundle and a flanking unstructured tail in the interaction with G-quadruplex DNA. J Biol Chem 2014; 289:21230-41. [PMID: 24952945 DOI: 10.1074/jbc.m114.565010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a number of functions in ribosome biogenesis and export, cell cycle control, and response to stress stimuli. NPM1 is the most frequently mutated gene in acute myeloid leukemia; mutations map to the C-terminal domain of the protein and cause its denaturation and aberrant cytoplasmic translocation. NPM1 C-terminal domain binds G-quadruplex regions at ribosomal DNA and at gene promoters, including the well characterized sequence from the nuclease-hypersensitive element III region of the c-MYC promoter. These activities are lost by the leukemic variant. Here we analyze the NPM1/G-quadruplex interaction, focusing on residues belonging to both the NPM1 terminal three-helix bundle and a lysine-rich unstructured tail, which has been shown to be necessary for high affinity recognition. We performed extended site-directed mutagenesis and measured binding rate constants through surface plasmon resonance analysis. These data, supported by molecular dynamics simulations, suggest that the unstructured tail plays a double role in the reaction mechanism. On the one hand, it facilitates the formation of an encounter complex through long range electrostatic interactions; on the other hand, it directly contacts the G-quadruplex scaffold through multiple and transient electrostatic interactions, significantly enlarging the contact surface.
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Affiliation(s)
- Alessandro Arcovito
- From the Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sara Chiarella
- Ce.S.I. Centro Scienze dell'Invecchiamento, "Fondazione Università D'Annunzio," 66013 Chieti, Italy, Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Della Longa
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, Università dell'Aquila, 67100 Coppito (L'Aquila), Italy
| | - Adele Di Matteo
- Istituto di Biologia, Medicina Molecolare e NanoBiotecnologie, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy, and
| | - Carlo Lo Sterzo
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, 00185 Rome, Italy
| | - Giovanni Luca Scaglione
- From the Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Luca Federici
- Ce.S.I. Centro Scienze dell'Invecchiamento, "Fondazione Università D'Annunzio," 66013 Chieti, Italy, Dipartimento di Scienze Sperimentali e Cliniche, Università di Chieti "G. D'Annunzio," 66013 Chieti, Italy
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44
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Scognamiglio PL, Di Natale C, Leone M, Poletto M, Vitagliano L, Tell G, Marasco D. G-quadruplex DNA recognition by nucleophosmin: New insights from protein dissection. Biochim Biophys Acta Gen Subj 2014; 1840:2050-9. [DOI: 10.1016/j.bbagen.2014.02.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 11/25/2022]
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45
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Mitrea DM, Grace CR, Buljan M, Yun MK, Pytel NJ, Satumba J, Nourse A, Park CG, Madan Babu M, White SW, Kriwacki RW. Structural polymorphism in the N-terminal oligomerization domain of NPM1. Proc Natl Acad Sci U S A 2014; 111:4466-71. [PMID: 24616519 PMCID: PMC3970533 DOI: 10.1073/pnas.1321007111] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleophosmin (NPM1) is a multifunctional phospho-protein with critical roles in ribosome biogenesis, tumor suppression, and nucleolar stress response. Here we show that the N-terminal oligomerization domain of NPM1 (Npm-N) exhibits structural polymorphism by populating conformational states ranging from a highly ordered, folded pentamer to a highly disordered monomer. The monomer-pentamer equilibrium is modulated by posttranslational modification and protein binding. Phosphorylation drives the equilibrium in favor of monomeric forms, and this effect can be reversed by Npm-N binding to its interaction partners. We have identified a short, arginine-rich linear motif in NPM1 binding partners that mediates Npm-N oligomerization. We propose that the diverse functional repertoire associated with NPM1 is controlled through a regulated unfolding mechanism signaled through posttranslational modifications and intermolecular interactions.
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Affiliation(s)
- Diana M. Mitrea
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Christy R. Grace
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Marija Buljan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Nicholas J. Pytel
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - John Satumba
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - M. Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
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46
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Savelyeva AV, Semenov DV, Stepanov GA, Baryakin DN, Kuligina EV, Rabinov IV, Koval OA, Richter VA. [The influence of recombinant nucleophosmin 1 on artificial RNA internalization into human adenocarcinoma MCF-7 cells]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014; 40:55-63. [PMID: 25898723 DOI: 10.1134/s1068162014010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study we obtained and characterized the recombinant analogue of multifunctional nucleolar phosphoprotein nucleophosmin 1 (NPM1) involved in crucial cellular processes such as transcription, reparation and mitosis. The influence ofnucleophosmin 1 on extrcellular RNAs accumulation in human adenocarcinoma cells MCF-7 was analyzed. It was found that incubation of AluY RNA (n > 300 nt), U24 snoRNA analogues (n ~ 80 nt) with Npm1-His6 resulted in RNA-protein non-covalent complexes formation, but not in case of the short oligoribonucleotide (n = 22 nt). It was shown that interaction of AluY RNA analogue with Npm1-His6 significantly increases transfection efficacy of the RNA into MCF-7 human cells. Altogether, these data allow us to conclude, that nucleophosmin 1 not only binds RNA with complex secondary structure, but also promotes uptake and internalization of such RNA by human cells.
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Hisaoka M, Nagata K, Okuwaki M. Intrinsically disordered regions of nucleophosmin/B23 regulate its RNA binding activity through their inter- and intra-molecular association. Nucleic Acids Res 2013; 42:1180-95. [PMID: 24106084 PMCID: PMC3902904 DOI: 10.1093/nar/gkt897] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Nucleophosmin (NPM1/B23) is a nucleolar protein implicated in growth-associated functions, in which the RNA binding activity of B23 plays essential roles in ribosome biogenesis. The C-terminal globular domain (CTD) of B23 has been believed to be the RNA binding domain because the splicing variant B23.2 lacking the CTD binds considerably less efficiently to RNA. However, the recognition of target RNAs by B23 remains poorly understood. Herein, we report a novel mechanism by which B23 recognizes specific RNA targets. We observed that the nucleolar retention of B23.3 lacking the basic region of B23.1 was lower than that of B23.1 because of its low RNA binding activity. Circular dichroism measurements indicated that the basic region and adjacent acidic regions of B23 are intrinsically disordered regions (IDRs). Biochemical analyses revealed that the basic IDR alone strongly binds to RNA with low specificity. The excessive RNA binding activity of the basic IDR was restrained by intra-molecular interaction with the acidic IDR of B23. Chemical cross-linking experiments and fluorescent labeling of bipartite tetracysteine-tagged proteins suggested that the inter- and intra-molecular interactions between the two IDRs contribute to the regulation of the RNA binding activity of CTD to control the cellular localization and functions of B23.
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Affiliation(s)
- Miharu Hisaoka
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan
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48
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Bañuelos S, Lectez B, Taneva SG, Ormaza G, Alonso-Mariño M, Calle X, Urbaneja MA. Recognition of intermolecular G-quadruplexes by full length nucleophosmin. Effect of a leukaemia-associated mutation. FEBS Lett 2013; 587:2254-9. [PMID: 23742937 DOI: 10.1016/j.febslet.2013.05.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/08/2013] [Accepted: 05/21/2013] [Indexed: 11/19/2022]
Abstract
Nucleophosmin (NPM) is a nucleolar protein involved in ribosome biogenesis. NPM1 gene is frequently mutated in acute myeloid leukaemia (AML), correlating with aberrant cytoplasmic localization of the protein. NPM attachment to the nucleolus in physiological conditions probably depends on binding to nucleic acids, and this recognition could be altered in AML. NPM associates to guanine-rich DNA sequences, able to fold as "G-quadruplexes". We have analyzed the interaction of pentameric, full length NPM with G-rich oligonucleotides, finding that the protein binds preferentially high-order G-quadruplexes. AML-associated mutation significantly hampers DNA binding, pointing to a possible mechanism contributing to pathological mislocalization of NPM.
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Affiliation(s)
- Sonia Bañuelos
- Biophysics Unit (CSIC/UPV-EHU), Department of Biochemistry and Molecular Biology, University of Basque Country (UPV-EHU), POB 644, 48080 Bilbao, Spain.
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49
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The folding pathway of a functionally competent C-terminal domain of nucleophosmin: protein stability and denatured state residual structure. Biochem Biophys Res Commun 2013; 435:64-8. [PMID: 23618861 DOI: 10.1016/j.bbrc.2013.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/07/2013] [Indexed: 11/23/2022]
Abstract
Nucleophosmin (NPM1) is a nucleolar protein implicated in ribosome biogenesis, centrosome duplication and cell cycle control; the NPM1 gene is the most frequent target for mutations in Acute Myeloid Leukemia. Mutations map to the C-terminal domain of the protein and cause its unfolding, loss of DNA binding properties and aberrant cellular localization. Here we investigate the folding pathway and denatured state properties of a NPM1 C-terminal domain construct encompassing the last 70 residues in the reference sequence. This construct is more stable than the previously characterized domain, which consisted of the last 53 residues. Data reveal that, similarly to what was discovered for the shorter construct, also the 70-residue construct of NPM1 displays a detectable residual structure in its denatured state. The higher stability of the latter domain allows us to conclude that the denatured state is robust to changes in solvent composition and that it consists of a discrete state in equilibrium with the expanded fully unfolded conformation. This observation, which might appear as a technicality, is in fact of general importance for the understanding of the folding of proteins. The implications of our results are discussed in the context of previous works on single domain helical proteins.
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50
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Federici L, Falini B. Nucleophosmin mutations in acute myeloid leukemia: a tale of protein unfolding and mislocalization. Protein Sci 2013; 22:545-56. [PMID: 23436734 DOI: 10.1002/pro.2240] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/15/2013] [Indexed: 12/14/2022]
Abstract
Nucleophosmin (NPM1) is an abundant, ubiquitously expressed protein mainly localized at nucleoli but continuously shuttling between nucleus and cytoplasm. NPM1 plays a role in several cellular functions, including ribosome biogenesis and export, centrosome duplication, chromatin remodeling, DNA repair, and response to stress stimuli. Much of the interest in this protein arises from its relevance in human malignancies. NPM1 is frequently overexpressed in solid tumors and is the target of several chromosomal translocations in hematologic neoplasms. Notably, NPM1 has been characterized as the most frequently mutated gene in acute myeloid leukemia (AML). Mutations alter the C-terminal DNA-binding domain of the protein and result in its aberrant nuclear export and stable cytosolic localization. In this review, we focus on the leukemia-associated NPM1 C-terminal domain and describe its structure, function, and the effect exerted by leukemic mutations. Finally, we discuss the possibility to target NPM1 for the treatment of cancer and, in particular, of AML patients with mutated NPM1 gene.
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Affiliation(s)
- Luca Federici
- Ce.S.I. Center of Excellence on Aging, University of Chieti "G. D'Annunzio", 66013 Chieti, Italy.
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