1
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Wei Q, Zhou J, Wang X, Li Z, Chen X, Chen K, Jiang R. Pan-cancer analysis of the prognostic and immunological role of nucleophosmin/nucleoplasmin 3 ( NPM3) and its potential significance in lung adenocarcinoma. CANCER PATHOGENESIS AND THERAPY 2023; 1:238-252. [PMID: 38327603 PMCID: PMC10846304 DOI: 10.1016/j.cpt.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 02/09/2024]
Abstract
Background Nucleophosmin/nucleoplasmin 3 (NPM3), a member of the NPM protein family, is widely expressed in various human tissues. Although previous studies identified elevated NPM3 expression in several cancers, a systematic pan-cancer analysis remains lacking. In this study, we conducted a comprehensive analysis of NPM3 to determine its role in tumorigenesis and tumor development. Methods Using data from The Cancer Genome Atlas (TCGA) and various bioinformatics analysis tools, we conducted a pan-cancer analysis of NPM3. Additionally, we collected gene expression and clinical data from 890 patients with lung adenocarcinoma (LUAD) from TCGA and the Gene Expression Omnibus database. We performed Cox regression analyses to explore the independent prognostic value of NPM3 expression in LUAD and plotted a nomogram to predict patient survival. We also used real-time quantitative polymerase chain reaction (RT-qPCR) to examine the expression levels of NPM3 in seven pairs of LUAD and paraneoplastic tissue samples. Results NPM3 expression was significantly increased in 20 types of cancer and was associated with poor prognosis in five types (P < 0.05). NPM3 expression was negatively correlated with DNA methylation and positively correlated with copy number variation. NPM3 was also significantly associated with immune cell infiltration in various cancers. Cox regression analyses revealed that NPM3 expression could serve as an independent prognostic marker of LUAD. Moreover, our nomogram demonstrated good predictive ability for the prognosis of patients with LUAD. Finally, the high expression of NPM3 in LUAD was verified using RT-qPCR. Conclusion NPM3 is a promising biomarker for predicting pan-cancer prognosis and immunotherapeutic efficacy.
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Affiliation(s)
- Qianhui Wei
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
| | - Jing Zhou
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
| | - Xinyue Wang
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
| | - Zhaona Li
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
| | - Xiuqiong Chen
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
| | - Kaidi Chen
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
| | - Richeng Jiang
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin 300202, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300202, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300202, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin 300202, China
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2
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Li J, Jiang H, Mu Y, Wei Z, Ma A, Sun M, Zhao J, Zhu C, Chen X. SRSF10 regulates proliferation of neural progenitor cells and affects neurogenesis in developing mouse neocortex. iScience 2023; 26:107042. [PMID: 37360696 PMCID: PMC10285642 DOI: 10.1016/j.isci.2023.107042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/25/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Alternative pre-mRNA splicing plays critical roles in brain development. SRSF10 is a splicing factor highly expressed in central nervous system and plays important roles in maintaining normal brain functions. However, its role in neural development is unclear. In this study, by conditional depleting SRSF10 in neural progenitor cells (NPCs) in vivo and in vitro, we found that dysfunction of SRSF10 leads to developmental defects of the brain, which manifest as abnormal ventricle enlargement and cortical thinning anatomically, as well as decreased NPCs proliferation and weakened cortical neurogenesis histologically. Furthermore, we proved that the function of SRSF10 on NPCs proliferation involved the regulation of PI3K-AKT-mTOR-CCND2 pathway and the alternative splicing of Nasp, a gene encoding isoforms of cell cycle regulators. These findings highlight the necessity of SRSF10 in the formation of a structurally and functionally normal brain.
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Affiliation(s)
- Junjie Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Hanyang Jiang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yawei Mu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Zixuan Wei
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Ankangzhi Ma
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Menghan Sun
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Jingjing Zhao
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, PR China
| | - Cuiqing Zhu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xianhua Chen
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
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3
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Mazorra-Carrillo JL, De León-Rodríguez A, Huerta-Ocampo JA, Velarde-Salcedo AJ, González de Mejía E, Barba de la Rosa AP. Proteomic analysis of chemically transformed NIH-3T3 cells reveals novel mechanisms of action of amaranth lunasin-like peptide. Food Res Int 2022; 157:111374. [DOI: 10.1016/j.foodres.2022.111374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
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4
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Wu YC, Hsu SP, Hu MC, Lan YT, Yeh ETH, Yang FM. PEP-sNASP Peptide Alleviates LPS-Induced Acute Lung Injury Through the TLR4/TRAF6 Axis. Front Med (Lausanne) 2022; 9:832713. [PMID: 35386914 PMCID: PMC8977741 DOI: 10.3389/fmed.2022.832713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 01/11/2023] Open
Abstract
Acute lung injury (ALI) is a severe inflammatory lung disease associated with macrophages. Somatic nuclear autoantigenic sperm protein (sNASP) is a negative regulator of Toll-like receptor (TLR) signaling that targets tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) in macrophages, which is required to maintain homeostasis of the innate immune response. In the present study, we generated a cell permeable PEP-sNASP peptide using the sNASP protein N-terminal domain, and examined its potential therapeutic effect in a mouse model of ALI induced by the intranasal administration of lipopolysaccharide (LPS) and elucidated the underlying molecular mechanisms in RAW 264.7 cells. In vivo, PEP-sNASP peptide treatment markedly ameliorated pathological injury, reduced the wet/dry (W/D) weight ratio of the lungs and the production of proinflammatory cytokines (interleukin (IL)-1β, IL-6, and TNF-α). In vitro, we demonstrated that when the PEP-sNASP peptide was transduced into RAW 264.7 cells, it bound to TRAF6, which markedly decreased LPS-induced proinflammatory cytokines by inhibiting TRAF6 autoubiquitination, nuclear factor (NF)-κB activation, reactive oxygen species (ROS) and cellular nitric oxide (NO) levels. Furthermore, the PEP-sNASP peptide also inhibited NLR family pyrin domain containing 3 (NLRP3) inflammasome activation. Our results therefore suggest that the PEP-sNASP may provide a potential protein therapy against oxidative stress and pulmonary inflammation via selective TRAF6 signaling.
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Affiliation(s)
- Yu-Chih Wu
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sung-Po Hsu
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Meng-Chun Hu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Ting Lan
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Edward T H Yeh
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AK, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AK, United States
| | - Feng-Ming Yang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
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5
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Distinct histone H3-H4 binding modes of sNASP reveal the basis for cooperation and competition of histone chaperones. Genes Dev 2021; 35:1610-1624. [PMID: 34819355 PMCID: PMC8653785 DOI: 10.1101/gad.349100.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023]
Abstract
In this study, Liu et al. investigated how sNASP binds H3–H4 in the presence and absence of ASF1, two major histone H3–H4 chaperones found in distinct and common complexes, during chromosomal duplication. They show that, in the presence of ASF1, sNASP principally recognizes a partially unfolded Nα region of histone H3, and in the absence of ASF1, an additional sNASP binding site becomes available in the core domain of the H3–H4 complex, providing new mechanistic insights into coordinated histone binding and transfer by histone chaperones. Chromosomal duplication requires de novo assembly of nucleosomes from newly synthesized histones, and the process involves a dynamic network of interactions between histones and histone chaperones. sNASP and ASF1 are two major histone H3–H4 chaperones found in distinct and common complexes, yet how sNASP binds H3–H4 in the presence and absence of ASF1 remains unclear. Here we show that, in the presence of ASF1, sNASP principally recognizes a partially unfolded Nα region of histone H3, and in the absence of ASF1, an additional sNASP binding site becomes available in the core domain of the H3–H4 complex. Our study also implicates a critical role of the C-terminal tail of H4 in the transfer of H3–H4 between sNASP and ASF1 and the coiled-coil domain of sNASP in nucleosome assembly. These findings provide mechanistic insights into coordinated histone binding and transfer by histone chaperones.
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6
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Stephenson RA, Thomalla JM, Chen L, Kolkhof P, White RP, Beller M, Welte MA. Sequestration to lipid droplets promotes histone availability by preventing turnover of excess histones. Development 2021; 148:271212. [PMID: 34355743 DOI: 10.1242/dev.199381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Because both dearth and overabundance of histones result in cellular defects, histone synthesis and demand are typically tightly coupled. In Drosophila embryos, histones H2B, H2A and H2Av accumulate on lipid droplets (LDs), which are cytoplasmic fat storage organelles. Without LD binding, maternally provided H2B, H2A and H2Av are absent; however, how LDs ensure histone storage is unclear. Using quantitative imaging, we uncover when during oogenesis these histones accumulate, and which step of accumulation is LD dependent. LDs originate in nurse cells (NCs) and are transported to the oocyte. Although H2Av accumulates on LDs in NCs, the majority of the final H2Av pool is synthesized in oocytes. LDs promote intercellular transport of the histone anchor Jabba and thus its presence in the ooplasm. Ooplasmic Jabba then prevents H2Av degradation, safeguarding the H2Av stockpile. Our findings provide insight into the mechanism for establishing histone stores during Drosophila oogenesis and shed light on the function of LDs as protein-sequestration sites.
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Affiliation(s)
- Roxan A Stephenson
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | | - Lili Chen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Petra Kolkhof
- Institute for Mathematical Modeling of Biological Systems, Systems Biology of Lipid Metabolism, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Roger P White
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Mathias Beller
- Institute for Mathematical Modeling of Biological Systems, Systems Biology of Lipid Metabolism, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Michael A Welte
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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7
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Lian Y, Hao H, Xu J, Bo T, Liang A, Wang W. The histone chaperone Nrp1 is required for chromatin stability and nuclear division in Tetrahymena thermophila. Epigenetics Chromatin 2021; 14:34. [PMID: 34301312 PMCID: PMC8299592 DOI: 10.1186/s13072-021-00409-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022] Open
Abstract
Histone chaperones facilitate DNA replication and repair by promoting chromatin assembly, disassembly and histone exchange. Following histones synthesis and nucleosome assembly, the histones undergo posttranslational modification by different enzymes and are deposited onto chromatins by various histone chaperones. In Tetrahymena thermophila, histones from macronucleus (MAC) and micronucleus (MIC) have been comprehensively investigated, but the function of histone chaperones remains unclear. Histone chaperone Nrp1 in Tetrahymena contains four conserved tetratricopepeptide repeat (TPR) domains and one C-terminal nuclear localization signal. TPR2 is typically interrupted by a large acidic motif. Immunofluorescence staining showed that Nrp1 is located in the MAC and MICs, but disappeared in the apoptotic parental MAC and the degraded MICs during the conjugation stage. Nrp1 was also colocalized with α-tubulin around the spindle structure. NRP1 knockdown inhibited cellular proliferation and led to the loss of chromosome, abnormal macronuclear amitosis, and disorganized micronuclear mitosis during the vegetative growth stage. During sexual developmental stage, the gametic nuclei failed to be selected and abnormally degraded in NRP1 knockdown mutants. Affinity purification combined with mass spectrometry analysis indicated that Nrp1 is co-purified with core histones, heat shock proteins, histone chaperones, and DNA damage repair proteins. The physical direct interaction of Nrp1 and Asf1 was also confirmed by pull-down analysis in vitro. The results show that histone chaperone Nrp1 is involved in micronuclear mitosis and macronuclear amitosis in the vegetative growth stage and maintains gametic nuclei formation during the sexual developmental stage. Nrp1 is required for chromatin stability and nuclear division in Tetrahymena thermophila.
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Affiliation(s)
- Yinjie Lian
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China
| | - Huijuan Hao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China.,School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China
| | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China.
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8
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Pang MYH, Sun X, Ausió J, Ishibashi T. Histone H4 variant, H4G, drives ribosomal RNA transcription and breast cancer cell proliferation by loosening nucleolar chromatin structure. J Cell Physiol 2020; 235:9601-9608. [PMID: 32385931 DOI: 10.1002/jcp.29770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/09/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023]
Abstract
The hominidae-specific histone variant H4G is expressed in breast cancer patients in a stage-dependent manner. H4G localizes primarily in the nucleoli via its interaction with nucleophosmin (NPM1). H4G is involved in rDNA transcription and ribosome biogenesis, which facilitates breast cancer cell proliferation. However, the molecular mechanism underlying this process remains unknown. Here, we show that H4G is not stably incorporated into nucleolar chromatin, even with the chaperoning assistance of NPM1. H4G likely form transient nucleosome-like-structure that undergoes rapid dissociation. In addition, the nucleolar chromatin in H4GKO cells is more compact than WT cells. Altogether, our results suggest that H4G relaxes the nucleolar chromatin and enhances rRNA transcription by forming destabilized nucleosome in breast cancer cells.
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Affiliation(s)
- Matthew Y H Pang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Xulun Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
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9
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Long M, Sun X, Shi W, Yanru A, Leung STC, Ding D, Cheema MS, MacPherson N, Nelson CJ, Ausio J, Yan Y, Ishibashi T. A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. Nucleic Acids Res 2019; 47:8399-8409. [PMID: 31219579 PMCID: PMC6895281 DOI: 10.1093/nar/gkz547] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Histone variants, present in various cell types and tissues, are known to exhibit different functions. For example, histone H3.3 and H2A.Z are both involved in gene expression regulation, whereas H2A.X is a specific variant that responds to DNA double-strand breaks. In this study, we characterized H4G, a novel hominidae-specific histone H4 variant. We found that H4G is expressed in a variety of human cell lines and exhibit tumor-stage dependent overexpression in tissues from breast cancer patients. We found that H4G localized primarily to the nucleoli of the cell nucleus. This localization was controlled by the interaction of the alpha-helix 3 of the histone fold motif with a histone chaperone, nucleophosmin 1. In addition, we found that modulating H4G expression affects rRNA expression levels, protein synthesis rates and cell-cycle progression. Our data suggest that H4G expression alters nucleolar chromatin in a way that enhances rDNA transcription in breast cancer tissues.
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Affiliation(s)
- Mengping Long
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Xulun Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Wenjin Shi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - An Yanru
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Sophia T C Leung
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Dongbo Ding
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Nicol MacPherson
- Department of Medical Oncology, BC Cancer Vancouver Island Centre, Victoria, BC V8R 6V5, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Yan Yan
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
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10
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Tan HL, Lim KK, Yang Q, Fan JS, Sayed AMM, Low LS, Ren B, Lim TK, Lin Q, Mok YK, Liou YC, Chen ES. Prolyl isomerization of the CENP-A N-terminus regulates centromeric integrity in fission yeast. Nucleic Acids Res 2019; 46:1167-1179. [PMID: 29194511 DOI: 10.1093/nar/gkx1180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/22/2017] [Indexed: 01/15/2023] Open
Abstract
Centromeric identity and chromosome segregation are determined by the precise centromeric targeting of CENP-A, the centromere-specific histone H3 variant. The significance of the amino-terminal domain (NTD) of CENP-A in this process remains unclear. Here, we assessed the functional significance of each residue within the NTD of CENP-A from Schizosaccharomyces pombe (SpCENP-A) and identified a proline-rich 'GRANT' (Genomic stability-Regulating site within CENP-A N-Terminus) motif that is important for CENP-A function. Through sequential mutagenesis, we show that GRANT proline residues are essential for coordinating SpCENP-A centromeric targeting. GRANT proline-15 (P15), in particular, undergoes cis-trans isomerization to regulate chromosome segregation fidelity, which appears to be carried out by two FK506-binding protein (FKBP) family prolyl cis-trans isomerases. Using proteomics analysis, we further identified the SpCENP-A-localizing chaperone Sim3 as a SpCENP-A NTD interacting protein that is dependent on GRANT proline residues. Ectopic expression of sim3+ complemented the chromosome segregation defect arising from the loss of these proline residues. Overall, cis-trans proline isomerization is a post-translational modification of the SpCENP-A NTD that confers precise propagation of centromeric integrity in fission yeast, presumably via targeting SpCENP-A to the centromere.
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Affiliation(s)
- Hwei Ling Tan
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Kim Kiat Lim
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Qiaoyun Yang
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | | | - Liy Sim Low
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Bingbing Ren
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Yu-Keung Mok
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456 Singapore
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, 117597 Singapore
- National University Health System (NUHS), Singapore, 119228 Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456 Singapore
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11
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Itoh K, Reis AH, Hayhurst A, Sokol SY. Isolation of nanobodies against Xenopus embryonic antigens using immune and non-immune phage display libraries. PLoS One 2019; 14:e0216083. [PMID: 31048885 PMCID: PMC6497274 DOI: 10.1371/journal.pone.0216083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
The use of Xenopus laevis as a model for vertebrate developmental biology is limited by a lack of antibodies specific for embryonic antigens. This study evaluated the use of immune and non-immune phage display libraries for the isolation of single domain antibodies, or nanobodies, with specificities for Xenopus embryonic antigens. The immune nanobody library was derived from peripheral blood lymphocyte RNA obtained from a llama immunized with Xenopus gastrula homogenates. Screening this library by immunostaining of embryonic tissues with pooled periplasmic material and sib-selection led to the isolation of several monoclonal phages reactive with the cytoplasm and nuclei of gastrula cells. One antigen recognized by a group of nanobodies was identified using a reverse proteomics approach as nucleoplasmin, an abundant histone chaperone. As an alternative strategy, a semi-synthetic non-immune llama nanobody phage display library was panned on highly purified Xenopus proteins. This proof-of-principle approach isolated monoclonal nanobodies that specifically bind Nuclear distribution element-like 1 (Ndel1) in multiple immunoassays. Our results suggest that immune and non-immune phage display screens on crude and purified embryonic antigens can efficiently identify nanobodies useful to the Xenopus developmental biology community.
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Affiliation(s)
- Keiji Itoh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alice H Reis
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Sergei Y Sokol
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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12
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Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation. Gigascience 2019; 8:giy160. [PMID: 30535196 PMCID: PMC6381762 DOI: 10.1093/gigascience/giy160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/19/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. FINDINGS Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. CONCLUSION The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
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Affiliation(s)
- Sree Rohit Raj Kolora
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Amin Saffari
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Maria Beatriz Walter Costa
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Embrapa Agroenergia, Parque Estacaeo Biologica (PqEB), Asa Norte, Brasilia/DF, 70770-901, Brazil
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany
- Max Planck Institute for Physics of Complex Systems, Noethnitzerstrasse 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01397 Dresden, Germany
| | - Manjusha Chintalapati
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Gero Doose
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Jörg Overmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Christoph Bleidorn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, Potsdam, 14476, Germany
| | - Klaus Henle
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Katja Nowick
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Rui Faria
- Department of Animal and Plant Sciences, Alfred Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Augustusplatz 12, Leipzig, 04107, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
- Fraunhofer Institut Für Zelltherapie Und Immunologie, Perlickstrasse 1, Leipzig, 04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger strasse 17, Wien, 1090, Austria
- Center for non-Coding RNA in Technology and Health, University of Copenhagen, Gronnegardsvej 3, Frederiksberg C, 1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico, 87501, USA
| | - Martin Schlegel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
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Functional Analysis of Hif1 Histone Chaperone in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:1993-2006. [PMID: 29661843 PMCID: PMC5982827 DOI: 10.1534/g3.118.200229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Hif1 protein in the yeast Saccharomyces cerevisie is an evolutionarily conserved H3/H4-specific chaperone and a subunit of the nuclear Hat1 complex that catalyzes the acetylation of newly synthesized histone H4. Hif1, as well as its human homolog NASP, has been implicated in an array of chromatin-related processes including histone H3/H4 transport, chromatin assembly and DNA repair. In this study, we elucidate the functional aspects of Hif1. Initially we establish the wide distribution of Hif1 homologs with an evolutionarily conserved pattern of four tetratricopeptide repeats (TPR) motifs throughout the major fungal lineages and beyond. Subsequently, through targeted mutational analysis, we demonstrate that the acidic region that interrupts the TPR2 is essential for Hif1 physical interactions with the Hat1/Hat2-complex, Asf1, and with histones H3/H4. Furthermore, we provide evidence for the involvement of Hif1 in regulation of histone metabolism by showing that cells lacking HIF1 are both sensitive to histone H3 over expression, as well as synthetic lethal with a deletion of histone mRNA regulator LSM1. We also show that a basic patch present at the extreme C-terminus of Hif1 is essential for its proper nuclear localization. Finally, we describe a physical interaction with a transcriptional regulatory protein Spt2, possibly linking Hif1 and the Hat1 complex to transcription-associated chromatin reassembly. Taken together, our results provide novel mechanistic insights into Hif1 functions and establish it as an important protein in chromatin-associated processes.
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Onikubo T, Shechter D. Chaperone-mediated chromatin assembly and transcriptional regulation in Xenopus laevis. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2018; 60:271-276. [PMID: 27759155 DOI: 10.1387/ijdb.130188ds] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Chromatin is the complex of DNA and histone proteins that is the physiological form of the eukaryotic genome. Chromatin is generally repressive for transcription, especially so during early metazoan development when maternal factors are explicitly in control of new zygotic gene expression. In the important model organism Xenopus laevis, maturing oocytes are transcriptionally active with reduced rates of chromatin assembly, while laid eggs and fertilized embryos have robust rates of chromatin assembly and are transcriptionally repressed. As the DNA-to-cytoplasmic ratio decreases approaching the mid-blastula transition (MBT) and the onset of zygotic genome activation (ZGA), the chromatin assembly process changes with the concomitant reduction in maternal chromatin components. Chromatin assembly is mediated in part by histone chaperones that store maternal histones and release them into new zygotic chromatin. Here, we review literature on chromatin and transcription in frog embryos and cell-free extracts and highlight key insights demonstrating the roles of maternal and zygotic histone deposition and their relationship with transcriptional regulation. We explore the central historical and recent literature on the use of Xenopus embryos and the key contributions provided by experiments in cell-free oocyte and egg extracts for the interplay between histone chaperones, chromatin assembly, and transcriptional regulation. Ongoing and future studies in Xenopus cell free extracts will likely contribute essential new insights into the interplay between chromatin assembly and transcriptional regulation.
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Affiliation(s)
- Takashi Onikubo
- Department of Biochemistry. Albert Einstein College of Medicine, Bronx, NY, USA
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15
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Shaping Chromatin in the Nucleus: The Bricks and the Architects. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:1-14. [PMID: 29208640 DOI: 10.1101/sqb.2017.82.033753] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromatin organization in the nucleus provides a vast repertoire of information in addition to that encoded genetically. Understanding how this organization impacts genome stability and influences cell fate and tumorigenesis is an area of rapid progress. Considering the nucleosome, the fundamental unit of chromatin structure, the study of histone variants (the bricks) and their selective loading by histone chaperones (the architects) is particularly informative. Here, we report recent advances in understanding how relationships between histone variants and their chaperones contribute to tumorigenesis using cell lines and Xenopus development as model systems. In addition to their role in histone deposition, we also document interactions between histone chaperones and other chromatin factors that govern higher-order structure and control DNA metabolism. We highlight how a fine-tuned assembly line of bricks (H3.3 and CENP-A) and architects (HIRA, HJURP, and DAXX) is key in adaptation to developmental and pathological changes. An example of this conceptual advance is the exquisite sensitivity displayed by p53-null tumor cells to modulation of HJURP, the histone chaperone for CENP-A (CenH3 variant). We discuss how these findings open avenues for novel therapeutic paradigms in cancer care.
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16
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Abstract
The nucleoplasmin family of histone chaperones is identified by a pentamer-forming domain and multiple acidic tracts that mediate histone binding and chaperone activity. Within this family, a novel domain organization was recently discovered that consists of an N-terminal nucleoplasmin-like (NPL) domain and a C-terminal FKBP peptidyl-proline isomerase domain. Saccharomyces cerevisiae Fpr4 is one such protein. Here we report that in addition to its known histone prolyl isomerase activities, the Fpr4 FKBP domain binds to nucleosomes and nucleosome arrays in vitro. This ability is mediated by a collection of basic patches that enable the enzyme to stably associate with linker DNA. The interaction of the Fpr4 FKBP with recombinant chromatin complexes condenses nucleosome arrays independently of its catalytic activity. Based on phylogenetic comparisons we propose that the chromatin binding ability of ‘basic’ FKBPs is shared amongst related orthologues present in fungi, plants, and insects. Thus, a subclass of FKBP prolyl isomerase enzymes is recruited to linker regions of chromatin.
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17
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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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18
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De Munter S, Görnemann J, Derua R, Lesage B, Qian J, Heroes E, Waelkens E, Van Eynde A, Beullens M, Bollen M. Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions. FEBS Lett 2017; 591:415-424. [DOI: 10.1002/1873-3468.12548] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/03/2016] [Accepted: 12/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Sofie De Munter
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Janina Görnemann
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Rita Derua
- Protein Phosphorylation & Proteomics Lab; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
- SyBioMa; KU Leuven; Belgium
| | - Bart Lesage
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Junbin Qian
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Ewald Heroes
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Etienne Waelkens
- Protein Phosphorylation & Proteomics Lab; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
- SyBioMa; KU Leuven; Belgium
| | - Aleyde Van Eynde
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Monique Beullens
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics; KU Leuven Department of Cellular and Molecular Medicine; University of Leuven; Belgium
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Maksimov V, Nakamura M, Wildhaber T, Nanni P, Ramström M, Bergquist J, Hennig L. The H3 chaperone function of NASP is conserved in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:425-436. [PMID: 27402088 DOI: 10.1111/tpj.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Histones are abundant cellular proteins but, if not incorporated into chromatin, they are usually bound by histone chaperones. Here, we identify Arabidopsis NASP as a chaperone for histones H3.1 and H3.3. NASP interacts in vitro with monomeric H3.1 and H3.3 as well as with histone H3.1-H4 and H3.3-H4 dimers. However, NASP does not bind to monomeric H4. NASP shifts the equilibrium between histone dimers and tetramers towards tetramers but does not interact with tetramers in vitro. Arabidopsis NASP promotes [H3-H4]2 tetrasome formation, possibly by providing preassembled histone tetramers. However, NASP does not promote disassembly of in vitro preassembled tetrasomes. In contrast to its mammalian homolog, Arabidopsis NASP is a predominantly nuclear protein. In vivo, NASP binds mainly monomeric H3.1 and H3.3. Pulldown experiments indicated that NASP may also interact with the histone chaperone MSI1 and a HSC70 heat shock protein.
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Affiliation(s)
- Vladimir Maksimov
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Thomas Wildhaber
- Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057, Zurich, Switzerland
| | - Margareta Ramström
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
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20
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Scott DD, Oeffinger M. Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol 2016; 94:419-432. [PMID: 27673355 DOI: 10.1139/bcb-2016-0068] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
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Affiliation(s)
- Daniel D Scott
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
| | - Marlene Oeffinger
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
- c Département de biochimie et médecine moléculaire, Faculté de Médecine, Université de Montréal, QC H3T 1J4, Canada
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21
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Structural Insights into the Association of Hif1 with Histones H2A-H2B Dimer and H3-H4 Tetramer. Structure 2016; 24:1810-1820. [DOI: 10.1016/j.str.2016.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 08/01/2016] [Accepted: 08/01/2016] [Indexed: 11/22/2022]
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22
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A Quantitative Characterization of Nucleoplasmin/Histone Complexes Reveals Chaperone Versatility. Sci Rep 2016; 6:32114. [PMID: 27558753 PMCID: PMC4997359 DOI: 10.1038/srep32114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/02/2016] [Indexed: 01/29/2023] Open
Abstract
Nucleoplasmin (NP) is an abundant histone chaperone in vertebrate oocytes and embryos involved in storing and releasing maternal histones to establish and maintain the zygotic epigenome. NP has been considered a H2A-H2B histone chaperone, and recently it has been shown that it can also interact with H3-H4. However, its interaction with different types of histones has not been quantitatively studied so far. We show here that NP binds H2A-H2B, H3-H4 and linker histones with Kd values in the subnanomolar range, forming different complexes. Post-translational modifications of NP regulate exposure of the polyGlu tract at the disordered distal face of the protein and induce an increase in chaperone affinity for all histones. The relative affinity of NP for H2A-H2B and linker histones and the fact that they interact with the distal face of the chaperone could explain their competition for chaperone binding, a relevant process in NP-mediated sperm chromatin remodelling during fertilization. Our data show that NP binds H3-H4 tetramers in a nucleosomal conformation and dimers, transferring them to DNA to form disomes and tetrasomes. This finding might be relevant to elucidate the role of NP in chromatin disassembly and assembly during replication and transcription.
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Abstract
The union of haploid gametes at fertilization initiates the formation of the diploid zygote in sexually reproducing animals. This founding event of embryogenesis includes several fascinating cellular and nuclear processes, such as sperm-egg cellular interactions, sperm chromatin remodelling, centrosome formation or pronuclear migration. In comparison with other aspects of development, the exploration of animal fertilization at the functional level has remained so far relatively limited, even in classical model organisms. Here, we have reviewed our current knowledge of fertilization in Drosophila melanogaster, with a special emphasis on the genes involved in the complex transformation of the fertilizing sperm nucleus into a replicated set of paternal chromosomes.
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Affiliation(s)
- Benjamin Loppin
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Raphaëlle Dubruille
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Béatrice Horard
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
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24
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Ellard K, Serpa JJ, Petrotchenko EV, Borchers CH, Ausió J. Expression and purification of the full murine NPM2 and study of its interaction with protamines and histones. Biochem Biophys Rep 2016; 6:165-171. [PMID: 28955874 PMCID: PMC5600342 DOI: 10.1016/j.bbrep.2016.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/19/2016] [Accepted: 04/04/2016] [Indexed: 11/27/2022] Open
Abstract
Mouse nucleoplasmin M.NPM2 was recombinantly expressed and the protein consisting of the complete sequence was purified and characterized. Similar to its Xenopus laevis X.NPM2 counterpart, the protein forms stable pentameric complexes and exhibits an almost undistinguishable hydrodynamic ionic strength-dependent unfolding behavior. The interaction of N.PM2 with histones and mouse P1/P2 protamines revealed that these chromosomal proteins bind preferentially to the distal part of the nucleoplasmin pentamer. Moreover, the present work highlights the critical role played by histones H2B and H4 in the association of the histone H2A-H2B dimers and histone octamer with nucleoplasmin. Characterization of the entire mouse M.NPM2 protein. Determination of sites of interaction of M.NPM2 with histones and mouse protamines. Use of crosslinking mass spectrometry to determine protein-protein interactions. Analysis of the C-terminal NPM2 unfolding.
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Affiliation(s)
- Katherine Ellard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
| | - Jason J Serpa
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.,Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada V8Z 7X8
| | - Evgeniy V Petrotchenko
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.,Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada V8Z 7X8
| | - Christoph H Borchers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.,Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada V8Z 7X8
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
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Rozenfeld C, Butts IA, Tomkiewicz J, Zambonino-Infante JL, Mazurais D. Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L. Comp Biochem Physiol A Mol Integr Physiol 2016; 191:59-65. [DOI: 10.1016/j.cbpa.2015.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/19/2015] [Accepted: 09/18/2015] [Indexed: 11/28/2022]
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Nagatomo H, Kohri N, Akizawa H, Hoshino Y, Yamauchi N, Kono T, Takahashi M, Kawahara M. Requirement for nuclear autoantigenic sperm protein mRNA expression in bovine preimplantation development. Anim Sci J 2015; 87:457-61. [PMID: 26690724 DOI: 10.1111/asj.12538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/11/2015] [Accepted: 08/20/2015] [Indexed: 11/28/2022]
Abstract
Nuclear autoantigenic sperm protein (NASP) is associated with DNA replication, cell proliferation, and cell cycle progression through its specific binding to histones. The aim of this study was to examine the roles of NASP in bovine preimplantation embryonic development. Using NASP gene knockdown (KD), we confirmed the reduction of NASP messenger RNA (mRNA) expression during preimplantation development. NASP KD did not affect cleavage but significantly decreased development of embryos into the blastocyst stage. Furthermore, blastocyst hatching was significantly decreased in NASP KD embryos. Cell numbers in the inner cell mass of NASP KD blastocysts were also decreased compared to those of controls. These results suggest that NASP mRNA expression is required for preimplantation development into the blastocyst stage in cattle.
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Affiliation(s)
- Hiroaki Nagatomo
- Advanced Biotechnology Center, University of Yamanashi, Kofu, Japan
| | - Nanami Kohri
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroki Akizawa
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yumi Hoshino
- Laboratory of Animal Reproduction, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Nobuhiko Yamauchi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Tomohiro Kono
- Department of BioScience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masashi Takahashi
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Manabu Kawahara
- Laboratory of Animal Breeding and Reproduction, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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Bowman A, Lercher L, Singh HR, Zinne D, Timinszky G, Carlomagno T, Ladurner AG. The histone chaperone sNASP binds a conserved peptide motif within the globular core of histone H3 through its TPR repeats. Nucleic Acids Res 2015; 44:3105-17. [PMID: 26673727 PMCID: PMC4838342 DOI: 10.1093/nar/gkv1372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/25/2015] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic chromatin is a complex yet dynamic structure, which is regulated in part by the assembly and disassembly of nucleosomes. Key to this process is a group of proteins termed histone chaperones that guide the thermodynamic assembly of nucleosomes by interacting with soluble histones. Here we investigate the interaction between the histone chaperone sNASP and its histone H3 substrate. We find that sNASP binds with nanomolar affinity to a conserved heptapeptide motif in the globular domain of H3, close to the C-terminus. Through functional analysis of sNASP homologues we identified point mutations in surface residues within the TPR domain of sNASP that disrupt H3 peptide interaction, but do not completely disrupt binding to full length H3 in cells, suggesting that sNASP interacts with H3 through additional contacts. Furthermore, chemical shift perturbations from(1)H-(15)N HSQC experiments show that H3 peptide binding maps to the helical groove formed by the stacked TPR motifs of sNASP. Our findings reveal a new mode of interaction between a TPR repeat domain and an evolutionarily conserved peptide motif found in canonical H3 and in all histone H3 variants, including CenpA and have implications for the mechanism of histone chaperoning within the cell.
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Affiliation(s)
- Andrew Bowman
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Lukas Lercher
- Leibniz University Hannover, BMWZ-Institute of Organic Chemistry, Schneiderberg 38, 30167 Hannover, Germany
| | - Hari R Singh
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Daria Zinne
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Gyula Timinszky
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, BMWZ-Institute of Organic Chemistry, Schneiderberg 38, 30167 Hannover, Germany Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany European Molecular Biology Laboratory, SCB Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandt Strasse 5-13, 81377 Munich, Germany Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Feodor Lynen Strasse 17, 81377 Munich, Germany
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Parseghian MH. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS BIOPHYSICS 2015; 2:724-772. [PMID: 31289748 PMCID: PMC6615755 DOI: 10.3934/biophy.2015.4.724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.
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Developmentally Regulated Post-translational Modification of Nucleoplasmin Controls Histone Sequestration and Deposition. Cell Rep 2015; 10:1735-1748. [PMID: 25772360 DOI: 10.1016/j.celrep.2015.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 01/09/2015] [Accepted: 02/13/2015] [Indexed: 11/23/2022] Open
Abstract
Nucleoplasmin (Npm) is an abundant histone chaperone in vertebrate oocytes and embryos. During embryogenesis, regulation of Npm histone binding is critical for its function in storing and releasing maternal histones to establish and maintain the zygotic epigenome. Here, we demonstrate that Xenopus laevis Npm post-translational modifications (PTMs) specific to the oocyte and egg promote either histone deposition or sequestration, respectively. Mass spectrometry and Npm phosphomimetic mutations used in chromatin assembly assays identified hyperphosphorylation on the N-terminal tail as a critical regulator for sequestration. C-terminal tail phosphorylation and PRMT5-catalyzed arginine methylation enhance nucleosome assembly by promoting histone interaction with the second acidic tract of Npm. Electron microscopy reconstructions of Npm and TTLL4 activity toward the C-terminal tail demonstrate that oocyte- and egg-specific PTMs cause Npm conformational changes. Our results reveal that PTMs regulate Npm chaperoning activity by modulating Npm conformation and Npm-histone interaction, leading to histone sequestration in the egg.
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Scieglinska D, Krawczyk Z. Expression, function, and regulation of the testis-enriched heat shock HSPA2 gene in rodents and humans. Cell Stress Chaperones 2015; 20:221-35. [PMID: 25344376 PMCID: PMC4326386 DOI: 10.1007/s12192-014-0548-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/03/2014] [Accepted: 10/09/2014] [Indexed: 12/29/2022] Open
Abstract
The HSPA2 gene is a poorly characterized member of the HSPA (HSP70) family. HSPA2 was originally described as testis-specific and expressed at the highest level in pachytene spermatocytes of rodents, the expression of which is not induced by heat shock. HSPA2 is crucial for male fertility. However, recent advances have shown that HSPA2 is expressed in various tumors and in certain types of somatic tissues. In this review, we summarize the current knowledge on the HSPA2 expression pattern, including information on transcriptional, translational, posttranslational, and epigenetic mechanisms which regulate HSPA2 expression. We also present and discuss the current views concerning the functions of the HSPA2 protein in spermatogenetic, somatic, and cancer cells. The knowledge of the properties of HSPA2, although limited, shows this protein as a unique member of the HSPA family. However, understanding whether this protein could become a relevant cancer biomarker or a therapeutically applicable target requires extensive further studies.
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Affiliation(s)
- Dorota Scieglinska
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-101, Gliwice, Poland,
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31
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Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
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Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
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Wang WL, Anderson LC, Nicklay JJ, Chen H, Gamble MJ, Shabanowitz J, Hunt DF, Shechter D. Phosphorylation and arginine methylation mark histone H2A prior to deposition during Xenopus laevis development. Epigenetics Chromatin 2014; 7:22. [PMID: 25302076 PMCID: PMC4191874 DOI: 10.1186/1756-8935-7-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/14/2014] [Indexed: 01/21/2023] Open
Abstract
Background Stored, soluble histones in eggs are essential for early development, in particular during the maternally controlled early cell cycles in the absence of transcription. Histone post-translational modifications (PTMs) direct and regulate chromatin-templated transactions, so understanding the nature and function of pre-deposition maternal histones is essential to deciphering mechanisms of regulation of development, chromatin assembly, and transcription. Little is known about histone H2A pre-deposition modifications nor known about the transitions that occur upon the onset of zygotic control of the cell cycle and transcription at the mid-blastula transition (MBT). Results We isolated histones from staged Xenopus laevis oocytes, eggs, embryos, and assembled pronuclei to identify changes in histone H2A modifications prior to deposition and in chromatin. Soluble and chromatin-bound histones from eggs and embryos demonstrated distinct patterns of maternal and zygotic H2A PTMs, with significant pre-deposition quantities of S1ph and R3me1, and R3me2s. We observed the first functional distinction between H2A and H4 S1 phosphorylation, as we showed that H2A and H2A.X-F (also known as H2A.X.3) serine 1 (S1) is phosphorylated concomitant with germinal vesicle breakdown (GVBD) while H4 serine 1 phosphorylation occurs post-MBT. In egg extract H2A/H4 S1 phosphorylation is independent of the cell cycle, chromatin assembly, and DNA replication. H2AS1ph is highly enriched on blastula chromatin during repression of zygotic gene expression while H4S1ph is correlated with the beginning of maternal gene expression and the lengthening of the cell cycle, consistent with distinct biological roles for H2A and H4 S1 phosphorylation. We isolated soluble H2A and H2A.X-F from the egg and chromatin-bound in pronuclei and analyzed them by mass spectrometry analysis to quantitatively determine abundances of S1ph and R3 methylation. We show that H2A and H4 S1ph, R3me1 and R3me2s are enriched on nucleosomes containing both active and repressive histone PTMs in human A549 cells and Xenopus embryos. Conclusions Significantly, we demonstrated that H2A phosphorylation and H4 arginine methylation form a new class of bona fide pre-deposition modifications in the vertebrate embryo. We show that S1ph and R3me containing chromatin domains are not correlated with H3 regulatory PTMs, suggesting a unique role for phosphorylation and arginine methylation.
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Affiliation(s)
- Wei-Lin Wang
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | - Lissa C Anderson
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - Joshua J Nicklay
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - Hongshan Chen
- Department of Molecular Pharmacology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | - Matthew J Gamble
- Department of Molecular Pharmacology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - Donald F Hunt
- Department of Chemistry, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA ; Department of Pathology, Health Sciences Center, University of Virginia, Charlottesville, VA 22904, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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Nabeel-Shah S, Ashraf K, Pearlman RE, Fillingham J. Molecular evolution of NASP and conserved histone H3/H4 transport pathway. BMC Evol Biol 2014; 14:139. [PMID: 24951090 PMCID: PMC4082323 DOI: 10.1186/1471-2148-14-139] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where some functional diversity has been reported. In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers. Although a comprehensive phylogenetic analysis is lacking, NASP-family proteins that possess four TPR motifs are thought to be widely distributed across eukaryotes. RESULTS We characterize the molecular evolution of NASP by systematically identifying putative NASP orthologs across diverse eukaryotic lineages ranging from excavata to those of the crown group. We detect extensive silent divergence at the nucleotide level suggesting the presence of strong purifying selection acting at the protein level. We also observe a selection bias for high frequencies of acidic residues which we hypothesize is a consequence of their critical function(s), further indicating the role of functional constraints operating on NASP evolution. Our data indicate that TPR1 and TPR4 constitute the most rapidly evolving functional units of NASP and may account for the functional diversity observed among well characterized family members. We also show that NASP paralogs in ray-finned fish have different genomic environments with clear differences in their GC content and have undergone significant changes at the protein level suggesting functional diversification. CONCLUSION We draw four main conclusions from this study. First, wide distribution of NASP throughout eukaryotes suggests that it was likely present in the last eukaryotic common ancestor (LECA) possibly as an important innovation in the transport of H3/H4. Second, strong purifying selection operating at the protein level has influenced the nucleotide composition of NASP genes. Further, we show that selection has acted to maintain a high frequency of functionally relevant acidic amino acids in the region that interrupts TPR2. Third, functional diversity reported among several well characterized NASP family members can be explained in terms of quickly evolving TPR1 and TPR4 motifs. Fourth, NASP fish specific paralogs have significantly diverged at the protein level with NASP2 acquiring a NNR domain.
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Affiliation(s)
| | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St,, Toronto M5B 2K3, Canada.
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Ramos I, Fernández-Rivero N, Arranz R, Aloria K, Finn R, Arizmendi JM, Ausió J, Valpuesta JM, Muga A, Prado A. The intrinsically disordered distal face of nucleoplasmin recognizes distinct oligomerization states of histones. Nucleic Acids Res 2013; 42:1311-25. [PMID: 24121686 PMCID: PMC3902905 DOI: 10.1093/nar/gkt899] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of Nucleoplasmin (NP) as a H2A-H2B histone chaperone has been extensively characterized. To understand its putative interaction with other histone ligands, we have characterized its ability to bind H3-H4 and histone octamers. We find that the chaperone forms distinct complexes with histones, which differ in the number of molecules that build the assembly and in their spatial distribution. When complexed with H3-H4 tetramers or histone octamers, two NP pentamers form an ellipsoidal particle with the histones located at the center of the assembly, in stark contrast with the NP/H2A-H2B complex that contains up to five histone dimers bound to one chaperone pentamer. This particular assembly relies on the ability of H3-H4 to form tetramers either in solution or as part of the octamer, and it is not observed when a variant of H3 (H3C110E), unable to form stable tetramers, is used instead of the wild-type protein. Our data also suggest that the distal face of the chaperone is involved in the interaction with distinct types of histones, as supported by electron microscopy analysis of the different NP/histone complexes. The use of the same structural region to accommodate all type of histones could favor histone exchange and nucleosome dynamics.
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Affiliation(s)
- Isbaal Ramos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del PaísVasco, P. O. Box 644, 48080 Bilbao, Spain, Unidad de Biofísica (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barrio Sarriena s/n, 48080 Leioa Spain, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain and Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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Expression of Tra2 β in Cancer Cells as a Potential Contributory Factor to Neoplasia and Metastasis. Int J Cell Biol 2013; 2013:843781. [PMID: 23935626 PMCID: PMC3723085 DOI: 10.1155/2013/843781] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/09/2013] [Indexed: 01/17/2023] Open
Abstract
The splicing regulator proteins SRSF1 (also known as ASF/SF2) and SRSF3 (also known as SRP20) belong to the SR family of proteins and can be upregulated in cancer. The SRSF1 gene itself is amplified in some cancer cells, and cancer-associated changes in the expression of MYC also increase SRSF1 gene expression. Increased concentrations of SRSF1 protein promote prooncogenic splicing patterns of a number of key regulators of cell growth. Here, we review the evidence that upregulation of the SR-related Tra2β protein might have a similar role in cancer cells. The TRA2B gene encoding Tra2β is amplified in particular tumours including those of the lung, ovary, cervix, stomach, head, and neck. Both TRA2B RNA and Tra2β protein levels are upregulated in breast, cervical, ovarian, and colon cancer, and Tra2β expression is associated with cancer cell survival. The TRA2B gene is a transcriptional target of the protooncogene ETS-1 which might cause higher levels of expression in some cancer cells which express this transcription factor. Known Tra2β splicing targets have important roles in cancer cells, where they affect metastasis, proliferation, and cell survival. Tra2β protein is also known to interact directly with the RBMY protein which is implicated in liver cancer.
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