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Yang WL, Zhang WF, Wang Y, Lou Y, Cai Y, Zhu J. Origin recognition complex 6 overexpression promotes growth of glioma cells. Cell Death Dis 2024; 15:485. [PMID: 38971772 PMCID: PMC11227543 DOI: 10.1038/s41419-024-06764-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024]
Abstract
The discovery of novel oncotargets for glioma is of immense significance. We here explored the expression patterns, biological functions, and underlying mechanisms associated with ORC6 (origin recognition complex 6) in glioma. Through the bioinformatics analyses, we found a significant increase in ORC6 expression within human glioma tissues, correlating with poorer overall survival, higher tumor grade, and wild-type isocitrate dehydrogenase status. Additionally, ORC6 overexpression is detected in glioma tissues obtained from locally-treated patients and across various primary/established glioma cells. Further bioinformatics scrutiny revealed that genes co-expressed with ORC6 are enriched in multiple signaling cascades linked to cancer. In primary and immortalized (A172) glioma cells, depleting ORC6 using specific shRNA or Cas9-sgRNA knockout (KO) significantly decreased cell viability and proliferation, disrupted cell cycle progression and mobility, and triggered apoptosis. Conversely, enhancing ORC6 expression via a lentiviral construct augmented malignant behaviors in human glioma cells. ORC6 emerged as a crucial regulator for the expression of key oncogenic genes, including Cyclin A2, Cyclin B2, and DNA topoisomerase II (TOP2A), within glioma cells. Silencing or KO of ORC6 reduced the mRNA and protein levels of these genes, while overexpression of ORC6 increased their expression in primary glioma cells. Bioinformatics analyses further identified RBPJ as a potential transcription factor of ORC6. RBPJ shRNA decreased ORC6 expression in primary glioma cells, while its overexpression increased it. Additionally, significantly enhanced binding between the RBPJ protein and the proposed ORC6 promoter region was detected in glioma tissues and cells. In vivo experiments demonstrated a significant reduction in the growth of patient-derived glioma xenografts in the mouse brain subsequent to ORC6 KO. ORC6 depletion, inhibited proliferation, decreased expression of Cyclin A2/B2/TOP2A, and increased apoptosis were detected within these ORC6 KO intracranial glioma xenografts. Altogether, RBPJ-driven ORC6 overexpression promotes glioma cell growth, underscoring its significance as a promising therapeutic target.
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Affiliation(s)
- Wen-Lei Yang
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Feng Zhang
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yin Wang
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Yue Lou
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Cai
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Zhu
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Chen L, Zhang D, Chen Y, Zhu H, Liu Z, Yu Z, Xie J. ORC6 acts as an effective prognostic predictor for non‑small cell lung cancer and is closely associated with tumor progression. Oncol Lett 2024; 27:96. [PMID: 38288041 PMCID: PMC10823314 DOI: 10.3892/ol.2024.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
Origin recognition complexes (ORCs) are vital in the control of DNA replication and the progression of the cell cycle, however the precise function and mechanism of ORC6 in non-small cell lung cancer (NSCLC) is still not well understood. The present study used bioinformatics methods to assess the predictive significance of ORC6 expression in NSCLC. Moreover, the expression of ORC6 was further evaluated using reverse transcription-quantitative PCR and western blotting, and its functional significance in lung cancer was assessed via knockdown experiments using small interfering RNA. A significant association was demonstrated between the expression of ORC6 and the clinical features of NSCLC. In particular, elevated levels of ORC6 were significantly strongly correlated with an unfavorable prognosis. Multivariate analysis demonstrated that increased ORC6 expression independently contributed to the risk of overall survival (HR 1.304; P=0.015) in individuals diagnosed with NSCLC. Analysis of Kaplan-Meier plots demonstrated that ORC6 expression served as a valuable indicator for diagnosing and predicting the prognosis of NSCLC. Moreover, in vitro studies demonstrated that modified ORC6 expression had a significant impact on the proliferation, migration and metastasis of NSCLC cells. NSCLC cell lines (H1299 and mH1650) exhibited markedly higher ORC6 expression than normal lung cell lines. The results of the present study indicated a strong association between the expression of ORC6 and the clinicopathological characteristics of NSCLC, which suggested its potential as a reliable biomarker for predicting NSCLC. Furthermore, ORC6 may have important therapeutic implications in the management of NSCLC.
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Affiliation(s)
- Letian Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Dongdong Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Yujuan Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Huilan Zhu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Zhipeng Liu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Zhiping Yu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Junping Xie
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
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Liu SW, Luo JQ, Zhao LY, Ou NJ, Chao-Yang, Zhang YX, Bai HW, Sun HF, Zhang JX, Yao CC, Li P, Tian RH, Li Z, Zhu ZJ. scRNA-seq reveals that origin recognition complex subunit 6 regulates mouse spermatogonial cell proliferation and apoptosis via activation of Wnt/β-catenin signaling. Asian J Androl 2024; 26:46-56. [PMID: 37788012 PMCID: PMC10846824 DOI: 10.4103/aja202330] [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: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 10/04/2023] Open
Abstract
The regulation of spermatogonial proliferation and apoptosis is of great significance for maintaining spermatogenesis. The single-cell RNA sequencing (scRNA-seq) analysis of the testis was performed to identify genes upregulated in spermatogonia. Using scRNA-seq analysis, we identified the spermatogonia upregulated gene origin recognition complex subunit 6 ( Orc6 ), which is involved in DNA replication and cell cycle regulation; its protein expression in the human and mouse testis was detected by western blot and immunofluorescence. To explore the potential function of Orc6 in spermatogonia, the C18-4 cell line was transfected with control or Orc6 siRNA. Subsequently, 5-ethynyl-2-deoxyuridine (EdU) and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assays, flow cytometry, and western blot were used to evaluate its effects on proliferation and apoptosis. It was revealed that ORC6 could promote proliferation and inhibit apoptosis of C18-4 cells. Bulk RNA sequencing and bioinformatics analysis indicated that Orc6 was involved in the activation of wingless/integrated (Wnt)/β-catenin signaling. Western blot revealed that the expression of β-catenin protein and its phosphorylation (Ser675) were significantly decreased when silencing the expression of ORC6. Our findings indicated that Orc6 was upregulated in spermatogonia, whereby it regulated proliferation and apoptosis by activating Wnt/β-catenin signaling.
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Affiliation(s)
- Shi-Wei Liu
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Jia-Qiang Luo
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Liang-Yu Zhao
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Ning-Jing Ou
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Chao-Yang
- Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yu-Xiang Zhang
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hao-Wei Bai
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hong-Fang Sun
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Jian-Xiong Zhang
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Chen-Cheng Yao
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Peng Li
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Ru-Hui Tian
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zheng Li
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zi-Jue Zhu
- Department of Andrology, Center for Men’s Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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Lin YC, Liu D, Chakraborty A, Macias V, Brister E, Sonalkar J, Shen L, Mitra J, Ha T, Kajdacsy-Balla A, Prasanth KV, Prasanth SG. DNA Damage-Induced, S-Phase Specific Phosphorylation of Orc6 is Critical for the Maintenance of Genome Stability. Mol Cell Biol 2023; 43:143-156. [PMID: 37096556 PMCID: PMC10153009 DOI: 10.1080/10985549.2023.2196204] [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: 10/07/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 04/26/2023] Open
Abstract
The smallest subunit of the human Origin Recognition Complex, hOrc6, is required for DNA replication progression and plays an important role in mismatch repair (MMR) during S-phase. However, the molecular details of how hOrc6 regulates DNA replication and DNA damage response remain to be elucidated. Orc6 levels are elevated upon specific types of genotoxic stress, and it is phosphorylated at Thr229, predominantly during S-phase, in response to oxidative stress. Many repair pathways, including MMR, mediate oxidative DNA damage repair. Defects in MMR are linked to Lynch syndrome, predisposing patients to many cancers, including colorectal cancer. Orc6 levels are known to be elevated in colorectal cancers. Interestingly, tumor cells show reduced hOrc6-Thr229 phosphorylation compared to adjacent normal mucosa. Further, elevated expression of wild-type and the phospho-dead forms of Orc6 results in increased tumorigenicity, implying that in the absence of this "checkpoint" signal, cells proliferate unabated. Based on these results, we propose that DNA-damage-induced hOrc6-pThr229 phosphorylation during S-phase facilitates ATR signaling in the S-phase, halts fork progression, and enables assembly of repair factors to mediate efficient repair to prevent tumorigenesis. Our study provides novel insights into how hOrc6 regulates genome stability.
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Affiliation(s)
- Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dazhen Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Virgilia Macias
- Research Tissue Imaging Core, Department of Pathology, University of Illinois, Chicago, Illinois, USA
| | - Eileen Brister
- Research Tissue Imaging Core, Department of Pathology, University of Illinois, Chicago, Illinois, USA
| | - Jay Sonalkar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Linyuan Shen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jaba Mitra
- Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taekjip Ha
- Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andre Kajdacsy-Balla
- Research Tissue Imaging Core, Department of Pathology, University of Illinois, Chicago, Illinois, USA
| | - Kannanganattu V. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, UIUC, Urbana, Illinois, USA
| | - Supriya G. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, UIUC, Urbana, Illinois, USA
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Liu D, Sonalkar J, Prasanth SG. ORChestra coordinates the replication and repair music. Bioessays 2023; 45:e2200229. [PMID: 36811379 PMCID: PMC10023367 DOI: 10.1002/bies.202200229] [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: 11/29/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
Error-free genome duplication and accurate cell division are critical for cell survival. In all three domains of life, bacteria, archaea, and eukaryotes, initiator proteins bind replication origins in an ATP-dependent manner, play critical roles in replisome assembly, and coordinate cell-cycle regulation. We discuss how the eukaryotic initiator, Origin recognition complex (ORC), coordinates different events during the cell cycle. We propose that ORC is the maestro driving the orchestra to coordinately perform the musical pieces of replication, chromatin organization, and repair.
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Affiliation(s)
- Dazhen Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
| | - Jay Sonalkar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
| | - Supriya G. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
- Cancer center at Illinois, UIUC
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Meier-Gorlin Syndrome: Clinical Misdiagnosis, Genetic Testing and Functional Analysis of ORC6 Mutations and the Development of a Prenatal Test. Int J Mol Sci 2022; 23:ijms23169234. [PMID: 36012502 PMCID: PMC9408996 DOI: 10.3390/ijms23169234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Meier−Gorlin syndrome (MGS) is a rare genetic developmental disorder that causes primordial proportional dwarfism, microtia, the absence of or hypoplastic patellae and other skeletal anomalies. Skeletal symptoms overlapping with other syndromes make MGS difficult to diagnose clinically. We describe a 3-year-old boy with short stature, recurrent respiratory infections, short-rib dysplasia, tower head and facial dysmorphisms who was admitted to the Tomsk Genetic Clinic to verify a clinical diagnosis of Jeune syndrome. Clinical exome sequencing revealed two variants (compound heterozygosity) in the ORC6 gene: c.2T>C(p.Met1Thr) and c.449+5G>A. In silico analysis showed the pathogenicity of these two mutations and predicted a decrease in donor splicing site strength for c.449+5G>A. An in vitro minigene assay indicated that variant c.449+5G>A causes complete skipping of exon 4 in the ORC6 gene. The parents requested urgent prenatal testing for MGS for the next pregnancy, but it ended in a miscarriage. Our results may help prevent MGS misdiagnosis in the future. We also performed in silico and functional analyses of ORC6 mutations and developed a restriction fragment length polymorphism and haplotype-based short-tandem-repeat assay for prenatal genetic testing for MGS. These findings should elucidate MGS etiology and improve the quality of genetic counselling for affected families.
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Orc6 is a component of the replication fork and enables efficient mismatch repair. Proc Natl Acad Sci U S A 2022; 119:e2121406119. [PMID: 35622890 DOI: 10.1073/pnas.2121406119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance Origin recognition complex (ORC) is required for the initiation of DNA replication. Unlike other ORC components, the role of human Orc6 in replication remains to be resolved. We identified an unexpected role for hOrc6, which is to promote S-phase progression after prereplication complex assembly and DNA damage response. Orc6 localizes at the replication fork, is an accessory factor of the mismatch repair complex, and plays a fundamental role in genome surveillance during S phase.
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Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F. A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Nat Commun 2022; 13:1059. [PMID: 35217664 PMCID: PMC8881611 DOI: 10.1038/s41467-022-28695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/04/2022] [Indexed: 11/10/2022] Open
Abstract
The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to DNA initiates the ATP-dependent recruitment of Cdc6, Cdt1 and Mcm2-7 loading, but the structural details for timely ATPase site regulation and for how loading can be impeded by inhibitory signals, such as cyclin-dependent kinase phosphorylation, are unknown. Using cryo-electron microscopy, we have determined several structures of S. cerevisiae ORC·DNA·Cdc6 intermediates at 2.5-2.7 Å resolution. These structures reveal distinct ring conformations of the initiator·co-loader assembly and inactive ATPase site configurations for ORC and Cdc6. The Orc6 N-terminal domain laterally engages the ORC·Cdc6 ring in a manner that is incompatible with productive Mcm2-7 docking, while deletion of this Orc6 region alleviates the CDK-mediated inhibition of Mcm7 recruitment. Our findings support a model in which Orc6 promotes the assembly of an autoinhibited ORC·DNA·Cdc6 intermediate to block origin licensing in response to CDK phosphorylation and to avert DNA re-replication.
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Affiliation(s)
- Jan Marten Schmidt
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland
- University of Basel, Basel, 4051, Switzerland
- Novartis Institutes for Biomedical Research, Basel, 4033, Switzerland
| | - Ran Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ashish Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Olivia Hunker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland
| | - Franziska Bleichert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
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Investigation of the Interaction of Human Origin Recognition Complex Subunit 1 with G-Quadruplex DNAs of Human c-myc Promoter and Telomere Regions. Int J Mol Sci 2021; 22:ijms22073481. [PMID: 33801762 PMCID: PMC8036949 DOI: 10.3390/ijms22073481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Origin recognition complex (ORC) binds to replication origins in eukaryotic DNAs and plays an important role in replication. Although yeast ORC is known to sequence-specifically bind to a replication origin, how human ORC recognizes a replication origin remains unknown. Previous genome-wide studies revealed that guanine (G)-rich sequences, potentially forming G-quadruplex (G4) structures, are present in most replication origins in human cells. We previously suggested that the region comprising residues 413–511 of human ORC subunit 1, hORC1413–511, binds preferentially to G-rich DNAs, which form a G4 structure in the absence of hORC1413–511. Here, we investigated the interaction of hORC1413-511 with various G-rich DNAs derived from human c-myc promoter and telomere regions. Fluorescence anisotropy revealed that hORC1413–511 binds preferentially to DNAs that have G4 structures over ones having double-stranded structures. Importantly, circular dichroism (CD) and nuclear magnetic resonance (NMR) showed that those G-rich DNAs retain the G4 structures even after binding with hORC1413–511. NMR chemical shift perturbation analyses revealed that the external G-tetrad planes of the G4 structures are the primary binding sites for hORC1413–511. The present study suggests that human ORC1 may recognize replication origins through the G4 structure.
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Chou HC, Bhalla K, Demerdesh OE, Klingbeil O, Hanington K, Aganezov S, Andrews P, Alsudani H, Chang K, Vakoc CR, Schatz MC, McCombie WR, Stillman B. The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure. eLife 2021; 10:61797. [PMID: 33522487 PMCID: PMC7877914 DOI: 10.7554/elife.61797] [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: 08/05/2020] [Accepted: 01/30/2021] [Indexed: 12/23/2022] Open
Abstract
The origin recognition complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre-RC complexes at origins of DNA replication. Here, using tiling-sgRNA CRISPR screens, we report that each subunit of ORC and CDC6 is essential in human cells. Using an auxin-inducible degradation system, we created stable cell lines capable of ablating ORC2 rapidly, revealing multiple cell division cycle phenotypes. The primary defects in the absence of ORC2 were cells encountering difficulty in initiating DNA replication or progressing through the cell division cycle due to reduced MCM2-7 loading onto chromatin in G1 phase. The nuclei of ORC2-deficient cells were also large, with decompacted heterochromatin. Some ORC2-deficient cells that completed DNA replication entered into, but never exited mitosis. ORC1 knockout cells also demonstrated extremely slow cell proliferation and abnormal cell and nuclear morphology. Thus, ORC proteins and CDC6 are indispensable for normal cellular proliferation and contribute to nuclear organization.
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Affiliation(s)
- Hsiang-Chen Chou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, United States
| | - Kuhulika Bhalla
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Sergey Aganezov
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Habeeb Alsudani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Michael C Schatz
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | | | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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12
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Expansion and Functional Diversification of TFIIB-Like Factors in Plants. Int J Mol Sci 2021; 22:ijms22031078. [PMID: 33498602 PMCID: PMC7865254 DOI: 10.3390/ijms22031078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
As sessile organisms, plants have evolved unique patterns of growth and development, elaborate metabolism and special perception and signaling mechanisms to environmental cues. Likewise, plants have complex and highly special programs for transcriptional control of gene expression. A case study for the special transcription control in plants is the expansion of general transcription factors, particularly the family of Transcription Factor IIB (TFIIB)-like factors with 15 members in Arabidopsis. For more than a decade, molecular and genetic analysis has revealed important functions of these TFIIB-like factors in specific biological processes including gametogenesis, pollen tube growth guidance, embryogenesis, endosperm development, and plant-microbe interactions. The redundant, specialized, and diversified roles of these TFIIB-like factors challenge the traditional definition of general transcription factors established in other eukaryotes. In this review, we discuss general transcription factors in plants with a focus on the expansion and functional analysis of plant TFIIB-like proteins to highlight unique aspects of plant transcription programs that can be highly valuable for understanding the molecular basis of plant growth, development and responses to stress conditions.
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Prospect of reprogramming replication licensing for cancer drug development. Biomed Pharmacother 2021; 136:111190. [PMID: 33497909 DOI: 10.1016/j.biopha.2020.111190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic chromosomal DNA replication is preceded by replication licensing which involves the identification of the origin of replication by origin recognition complex (ORC). The ORC loads pre-replication complexes (pre-RCs) through a series of tightly regulated mechanisms where the ORC interacts with Cdc6 to recruit cdt1-MCM2-7 complexes to the origin of replication. In eukaryotes, adherence to regulatory mechanisms of the replication program is required to ensure that all daughter cells carry the exact copy of genetic material as the parent cell. Failure of which leads to the development of genome instability syndromes like cancer, diabetes, etc. In an event of such occurrence, preventing cells from carrying the defaulted genetic material and passing it to other cells hinges on the regulation of chromosomal DNA replication. Thus, understanding the mechanisms underpinning chromosomal DNA replication and particularly replication licensing can expose druggable enzymes, effector molecules, and secondary messengers that can be targeted for diagnosis and therapeutic purposes. Effectively drugging these molecular markers to reprogram pre-replication events can be used to control the fate of chromosomal DNA replication for the treatment of genome instability disorders and in this case, cancer. This review discusses available knowledge of replication licensing in the contest of molecular drug discovery for the treatment of cancer.
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