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Abstract
Formation of the 3' end of a eukaryotic mRNA is a key step in the production of a mature transcript. This process is mediated by a number of protein factors that cleave the pre-mRNA, add a poly(A) tail, and regulate transcription by protein dephosphorylation. Cleavage and polyadenylation specificity factor (CPSF) in humans, or cleavage and polyadenylation factor (CPF) in yeast, coordinates these enzymatic activities with each other, with RNA recognition, and with transcription. The site of pre-mRNA cleavage can strongly influence the translation, stability, and localization of the mRNA. Hence, cleavage site selection is highly regulated. The length of the poly(A) tail is also controlled to ensure that every transcript has a similar tail when it is exported from the nucleus. In this review, we summarize new mechanistic insights into mRNA 3'-end processing obtained through structural studies and biochemical reconstitution and outline outstanding questions in the field.
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Affiliation(s)
- Vytautė Boreikaitė
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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2
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Russell BL, Ntwasa M. Expression, purification, and characterisation of the p53 binding domain of Retinoblastoma binding protein 6 (RBBP6). PLoS One 2023; 18:e0277478. [PMID: 36763571 PMCID: PMC9916574 DOI: 10.1371/journal.pone.0277478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2023] Open
Abstract
RBBP6 is a 250 kDa eukaryotic protein known to be a negative regulator of p53 and essential for embryonic development. Furthermore, RBBP6 is a critical element in carcinogenesis and has been identified as a potential biomarker for certain cancers. RBBP6's ability to interact with p53 and cause its degradation makes it a potential drug target in cancer therapy. Therefore, a better understating of the p53 binding domain of RBBP6 is needed. This study presents a three-part purification protocol for the polyhistidine-tagged p53 binding domain of RBBP6, expressed in Escherichia coli bacterial cells. The purified recombinant domain was shown to have structure and is functional as it could bind endogenous p53. We characterized it using clear native PAGE and far-UV CD and found that it exists in a single form, most likely monomer. We predict that its secondary structure is predominantly random coil with 19% alpha-helices, 9% beta-strand and 14% turns. When we exposed the recombinant domain to increasing temperature or known denaturants, our investigation suggested that the domain undergoes relatively small structural changes, especially with increased temperature. Moreover, we notice a high percentage recovery after returning the domain close to starting conditions. The outcome of this study is a pure, stable, and functional recombinant RBBP6-p53BD that is primarily intrinsically disordered.
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Affiliation(s)
- Bonnie L. Russell
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Roodepoort, South Africa
- Innovation Hub, Buboo (Pty) Ltd, Pretoria, South Africa
| | - Monde Ntwasa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Roodepoort, South Africa
- * E-mail:
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3
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Zhai F, Wang J, Yang W, Ye M, Jin X. The E3 Ligases in Cervical Cancer and Endometrial Cancer. Cancers (Basel) 2022; 14:5354. [PMID: 36358773 PMCID: PMC9658772 DOI: 10.3390/cancers14215354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 07/28/2023] Open
Abstract
Endometrial (EC) and cervical (CC) cancers are the most prevalent malignancies of the female reproductive system. There is a global trend towards increasing incidence and mortality, with a decreasing age trend. E3 ligases label substrates with ubiquitin to regulate their activity and stability and are involved in various cellular functions. Studies have confirmed abnormal expression or mutations of E3 ligases in EC and CC, indicating their vital roles in the occurrence and progression of EC and CC. This paper provides an overview of the E3 ligases implicated in EC and CC and discusses their underlying mechanism. In addition, this review provides research advances in the target of ubiquitination processes in EC and CC.
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Affiliation(s)
- Fengguang Zhai
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jie Wang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Weili Yang
- Department of Gynecology, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
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4
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Spada S, Luke B, Danckwardt S. The Bidirectional Link Between RNA Cleavage and Polyadenylation and Genome Stability: Recent Insights From a Systematic Screen. Front Genet 2022; 13:854907. [PMID: 35571036 PMCID: PMC9095915 DOI: 10.3389/fgene.2022.854907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The integrity of the genome is governed by multiple processes to ensure optimal survival and to prevent the inheritance of deleterious traits. While significant progress has been made to characterize components involved in the DNA Damage Response (DDR), little is known about the interplay between RNA processing and the maintenance of genome stability. Here, we describe the emerging picture of an intricate bidirectional coupling between RNA processing and genome integrity in an integrative manner. By employing insights from a recent large-scale RNAi screening involving the depletion of more than 170 components that direct (alternative) polyadenylation, we provide evidence of bidirectional crosstalk between co-transcriptional RNA 3′end processing and the DDR in a manner that optimizes genomic integrity. We provide instructive examples illustrating the wiring between the two processes and show how perturbations at one end are either compensated by buffering mechanisms at the other end, or even propel the initial insult and thereby become disease-eliciting as evidenced by various disorders.
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Affiliation(s)
- Stefano Spada
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Centre for Healthy Aging (CHA) Mainz, Mainz, Germany
- *Correspondence: Sven Danckwardt,
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5
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RBBP6 activates the pre-mRNA 3' end processing machinery in humans. Genes Dev 2022; 36:210-224. [PMID: 35177536 PMCID: PMC8887125 DOI: 10.1101/gad.349223.121] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
Abstract
In this study, Boreikaite et al. reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. 3′ end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3′ end of the mature transcript, which is important for mRNA localization, translation, and stability. Cleavage must therefore be tightly regulated. Here, we reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. Unlike its yeast homolog Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to humans. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in mRNA processing.
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Mabonga L, Masamba P, Kappo AP. Inhibitory potential of a benzoxazole derivative, 4FI against SNRPG∼RING finger domain protein complex as a lead compound in the discovery of anti-cancer drugs: A molecular dynamics simulation approach. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Zhang Y, Liu L, Qiu Q, Zhou Q, Ding J, Lu Y, Liu P. Alternative polyadenylation: methods, mechanism, function, and role in cancer. J Exp Clin Cancer Res 2021; 40:51. [PMID: 33526057 PMCID: PMC7852185 DOI: 10.1186/s13046-021-01852-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Occurring in over 60% of human genes, alternative polyadenylation (APA) results in numerous transcripts with differing 3'ends, thus greatly expanding the diversity of mRNAs and of proteins derived from a single gene. As a key molecular mechanism, APA is involved in various gene regulation steps including mRNA maturation, mRNA stability, cellular RNA decay, and protein diversification. APA is frequently dysregulated in cancers leading to changes in oncogenes and tumor suppressor gene expressions. Recent studies have revealed various APA regulatory mechanisms that promote the development and progression of a number of human diseases, including cancer. Here, we provide an overview of four types of APA and their impacts on gene regulation. We focus particularly on the interaction of APA with microRNAs, RNA binding proteins and other related factors, the core pre-mRNA 3'end processing complex, and 3'UTR length change. We also describe next-generation sequencing methods and computational tools for use in poly(A) signal detection and APA repositories and databases. Finally, we summarize the current understanding of APA in cancer and provide our vision for future APA related research.
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Affiliation(s)
- Yi Zhang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Lian Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Qiongzi Qiu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Qing Zhou
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Jinwang Ding
- Department of Head and Neck Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, Zhejiang, China.
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310029, Zhejiang, China.
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China.
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Cancer Center, Zhejiang University, Hangzhou, 310029, Zhejiang, China.
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RBBP6 interactome: RBBP6 isoform 3/DWNN and Nek6 interaction is critical for cell cycle regulation and may play a role in carcinogenesis. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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9
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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10
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Wang QS, Wei SR, Xiao HL. RBBP6 induces non-small cell lung cancer cell proliferation and high expression is associated with poor prognosis. Oncol Lett 2020; 19:2895-2901. [PMID: 32218844 PMCID: PMC7068609 DOI: 10.3892/ol.2020.11403] [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: 04/08/2019] [Accepted: 01/07/2020] [Indexed: 12/02/2022] Open
Abstract
Lung cancer is the most common cause of cancer-associated mortality in China with 85% of patients having non-small cell lung cancer (NSCLC). Identifying NSCLC driver genes and prognostic markers is critical to reducing these numbers. The studies of retinoblastoma binding protein 6 (RBBP6) performed on NSCLC is limited. The present study aimed to investigate the molecular function and the prognostic potential of RBBP6 in NSCLC using the A549 cell line and patient samples, respectively. The functional effect on cancer cell proliferation and prognostic value of RBBP6 were examined in vitro and in vivo using reverse transcription-quantitative PCR, immunofluorescence, immunohistochemistry (IHC) and xenograft implantation. The results demonstrated that RBBP6 mRNA expression was significantly higher in NSCLC tissues compared with in adjacent normal samples. When RBBP6 mRNA expression was interfered with using short hairpin RNA, A549 cell proliferation and xenograft tumor growth were reduced. Additionally, IHC and survival analysis demonstrated that patients with NSCLC with high expression levels of RBBP6 had a shorter median overall survival time compared with patients with low RBBP6 expression (31 vs. 51.5 months), and this was more prominent in stage I–II patients (43 vs. >67 months). High expression levels of RBBP6 indicated poor prognosis in patients with NSCLC. This may be due to the ability of RBBP6 to promote cancer cell proliferation. RBBP6 may be a potential prognostic biomarker and a therapeutic target for NSCLC.
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Affiliation(s)
- Qiu-Shi Wang
- Department of Pathology, Daping Hospital and Research Institute of Surgery, Army Medical University, Chongqing 400042, P.R. China.,Department of Clinical Biobank, Daping Hospital and Research Institute of Surgery, Army Medical University, Chongqing 400042, P.R. China
| | - Shi-Rong Wei
- Department of Pathology, Daping Hospital and Research Institute of Surgery, Army Medical University, Chongqing 400042, P.R. China
| | - Hua-Liang Xiao
- Department of Pathology, Daping Hospital and Research Institute of Surgery, Army Medical University, Chongqing 400042, P.R. China
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11
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RBBP6, a RING finger-domain E3 ubiquitin ligase, induces epithelial-mesenchymal transition and promotes metastasis of colorectal cancer. Cell Death Dis 2019; 10:833. [PMID: 31685801 PMCID: PMC6828677 DOI: 10.1038/s41419-019-2070-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022]
Abstract
RBBP6 has been implicated in tumorigenesis but its role in tumor metastasis and progression has not been evaluated. Interestingly, here we show that RBBP6 is upregulated in colorectal cancer (CRC) where its expression level is positively correlated with distant metastasis. In this study, we identified RBBP6, a RING Finger-domain E3 ubiquitin ligase, served as an independent prognostic factor and predicted poor outcome for CRC patients. RBBP6 promoted cell proliferation, migration, and invasion in CRC cells and promoted tumor growth, lung metastasis, and liver metastasis in mouse models. Mechanistically, we revealed that RBBP6 bound and ubiquitylated IκBα, an inhibitor of the NF-κB-signaling pathway. RBBP6-mediated ubiquitination and degradation of IκBα significantly enhanced p65 nuclear translocation, which triggered the activation of NF-κB pathway and then induced the epithelial–mesenchymal transition (EMT) process and cell metastasis. Furthermore, by DNA methylation results and ChIP analysis, we demonstrated that the promoter of RBBP6 was hypomethylated, and was activated by multi-oncogenic transcription factors. In conclusion, our findings suggest that RBBP6 may be a potential prognostic biomarker and therapeutic target for CRC invasion and metastasis.
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12
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1571. [PMID: 31657151 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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13
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Yuan F, Hankey W, Wagner EJ, Li W, Wang Q. Alternative polyadenylation of mRNA and its role in cancer. Genes Dis 2019; 8:61-72. [PMID: 33569514 PMCID: PMC7859462 DOI: 10.1016/j.gendis.2019.10.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3′ end of RNA polymerase II transcripts from over 60% of human genes. APA is derived from the existence of multiple polyadenylation signals (PAS) within the same transcript, and results in the differential inclusion of sequence information at the 3′ end. While APA can occur between two PASs allowing for generation of transcripts with distinct coding potential from a single gene, most APA occurs within the untranslated region (3′UTR) and changes the length and content of these non-coding sequences. APA within the 3′UTR can have tremendous impact on its regulatory potential of the mRNA through a variety of mechanisms, and indeed this layer of gene expression regulation has profound impact on processes vital to cell growth and development. Recent studies have particularly highlighted the importance of APA dysregulation in cancer onset and progression. Here, we review the current knowledge of APA and its impacts on mRNA stability, translation, localization and protein localization. We also discuss the implications of APA dysregulation in cancer research and therapy.
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Affiliation(s)
- Fuwen Yuan
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - William Hankey
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.,Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University School of Medicine, Durham, NC, 27710, USA
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14
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Abstract
Retinoblastoma binding protein 6 (RBBP6) is a cancer-related protein that has been implicated in the regulation of cell cycle and apoptosis. RBBP6 isoform 1 has been demonstrated to interact with two tumour suppressors, p53 and pRB. Isoform 1 been shown to regulate p53 through its ubiquitin ligase activity, thus implicating in cell cycle regulation and apoptosis. Isoforms 1 and 2 are multidomain proteins containing a domain with no name (DWNN) domain, a Zinc Finger, a RING Finger, an Rb-binding domain and a p53-binding domain. The RBBP6 isoform 3 comprises the DWNN domain only. Isoform 4 lacks the Rb-binding domain but its role is less understood. RBBP6 isoform 3 has been reported as a cell cycle regulator with anticancer potential. There have been several studies that have clearly demonstrated that RBBP6 may be an important biomarker for cancer diagnosis and a potential drug target for cancer treatment. This work focused on differential expression of RBBP6 transcripts in different cancers, providing detailed analysis of their potential as diagnostic biomarkers for different cancers. These cancers include breast, liver, cervical and colon carcinomas. The expression of RBBP6 transcripts may further provide better understanding of the role of the RBBP6 in carcinogenesis and cell homeostasis.
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15
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Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ. Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell 2018; 175:1917-1930.e13. [PMID: 30550789 PMCID: PMC6366944 DOI: 10.1016/j.cell.2018.08.044] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/17/2018] [Accepted: 08/17/2018] [Indexed: 01/21/2023]
Abstract
Ebola virus (EBOV) infection often results in fatal illness in humans, yet little is known about how EBOV usurps host pathways during infection. To address this, we used affinity tag-purification mass spectrometry (AP-MS) to generate an EBOV-host protein-protein interaction (PPI) map. We uncovered 194 high-confidence EBOV-human PPIs, including one between the viral transcription regulator VP30 and the host ubiquitin ligase RBBP6. Domain mapping identified a 23 amino acid region within RBBP6 that binds to VP30. A crystal structure of the VP30-RBBP6 peptide complex revealed that RBBP6 mimics the viral nucleoprotein (NP) binding to the same interface of VP30. Knockdown of endogenous RBBP6 stimulated viral transcription and increased EBOV replication, whereas overexpression of either RBBP6 or the peptide strongly inhibited both. These results demonstrate the therapeutic potential of biologics that target this interface and identify additional PPIs that may be leveraged for novel therapeutic strategies.
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Affiliation(s)
- Jyoti Batra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Dandan Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Olena Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Laura Satkamp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Toni M Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel I Small
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Eusondia Arnett
- Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Ann Reyes
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Robyn Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Paige Haas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Carson B Schmidt
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Douglas J LaCount
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
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16
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Teng F, Ruan HJ, Xu J, Ni J, Qian B, Shen R, Gao LJ. RBBP6 promotes human cervical carcinoma malignancy via JNK signaling pathway. Biomed Pharmacother 2018; 101:399-405. [DOI: 10.1016/j.biopha.2018.02.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 02/08/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023] Open
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Varghese VK, Shukla V, Kabekkodu SP, Pandey D, Satyamoorthy K. DNA methylation regulated microRNAs in human cervical cancer. Mol Carcinog 2017; 57:370-382. [PMID: 29077234 DOI: 10.1002/mc.22761] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 01/19/2023]
Abstract
Regulation of miRNA gene expression by DNA promoter methylation may represent a key mechanism to drive cervical cancer progression. In order to understand the impact of DNA promoter methylation on miRNAs at various stages of cervical carcinogenesis, we performed DNA methylation microarray on Normal Cervical Epithelium (NCE), Cervical Intraepithelial Neoplasia (CIN I-III) and Squamous Cell Carcinoma (SCC) tissues to identify differentially methylated miRNAs followed by validation by bisulfite sequencing. Further, expression of miRNAs was analyzed by qRT-PCR in clinical tissues and cervical cancer cell lines. Transcriptional activity was determined by luciferase assay. We identified a total of 69 hypermethylated and hypomethylated miRNA promoters encompassing 78 CpG islands in all except Y chromosome, among the three groups. The candidate DNA promoters of miR-424 were significantly hypermethylated and miR-200b and miR-34c were significantly hypomethylated in SCC compared to NCE (P < 0.05). Expression of miR-424, miR-200b, and miR-34c were inversely correlated with promoter DNA methylation in tissue samples. Treatment of cell lines with 5-aza-2'-deoxycytidine showed differential expression in all three miRNAs. We observed a decrease in miRNA promoter activity following in vitro SssI methylase treatment of miR-424, miR-200b, and miR-34c. Luciferase assay demonstrated that miR-200b and miR-424 functionally interacts with 3'-UTR of HIPK3 and RBBP6 respectively and decreased their activity in presence of miR-200b and miR-424 mimics transfected in SiHa cells. Taken together, we have identified deregulation of miRNAs by aberrant DNA promoter methylation, leading to its transcriptional silencing during cervical carcinogenesis, which can be potential targets for diagnosis and therapy.
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Affiliation(s)
- Vinay K Varghese
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Shama P Kabekkodu
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Deeksha Pandey
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
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18
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Monchusi B, Ntwasa M. Methyl pyruvate protects a normal lung fibroblast cell line from irinotecan-induced cell death: Potential use as adjunctive to chemotherapy. PLoS One 2017; 12:e0182789. [PMID: 28797070 PMCID: PMC5552298 DOI: 10.1371/journal.pone.0182789] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/24/2017] [Indexed: 12/02/2022] Open
Abstract
The Warburg Effect, characterized by increased rate of glycolysis even under normoxic conditions, is one of the hallmarks of cancer. Relatively lower oxidative phosphorylation (OXPHOS) is also a characteristic feature in cancer cells. We hypothesized that interference with this phenomenon, by introducing exogenous pyruvate, would upset this cancer phenotype and boost the energy requirements of normal cells. We find that methyl pyruvate protects irinotecan-treated normal lung fibroblast cell line (MRC-5) probably by turning off the p53/p21 axis of the apoptotic pathways. When the MRC-5 fibroblasts recover in drug-free medium, the intrinsic apoptotic pathway is also turned off and the cells survive with no discernible exponential growth during the observation period. In contrast, the mere introduction of exogenous pyruvate kills the lung cancer cell line (A549). Although, functional p53 is important in the drug-induced cancer cell death, it is probably not essential because cancer cell lines with mutated p53 also die albeit less efficiently. We conclude that methyl pyruvate may preferentially kill cancer cells and protect normal cells during chemotherapy.
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Affiliation(s)
- Bernice Monchusi
- School of Molecular & Cell Biology, Gatehouse 514, University of the Witwatersrand, Wits, Johannesburg, Republic of South Africa
| | - Monde Ntwasa
- Department of Life & Consumer Sciences, 211 Calabash Building, University of South Africa, Florida, Johannesburg, Republic of South Africa
- * E-mail:
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19
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Mcm10: A Dynamic Scaffold at Eukaryotic Replication Forks. Genes (Basel) 2017; 8:genes8020073. [PMID: 28218679 PMCID: PMC5333062 DOI: 10.3390/genes8020073] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
To complete the duplication of large genomes efficiently, mechanisms have evolved that coordinate DNA unwinding with DNA synthesis and provide quality control measures prior to cell division. Minichromosome maintenance protein 10 (Mcm10) is a conserved component of the eukaryotic replisome that contributes to this process in multiple ways. Mcm10 promotes the initiation of DNA replication through direct interactions with the cell division cycle 45 (Cdc45)-minichromosome maintenance complex proteins 2-7 (Mcm2-7)-go-ichi-ni-san GINS complex proteins, as well as single- and double-stranded DNA. After origin firing, Mcm10 controls replication fork stability to support elongation, primarily facilitating Okazaki fragment synthesis through recruitment of DNA polymerase-α and proliferating cell nuclear antigen. Based on its multivalent properties, Mcm10 serves as an essential scaffold to promote DNA replication and guard against replication stress. Under pathological conditions, Mcm10 is often dysregulated. Genetic amplification and/or overexpression of MCM10 are common in cancer, and can serve as a strong prognostic marker of poor survival. These findings are compatible with a heightened requirement for Mcm10 in transformed cells to overcome limitations for DNA replication dictated by altered cell cycle control. In this review, we highlight advances in our understanding of when, where and how Mcm10 functions within the replisome to protect against barriers that cause incomplete replication.
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20
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Ntwasa M. Retinoblastoma Binding Protein 6, Another p53 Monitor. Trends Cancer 2016; 2:635-637. [DOI: 10.1016/j.trecan.2016.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 11/25/2022]
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21
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Dlamini Z, Rupnarain C, Naicker S, Hull R, Mbita Z. Expression analysis and association of RBBP6 with apoptosis in colon cancers. J Mol Histol 2016; 47:169-82. [DOI: 10.1007/s10735-016-9663-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
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22
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Shi Y, Manley JL. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev 2015; 29:889-97. [PMID: 25934501 PMCID: PMC4421977 DOI: 10.1101/gad.261974.115] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Recent studies have significantly reshaped current models for the protein–RNA interactions involved in poly(A) site recognition. Here, Shi and Manley review the recent advances in this area and provide a perspective for future studies. The key RNA sequence elements and protein factors necessary for 3′ processing of polyadenylated mRNA precursors are well known. Recent studies, however, have significantly reshaped current models for the protein–RNA interactions involved in poly(A) site recognition, painting a picture more complex than previously envisioned and also providing new insights into regulation of this important step in gene expression. Here we review the recent advances in this area and provide a perspective for future studies.
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Affiliation(s)
- Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California at Irvine, Irvine, California 92697, USA;
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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23
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Hull R, Oosthuysen B, Cajee UF, Mokgohloa L, Nweke E, Antunes RJ, Coetzer THT, Ntwasa M. The Drosophila retinoblastoma binding protein 6 family member has two isoforms and is potentially involved in embryonic patterning. Int J Mol Sci 2015; 16:10242-66. [PMID: 25955646 PMCID: PMC4463644 DOI: 10.3390/ijms160510242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/13/2015] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma binding protein 6 (RBBP6) is implicated in esophageal, lung, hepatocellular and colon cancers. Furthermore, RBBP6 was identified as a strong marker for colon cancer prognosis and as a predisposing factor in familial myeloproliferative neoplasms. Functionally, the mammalian protein interacts with p53 and enhances the activity of Mdm2, the prototypical negative regulator of p53. However, since RBBP6 (known as PACT in mice) exists in multiple isoforms and pact-/- mice exhibit a more severe phenotype than mdm2-/- mutants, it must possess some Mdm2-independent functions. The function of the invertebrate homologue is poorly understood. This is complicated by the absence of the Mdm2 gene in both Drosophila and Caenorhabditis elegans. We have experimentally identified the promoter region of Snama, the Drosophila homologue, analyzed potential transcription factor binding sites and confirmed the existence of an additional isoform. Using band shift and co-immunoprecipitation assays combined with mass spectrometry, we found evidence that this gene may be regulated by, amongst others, DREF, which regulates hundreds of genes related to cell proliferation. The potential transcription factors for Snama fall into distinct functional groups, including anteroposterior embryonic patterning and nucleic acid metabolism. Significantly, previous work in mice shows that pact-/- induces an anteroposterior phenotype in embryos when rescued by simultaneous deletion of p53. Taken together, these observations indicate the significance of RBBP6 proteins in carcinogenesis and in developmental defects.
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Affiliation(s)
- Rodney Hull
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Brent Oosthuysen
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Umar-Faruq Cajee
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Lehlogonolo Mokgohloa
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Ekene Nweke
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Ricardo Jorge Antunes
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Theresa H T Coetzer
- School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg campus); 3209 Scottsville, South Africa.
| | - Monde Ntwasa
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
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Di Giammartino DC, Li W, Ogami K, Yashinskie JJ, Hoque M, Tian B, Manley JL. RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs. Genes Dev 2014; 28:2248-60. [PMID: 25319826 PMCID: PMC4201286 DOI: 10.1101/gad.245787.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Campigli Di Giammartino et al. find that RBBP6 is a component of a large multisubunit protein complex that mediates polyadenylation of mRNA precursors. Genome-wide analyses following RBBP6 knockdown revealed decreased transcript levels, especially of mRNAs with AU-rich 3′ UTRs such as c-Fos and c-Jun, and increased usage of distal poly(A) sites. Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding protein 6), identified initially as an Rb- and p53-binding protein, is a component of this complex and functions in 3′ processing in vitro and in vivo. RBBP6 associates with other core factors, and this interaction is mediated by an unusual ubiquitin-like domain, DWNN (“domain with no name”), that is required for 3′ processing activity. The DWNN is also expressed, via alternative RNA processing, as a small single-domain protein (isoform 3 [iso3]). Importantly, we show that iso3, known to be down-regulated in several cancers, competes with RBBP6 for binding to the core machinery, thereby inhibiting 3′ processing. Genome-wide analyses following RBBP6 knockdown revealed decreased transcript levels, especially of mRNAs with AU-rich 3′ untranslated regions (UTRs) such as c-Fos and c-Jun, and increased usage of distal poly(A) sites. Our results implicate RBBP6 and iso3 as novel regulators of 3′ processing, especially of RNAs with AU-rich 3′ UTRs.
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Affiliation(s)
| | - Wencheng Li
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Koichi Ogami
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jossie J Yashinskie
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Mainul Hoque
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA;
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Morisaki T, Yashiro M, Kakehashi A, Inagaki A, Kinoshita H, Fukuoka T, Kasashima H, Masuda G, Sakurai K, Kubo N, Muguruma K, Ohira M, Wanibuchi H, Hirakawa K. Comparative proteomics analysis of gastric cancer stem cells. PLoS One 2014; 9:e110736. [PMID: 25379943 PMCID: PMC4224387 DOI: 10.1371/journal.pone.0110736] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/16/2014] [Indexed: 02/07/2023] Open
Abstract
Cancer stem cells (CSCs) are responsible for cancer progression, metastasis, and recurrence. To date, the specific markers of CSCs remain undiscovered. The aim of this study was to identify novel biomarkers of gastric CSCs for clinical diagnosis using proteomics technology. CSC-like SP cells, OCUM-12/SP cells, OCUM-2MD3/SP cells, and their parent OCUM-12 cells and OCUM-2MD3 cells were used in this study. Protein lysates from each cell line were analyzed using QSTAR Elite Liquid Chromatography with Tandem Mass Spectrometry, coupled with isobaric tags for relative and absolute quantitation technology. Candidate proteins detected by proteomics technology were validated by immunohistochemical analysis of 300 gastric cancers. Based on the results of LC-MS/MS, eight proteins, including RBBP6, GLG1, VPS13A, DCTPP1, HSPA9, HSPA4, ALDOA, and KRT18, were up-regulated in both OCUM-12/SP cells and OCUM-2MD3/SP cells when compared to their corresponding parent cells. RT-PCR analysis indicated that the expression level of RBBP6, HSPA4, DCTPP1, HSPA9, VPS13A, ALDOA, GLG1, and CK18 was high in OCUM-12/SP and OCUM-2MD3/SP, in compared with the control of parent OCUM-12 and OCUM-2MD3. These proteins were significantly associated with advanced invasion depth, lymph node metastasis, distant metastasis, or advanced clinical stage. RBBP6, DCTPP1, HSPA4, and ALDOA expression in particular were significantly associated with a poor prognosis in the 300 gastric cancer patients. RBBP6 was determined to be an independent prognostic factor. The motility-stimulating ability of OCUM-12/SP cells and OCUM-2MD3/SP cells was inhibited by RBBP6 siRNA. These findings might suggest that the eight proteins, RBBP6, GLG1, VPS13A, DCTPP1, HSPA9, HSPA4, ALDOA, and KRT18, utilizing comparative proteomics analysis, were perceived to be potential CSC markers of gastric cancer. Of the eight candidate proteins, RBBP6 was suggested to be a promising prognostic biomarker and a therapeutic target for gastric cancer.
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Affiliation(s)
- Tamami Morisaki
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masakazu Yashiro
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka, Japan
- * E-mail:
| | - Anna Kakehashi
- Department of Pathology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Azusa Inagaki
- Department of Pathology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Haruhito Kinoshita
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Tatsunari Fukuoka
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hiroaki Kasashima
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Go Masuda
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Katsunobu Sakurai
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Naoshi Kubo
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Kazuya Muguruma
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masaichi Ohira
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hideki Wanibuchi
- Department of Pathology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Kosei Hirakawa
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
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26
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Di Giammartino DC, Manley JL. New links between mRNA polyadenylation and diverse nuclear pathways. Mol Cells 2014; 37:644-9. [PMID: 25081038 PMCID: PMC4179132 DOI: 10.14348/molcells.2014.0177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 06/28/2014] [Indexed: 11/27/2022] Open
Abstract
The 3' ends of most eukaryotic messenger RNAs must undergo a maturation step that includes an endonuc-leolytic cleavage followed by addition of a polyadenylate tail. While this reaction is catalyzed by the action of only two enzymes it is supported by an unexpectedly large number of proteins. This complexity reflects the necessity of coordinating this process with other nuclear events, and growing evidence indicates that even more factors than previously thought are necessary to connect 3' processing to additional cellular pathways. In this review we summarize the current understanding of the molecular machinery involved in this step of mRNA maturation, focusing on new core and auxiliary proteins that connect polyadenylation to splicing, DNA damage, transcription and cancer.
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Affiliation(s)
| | - James L Manley
- Columbia University, Department of Biological Sciences, New York NY, 10027, USA
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Efficient mRNA polyadenylation requires a ubiquitin-like domain, a zinc knuckle, and a RING finger domain, all contained in the Mpe1 protein. Mol Cell Biol 2014; 34:3955-67. [PMID: 25135474 DOI: 10.1128/mcb.00077-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Almost all eukaryotic mRNAs must be polyadenylated at their 3' ends to function in protein synthesis. This modification occurs via a large nuclear complex that recognizes signal sequences surrounding a poly(A) site on mRNA precursor, cleaves at that site, and adds a poly(A) tail. While the composition of this complex is known, the functions of some subunits remain unclear. One of these is a multidomain protein called Mpe1 in the yeast Saccharomyces cerevisiae and RBBP6 in metazoans. The three conserved domains of Mpe1 are a ubiquitin-like (UBL) domain, a zinc knuckle, and a RING finger domain characteristic of some ubiquitin ligases. We show that mRNA 3'-end processing requires all three domains of Mpe1 and that more than one region of Mpe1 is involved in contact with the cleavage/polyadenylation factor in which Mpe1 resides. Surprisingly, both the zinc knuckle and the RING finger are needed for RNA-binding activity. Consistent with a role for Mpe1 in ubiquitination, mutation of Mpe1 decreases the association of ubiquitin with Pap1, the poly(A) polymerase, and suppressors of mpe1 mutants are linked to ubiquitin ligases. Furthermore, an inhibitor of ubiquitin-mediated interactions blocks cleavage, demonstrating for the first time a direct role for ubiquitination in mRNA 3'-end processing.
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28
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Hu D, Zhang S, Zhao Y, Wang S, Wang Q, Song X, Lu D, Mao Y, Chen H. Association of genetic variants in the retinoblastoma binding protein 6 gene with the risk of glioma: a case-control study in a Chinese Han population. J Neurosurg 2014; 121:1209-18. [PMID: 25127414 DOI: 10.3171/2014.6.jns132240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECT The retinoblastoma binding protein 6 (RBBP6) gene plays an important role in the induction of apoptosis and regulation of the cell cycle, and interacts with both p53 and retinoblastoma protein in carcinogenesis. Recently, many studies investigating the function of the RBBP6 gene, including its roles in lung cancer and breast cancer, have been reported. However, the association between RBBP6 variants and glioma was unknown. Therefore, to uncover the association between single nucleotide polymorphisms (SNPs) of RBBP6 and glioma, a hospital-based case-control study was performed in a Chinese Han population. METHODS Ten common tagging SNPs of the RBBP6 gene (covering 100% of all SNPs) were genotyped with the Sequenom MassARRY iPLEX platform, including 992 cases and 1008 controls, according to the HapMap database based on a pairwise linkage disequilibrium r(2) threshold of 0.8, minor allele frequency of 0.05, and Hardy-Weinberg equilibrium of 0.05. RESULTS The authors found that 4 SNPs were significantly associated with glioma (rs2033214, p = 0.013, adjusted OR 2.46, 95% CI 1.18-5.14; rs11860248, p = 8.64 × 10-(6), adjusted OR 1.59, 95% CI 1.23-2.05; rs9933544, p = 3.65 × 10(-4), adjusted OR 1.39, 95% CI 1.13-1.87; rs13332653, p = 0.004, adjusted OR 1.49, 95% CI 1.14-1.95). Stratification analyses revealed that rs2033214 was only significantly associated with low-grade gliomas; rs9933544 and rs13332653 were only significantly associated with glioblastoma multiforme; and rs11860248 was significantly associated with both low-grade gliomas and glioblastoma multiforme, compared with the common wild-type homozygous genotype. Further stratified analysis revealed that rs11860248 was more pronounced in certain subgroups: adults, males, histological types, and family history of cancer. What's more, the haplotype and diplotype analyses consistently revealed that the subjects carrying 1 copy of haplotype CCGCC had a 53% increased glioma risk compared with their corresponding noncarriers (p = 0.018, adjusted OR 1.53, 95% CI 1.08-2.17). CONCLUSIONS The authors' results suggested that RBBP6 gene variants are associated with glioma and contribute to glioma susceptibility, which was first reported elsewhere. Individuals with the so-called risk alleles might have an increased risk of glioma. These results might provide new insight into the occurrence of glioma.
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Affiliation(s)
- Dezhi Hu
- State Key Laboratory of Genetic Engineering, Fudan-VARI Genetic Epidemiology Center and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences andInstitutes for Biomedical Sciences, Fudan University, and
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29
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The RBBP6/ZBTB38/MCM10 axis regulates DNA replication and common fragile site stability. Cell Rep 2014; 7:575-587. [PMID: 24726359 DOI: 10.1016/j.celrep.2014.03.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/17/2014] [Accepted: 03/09/2014] [Indexed: 11/23/2022] Open
Abstract
Faithful DNA replication is essential for the maintenance of genome integrity. Incomplete genome replication leads to DNA breaks and chromosomal rearrangements, which are causal factors in cancer and other human diseases. Despite their importance, the molecular mechanisms that control human genome stability are incompletely understood. Here, we report a pathway that is required for human genome replication and stability. This pathway has three components: an E3 ubiquitin ligase, a transcriptional repressor, and a replication protein. The E3 ubiquitin ligase RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38. This repressor negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Cells lacking RBBP6 experience reduced replication fork progression and increased damage at common fragile sites due to ZBTB38 accumulation and MCM10 downregulation. Our results uncover a pathway that ensures genome-wide DNA replication and chromosomal stability.
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Saidu NEB, Abu Asali I, Czepukojc B, Seitz B, Jacob C, Montenarh M. Comparison between the effects of diallyl tetrasulfide on human retina pigment epithelial cells (ARPE-19) and HCT116 cells. Biochim Biophys Acta Gen Subj 2013; 1830:5267-76. [PMID: 23948592 DOI: 10.1016/j.bbagen.2013.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Diallyl mono- and polysulfanes from garlic are known to induce an adaptive cell response and the formation of antioxidants in cancer cells. In the case of a severe ER stress and a failure in the response, cancer cells eventually go into apoptosis. Only little is known about the response of normal cells upon treatment. METHODS Normal ARPE-19 cells were treated with diallyl tetrasulfide to study their cellular response and the results were compared with those of HCT116 cancer cells. Cell viability was checked by an MTT assay and cytofluorimetry. The formation of superoxide radicals, H2O2 and thiols were determined and proteins involved in the ER stress response were also detected by Western blot analysis. RESULTS We found that diallyl tetrasulfide induced reactive oxygen species (ROS) in normal cells similar to cancer cells in a time (0 to 60min) and dose dependent manner (0 to 50μM). The level of heme oxigenase-1 (HO-1) was up-regulated in both cell types. Initially, we found a decrease in the total thiol level in both cell types but in contrast to cancer cells, normal cells recovered from the decrease in the total thiol concentration within 60min of treatment. CONCLUSIONS The recovery of the thiol concentration in normal cells treated with diallyl tetrasulfide seems to be responsible for the failure to induce the ER stress signalling pathway and finally apoptosis in normal cells. GENERAL SIGNIFICANCE The difference in the recovery of the thiol status might be an explanation for the anti-carcinogenic effects of garlic compounds.
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Chen J, Tang H, Wu Z, Zhou C, Jiang T, Xue Y, Huang G, Yan D, Peng Z. Overexpression of RBBP6, alone or combined with mutant TP53, is predictive of poor prognosis in colon cancer. PLoS One 2013; 8:e66524. [PMID: 23799110 PMCID: PMC3684577 DOI: 10.1371/journal.pone.0066524] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/06/2013] [Indexed: 01/15/2023] Open
Abstract
Retinoblastoma binding protein 6 (RBBP6) plays an important role in chaperone-mediated ubiquitination and interacts with TP53 in carcinogenesis. However, the clinicopathologic significance of RBBP6 expression in colon cancer is unknown; in particular, the prognostic value of RBBP6 combined with TP53 expression has not been explored. Therefore, quantitative real-time PCR and western blot analyses were performed to detect RBBP6 expression in colon cancer tissues. RBBP6 and TP53 expression were assessed by immunohistochemistry in a tissue microarray format, in which the primary colon cancer tissue was paired with noncancerous tissue. Tissue specimens were obtained from 203 patients. We found that RBBP6 was overexpressed in colon tumorous tissues and was significantly associated with clinical stage, depth of tumor invasion, lymph node metastasis (LNM), distant metastasis, and histologic grade. Further studies revealed that a corresponding correlation between RBBP6 overexpression and mutant TP53 was evident in colon cancer (r = 0.450; P<0.001). RBBP6 expression was an independent prognostic factor for overall survival (OS) and disease free survival (DFS). Interestingly, patients with tumors that had both RBBP6 overexpression and mutant TP53 protein accumulation relapsed and died within a significantly short period after surgery (P<0.001). Multivariate analysis showed that patients with LNM and patients with both RBBP6- and TP53-positive tumors had extremely poor OS (HR 6.75; 95% CI 2.63–17.35; P<0.001) and DFS (HR 8.08; 95% CI 2.80–23.30; P<0.001). These clinical findings indicate that the assessment of both RBBP6 and mutant TP53 expression will be helpful in predicting colon cancer prognosis.
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Affiliation(s)
- Jian Chen
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Huamei Tang
- Department of Pathology, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Zehua Wu
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Chongzhi Zhou
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Tao Jiang
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Yingming Xue
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Guoyu Huang
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
| | - Dongwang Yan
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
- * E-mail:
| | - Zhihai Peng
- Department of General Surgery, Shanghai Jiaotong University Affiliated First People’s Hospital, Shanghai, People’s Republic of China
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The C. elegans Homolog of RBBP6 (RBPL-1) regulates fertility through controlling cell proliferation in the germline and nutrient synthesis in the intestine. PLoS One 2013; 8:e58736. [PMID: 23536819 PMCID: PMC3594146 DOI: 10.1371/journal.pone.0058736] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/05/2013] [Indexed: 02/04/2023] Open
Abstract
RBBP6 (retinoblastoma binding protein 6, also known as PACT or P2P-R in humans) is a multi-domain protein that functions in multiple processes, such as mitosis, cell differentiation, and cell apoptosis. RBBP6 is evolutionarily conserved and is present in unicellular organisms to mammals. Studies of RBBP6 have mostly focused on its RB- and p53-binding domains, which are found exclusively in mammals. Here, we investigated the C. elegans homolog of RBBP6 to explore the functional roles of its other domains. We found that RBPL-1, the homolog of RBBP6 in C. elegans, is indispensable for worm development. RNAi silencing of rbpl-1 led to embryonic lethality, as well as defects in oocyte production and intestine development. rbpl-1 RNAi worms showed defects in germ cell proliferation, suggesting that RBPL-1 regulates mitosis. Moreover, RNAi silencing of rbpl-1 inhibited nutrient synthesis in the worm intestine. RBPL-1, as a nucleolus protein, was found to be expressed in diverse tissues and necessary for both germline and soma development. Using microarray analysis, we identified ≈700 genes whose expression levels were changed at least 10-fold in rbpl-1 worms. We propose that RBPL-1, like its yeast homolog, may regulate gene expression as an mRNA cleavage and polyadenylation factor. Taken together, the findings from this study reveal that RBPL-1 plays a pivotal role in C. elegans germline and soma development, suggesting that the functions of RBBP6 are conserved in diverse eukaryotic species.
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Cajee UF, Hull R, Ntwasa M. Modification by ubiquitin-like proteins: significance in apoptosis and autophagy pathways. Int J Mol Sci 2012; 13:11804-11831. [PMID: 23109884 PMCID: PMC3472776 DOI: 10.3390/ijms130911804] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 09/13/2012] [Indexed: 01/31/2023] Open
Abstract
Ubiquitin-like proteins (Ubls) confer diverse functions on their target proteins. The modified proteins are involved in various biological processes, including DNA replication, signal transduction, cell cycle control, embryogenesis, cytoskeletal regulation, metabolism, stress response, homeostasis and mRNA processing. Modifiers such as SUMO, ATG12, ISG15, FAT10, URM1, and UFM have been shown to modify proteins thus conferring functions related to programmed cell death, autophagy and regulation of the immune system. Putative modifiers such as Domain With No Name (DWNN) have been identified in recent times but not fully characterized. In this review, we focus on cellular processes involving human Ubls and their targets. We review current progress in targeting these modifiers for drug design strategies.
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Affiliation(s)
- Umar-Faruq Cajee
- School of Molecular & Cell Biology, Gatehouse 512, University of the Witwatersrand, Johannesburg, 2050, South Africa; E-Mails: (U.-F.C.); (R.H.)
| | - Rodney Hull
- School of Molecular & Cell Biology, Gatehouse 512, University of the Witwatersrand, Johannesburg, 2050, South Africa; E-Mails: (U.-F.C.); (R.H.)
| | - Monde Ntwasa
- School of Molecular & Cell Biology, Gatehouse 512, University of the Witwatersrand, Johannesburg, 2050, South Africa; E-Mails: (U.-F.C.); (R.H.)
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Mbita Z, Meyer M, Skepu A, Hosie M, Rees J, Dlamini Z. De-regulation of the RBBP6 isoform 3/DWNN in human cancers. Mol Cell Biochem 2011; 362:249-62. [PMID: 22139301 DOI: 10.1007/s11010-011-1150-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/03/2011] [Indexed: 01/30/2023]
Abstract
Retinoblastoma binding protein 6 (RBBP6) is a nuclear protein, previously implicated in the regulation of cell cycle and apoptosis. The human RBBP6 gene codes for three protein isoforms and isoform 3 consists of the domain with no name domain only whilst the other two isoforms, 1 and 2 comprise of additional zinc, RING, retinoblastoma and p53 binding domains. In this study, the localization of RBBP6 using RBBP6 variant 3 mRNA-specific probe was performed to investigate the expression levels of the gene in different tumours and find a link between RBBP6 and human carcinogenesis. Using FISH, real-time PCR and Western blotting analysis our results show that RBBP6 isoform 3 is down-regulated in human cancers. RBBP6 isoform 3 knock-down resulted in reduced G2/M cell cycle arrest whilst its over-expression resulted in increased G2/M cell cycle arrest using propidium iodide DNA staining. The results further demonstrate that the RBBP6 isoform 3 may be the cell cycle regulator and involved in mitotic apoptosis not the isoform 1 as previously reported for mice. In conclusion, these findings suggest that RBBP6 isoform 3 is a cell cycle regulator and may be de-regulated in carcinogenesis.
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Affiliation(s)
- Zukile Mbita
- College of Agriculture and Environmental Science, University of South Africa, Florida Campus, Johannesburg, South Africa
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Kappo MA, Ab E, Hassem F, Atkinson RA, Faro A, Muleya V, Mulaudzi T, Poole JO, McKenzie JM, Chibi M, Moolman-Smook JC, Rees DJG, Pugh DJR. Solution structure of RING finger-like domain of retinoblastoma-binding protein-6 (RBBP6) suggests it functions as a U-box. J Biol Chem 2011; 287:7146-58. [PMID: 22130672 DOI: 10.1074/jbc.m110.217059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Retinoblastoma-binding protein-6 (RBBP6) plays a facilitating role, through its RING finger-like domain, in the ubiquitination of p53 by Hdm2 that is suggestive of E4-like activity. Although the presence of eight conserved cysteine residues makes it highly probable that the RING finger-like domain coordinates two zinc ions, analysis of the primary sequence suggests an alternative classification as a member of the U-box family, the members of which do not bind zinc ions. We show here that despite binding two zinc ions, the domain adopts a homodimeric structure highly similar to those of a number of U-boxes. Zinc ions could be replaced by cadmium ions without significantly disrupting the structure or the stability of the domain, although the rate of substitution was an order of magnitude slower than any previous measurement, suggesting that the structure is particularly stable, a conclusion supported by the high thermal stability of the domain. A hallmark of U-box-containing proteins is their association with chaperones, with which they cooperate in eliminating irretrievably unfolded proteins by tagging them for degradation by the proteasome. Using a yeast two-hybrid screen, we show that RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. Taken together with the structural similarities to U-box-containing proteins, our data suggest that RBBP6 plays a role in chaperone-mediated ubiquitination and possibly in protein quality control.
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Affiliation(s)
- Mautin A Kappo
- Biotechnology Department, University of the Western Cape, Bellville 7535, South Africa
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Motadi LR, Bhoola KD, Dlamini Z. Expression and function of retinoblastoma binding protein 6 (RBBP6) in human lung cancer. Immunobiology 2011; 216:1065-73. [DOI: 10.1016/j.imbio.2011.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 04/12/2011] [Accepted: 05/07/2011] [Indexed: 12/24/2022]
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Peidis P, Voukkalis N, Aggelidou E, Georgatsou E, Hadzopoulou-Cladaras M, Scott RE, Nikolakaki E, Giannakouros T. SAFB1 interacts with and suppresses the transcriptional activity of p53. FEBS Lett 2010; 585:78-84. [DOI: 10.1016/j.febslet.2010.11.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 11/23/2010] [Accepted: 11/24/2010] [Indexed: 01/04/2023]
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Vaz Meirelles G, Ferreira Lanza DC, da Silva JC, Santana Bernachi J, Paes Leme AF, Kobarg J. Characterization of hNek6 interactome reveals an important role for its short N-terminal domain and colocalization with proteins at the centrosome. J Proteome Res 2010; 9:6298-316. [PMID: 20873783 DOI: 10.1021/pr100562w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Physical protein-protein interactions are fundamental to all biological processes and are organized in complex networks. One branch of the kinome network is the evolutionarily conserved NIMA-related serine/threonine kinases (Neks). Most of the 11 mammalian Neks studied so far are related to cell cycle regulation, and due to association with diverse human pathologies, Neks are promising chemotherapeutic targets. Human Nek6 was associated to carcinogenesis, but its interacting partners and signaling pathways remain elusive. Here we introduce hNek6 as a highly connected member in the human kinase interactome. In a more global context, we performed a broad data bank comparison based on degree distribution analysis and found that the human kinome is enriched in hubs. Our networks include a broad set of novel hNek6 interactors as identified by our yeast two-hybrid screens classified into 18 functional categories. All of the tested interactions were confirmed, and the majority of tested substrates were phosphorylated in vitro by hNek6. Notably, we found that hNek6 N-terminal is important to mediate the interactions with its partners. Some novel interactors also colocalized with hNek6 and γ-tubulin in human cells, pointing to a possible centrosomal interaction. The interacting proteins link hNek6 to novel pathways, for example, Notch signaling and actin cytoskeleton regulation, or give new insights on how hNek6 may regulate previously proposed pathways such as cell cycle regulation, DNA repair response, and NF-κB signaling. Our findings open new perspectives in the study of hNek6 role in cancer by analyzing its novel interactions in specific pathways in tumor cells, which may provide important implications for drug design and cancer therapy.
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Affiliation(s)
- Gabriela Vaz Meirelles
- Laboratório Nacional de Biociências, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Glycolytic flux occurs in Drosophila melanogaster recovering from camptothecin treatment. Anticancer Drugs 2010; 21:945-57. [PMID: 20717003 DOI: 10.1097/cad.0b013e32833e2f60] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Camptothecin (CPT) and CPT-derived drugs are widely used against gynaecological and colorectal cancers. On account of their mechanism of action these drugs target rapidly dividing cells and may have an adverse effect on normal tissues. We sought to investigate their impact on normal cells by using Drosophila as a model. We investigated the possible involvement of Drosophila homologue of p53 (Dmp53) and a member of the retinoblastoma binding protein 6 family, known as Snama. On account of its molecular features and experimental evidence gleaned from mammalian studies we propose Snama as a candidate in Dmp53 regulation. We have used proteomics and core molecular biology techniques on embryos and on adult flies. We found that flies that recover from CPT treatment display a metabolic programme characterized by glycolytic flux, depletion of Dmp53 and increase of Snama transcripts. When we introduced methyl pyruvate in the diet to bypass the glycolytic pathway, we noticed differential expression of Dmp53 and Snama and improvement in reproduction and embryonic development. The development of embryos into the pupal stage was significantly improved to 40% (P=0.02) when CPT was given to mothers in combination with methyl pyruvate. This investigation highlights the importance of energy production mechanisms in cells that recover from chemotherapy and differences between the metabolic programmes used by recovering cells and those adopted by cancer cells.
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Peidis P, Giannakouros T, Burow ME, Williams RW, Scott RE. Systems genetics analyses predict a transcription role for P2P-R: molecular confirmation that P2P-R is a transcriptional co-repressor. BMC SYSTEMS BIOLOGY 2010; 4:14. [PMID: 20184719 PMCID: PMC2843647 DOI: 10.1186/1752-0509-4-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 02/25/2010] [Indexed: 12/31/2022]
Abstract
Background The 250 kDa P2P-R protein (also known as PACT and Rbbp6) was cloned over a decade ago and was found to bind both the p53 and Rb1 tumor suppressor proteins. In addition, P2P-R has been associated with multiple biological functions, such as mitosis, mRNA processing, translation and ubiquitination. In the current studies, the online GeneNetwork system was employed to further probe P2P-R biological functions. Molecular studies were then performed to confirm the GeneNetwork evaluations. Results GeneNetwork and associated gene ontology links were used to investigate the coexpression of P2P-R with distinct functional sets of genes in an adipocyte genetic reference panel of HXB/BXH recombinant strains of rats and an eye genetic reference panel of BXD recombinant inbred strains of mice. The results establish that biological networks of 75 and 135 transcription-associated gene products that include P2P-R are co-expressed in a genetically-defined manner in rat adipocytes and in the mouse eye, respectively. Of this large set of transcription-associated genes, >10% are associated with hormone-mediated transcription. Since it has been previously reported that P2P-R can bind the SRC-1 transcription co-regulatory factor (steroid receptor co-activator 1, [Ncoa1]), the possible effects of P2P-R on estrogen-induced transcription were evaluated. Estrogen-induced transcription was repressed 50-70% by the transient transfection of P2P-R plasmid constructs into four different cell types. In addition, knockdown of P2P-R expression using an antisense oligonucleotide increased estrogen-mediated transcription. Co-immunoprecipitation assays confirmed that P2P-R interacts with SRC-1 and also demonstrated that P2P-R interacts with estrogen receptor α. Conclusions The findings presented in this study provide strong support for the value of systems genetics, especially GeneNetwork, in discovering new functions of genes that can be confirmed by molecular analysis. More specifically, these data provide evidence that the expression of P2P-R co-varies in a genetically-defined manner with large transcription networks and that P2P-R can function as a co-repressor of estrogen-dependent transcription.
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Affiliation(s)
- Philippos Peidis
- Laboratory of Biochemistry, Department of Chemistry, The Aristotle University, 54124 Thessaloniki, Greece
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Ahlander J, Bosco G. The RB/E2F pathway and regulation of RNA processing. Biochem Biophys Res Commun 2009; 384:280-3. [PMID: 19401190 DOI: 10.1016/j.bbrc.2009.04.107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 04/19/2009] [Indexed: 12/11/2022]
Abstract
The retinoblastoma tumor suppressor protein (RB) is inactivated in a majority of cancers. RB restricts cell proliferation by inhibiting the E2F family of transcription factors. The current model for RB/E2F function describes its role in regulating transcription at gene promoters. Whether the RB or E2F proteins might play a role in gene expression beyond transcription initiation is not well known. This review describes evidence that points to a novel role for the RB/E2F network in the regulation of RNA processing, and we propose a model as a framework for future research. The elucidation of a novel role of RB in RNA processing will have a profound impact on our understanding of the role of this tumor suppressor family in cell and developmental biology.
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Affiliation(s)
- Joseph Ahlander
- Department of Molecular and Cellular Biology, 1007 East Lowell Street, University of Arizona, Tucson, AZ 85721, USA
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Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR, Frank J, Manley JL. Molecular architecture of the human pre-mRNA 3' processing complex. Mol Cell 2009; 33:365-76. [PMID: 19217410 DOI: 10.1016/j.molcel.2008.12.028] [Citation(s) in RCA: 414] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 10/24/2008] [Accepted: 12/12/2008] [Indexed: 01/17/2023]
Abstract
Pre-mRNA 3' end formation is an essential step in eukaryotic gene expression. Over half of human genes produce alternatively polyadenylated mRNAs, suggesting that regulated polyadenylation is an important mechanism for posttranscriptional gene control. Although a number of mammalian mRNA 3' processing factors have been identified, the full protein composition of the 3' processing machinery has not been determined, and its structure is unknown. Here we report the purification and subsequent proteomic and structural characterization of human mRNA 3' processing complexes. Remarkably, the purified 3' processing complex contains approximately 85 proteins, including known and new core 3' processing factors and over 50 proteins that may mediate crosstalk with other processes. Electron microscopic analyses show that the core 3' processing complex has a distinct "kidney" shape and is approximately 250 A in length. Together, our data has revealed the complexity and molecular architecture of the pre-mRNA 3' processing complex.
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Affiliation(s)
- Yongsheng Shi
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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Lechner JF, Reen RK, Dombkowski AA, Cukovic D, Salagrama S, Wang LS, Stoner GD. Effects of a Black Raspberry Diet on Gene Expression in the Rat Esophagus. Nutr Cancer 2008; 60 Suppl 1:61-9. [DOI: 10.1080/01635580802393118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Chibi M, Meyer M, Skepu A, G Rees DJ, Moolman-Smook JC, Pugh DJR. RBBP6 interacts with multifunctional protein YB-1 through its RING finger domain, leading to ubiquitination and proteosomal degradation of YB-1. J Mol Biol 2008; 384:908-16. [PMID: 18851979 DOI: 10.1016/j.jmb.2008.09.060] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 09/19/2008] [Accepted: 09/22/2008] [Indexed: 01/17/2023]
Abstract
RBBP6 (retinoblastoma binding protein 6) is a 250-kDa multifunctional protein that interacts with both p53 and pRb and has been implicated in mRNA processing. It has also been identified as a putative E3 ubiquitin ligase due to the presence of a RING finger domain, although no substrate has been identified up to now. Using the RING finger domain as bait in a yeast two-hybrid screen, we identified YB-1 (Y-box binding protein 1) as a binding partner of RBBP6, localising the interaction to the last 62 residues of YB-1. We showed, furthermore, that both full-length RBBP6 and the isolated RING finger domain were able to ubiquitinate YB-1, resulting in its degradation in the proteosome. As a result, RBBP6 was able to suppress the levels of YB-1 in vivo and to reduce its transactivational ability. In the light of the important role that YB-1 appears to play in tumourigenesis, our results suggest that RBBP6 may be a relevant target for therapeutic drugs aimed at modifying the activity of YB-1.
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Affiliation(s)
- Moredreck Chibi
- Biotechnology Department, University of the Western Cape, Bellville, South Africa
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Wang J, Yuan Y, Zhou Y, Guo L, Zhang L, Kuai X, Deng B, Pan Z, Li D, He F. Protein Interaction Data Set Highlighted with Human Ras-MAPK/PI3K Signaling Pathways. J Proteome Res 2008; 7:3879-89. [DOI: 10.1021/pr8001645] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Longhua Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xuezhang Kuai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Binwei Deng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhi Pan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Li L, Deng B, Xing G, Teng Y, Tian C, Cheng X, Yin X, Yang J, Gao X, Zhu Y, Sun Q, Zhang L, Yang X, He F. PACT is a negative regulator of p53 and essential for cell growth and embryonic development. Proc Natl Acad Sci U S A 2007; 104:7951-6. [PMID: 17470788 PMCID: PMC1876553 DOI: 10.1073/pnas.0701916104] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The tumor suppressor p53 regulates cell cycle progression and apoptosis in response to various types of stress, whereas excess p53 activity creates unwanted effects. Tight regulation of p53 is essential for maintaining normal cell growth. p53-associated cellular protein-testes derived (PACT, also known as P2P-R, RBBP6) is a 250-kDa Ring finger-containing protein that can directly bind to p53. PACT is highly up-regulated in esophageal cancer and may be a promising target for immunotherapy. However, the physiological role of the PACT-p53 interaction remains largely unclear. Here, we demonstrate that the disruption of PACT in mice leads to early embryonic lethality before embryonic day 7.5 (E7.5), accompanied by an accumulation of p53 and widespread apoptosis. p53-null mutation partially rescues the lethality phenotype and prolonged survival to E11.5. Endogenous PACT can interact with Hdm2 and enhance Hdm2-mediated ubiquitination and degradation of p53 as a result of the increase of the p53-Hdm2 affinity. Consequently, PACT represses p53-dependent gene transcription. Knockdown of PACT significantly attenuates the p53-Hdm2 interaction, reduces p53 polyubiquitination, and enhances p53 accumulation, leading to both apoptosis and cell growth retardation. Taken together, our data demonstrate that the PACT-p53 interaction plays a critical role in embryonic development and tumorigenesis and identify PACT as a member of negative regulators of p53.
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Affiliation(s)
- Li Li
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
- Genetic Laboratory of Development and Diseases and
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, 20 Dongdajie, Beijing 100071, People's Republic of China; and
| | - Binwei Deng
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Guichun Xing
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Yan Teng
- Genetic Laboratory of Development and Diseases and
| | - Chunyan Tian
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Xuan Cheng
- Genetic Laboratory of Development and Diseases and
| | - Xiushan Yin
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Juntao Yang
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Xue Gao
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Yunping Zhu
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Qihong Sun
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
| | - Lingqiang Zhang
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
- To whom correspondence may be addressed. E-mail: , , or
| | - Xiao Yang
- Genetic Laboratory of Development and Diseases and
- To whom correspondence may be addressed. E-mail: , , or
| | - Fuchu He
- *State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, People's Republic of China
- To whom correspondence may be addressed. E-mail: , , or
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47
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Jones C, Reifegerste R, Moses K. Characterization of Drosophila mini-me, a gene required for cell proliferation and survival. Genetics 2006; 173:793-808. [PMID: 16547096 PMCID: PMC1526529 DOI: 10.1534/genetics.106.056762] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the developing Drosophila eye, the morphogenetic furrow is a developmental organizing center for patterning and cell proliferation. The furrow acts both to limit eye size and to coordinate the number of cells to the number of facets. Here we report the molecular and functional characterization of Drosophila mini-me (mnm), a potential regulator of cell proliferation and survival in the developing eye. We first identified mnm as a dominant modifier of hedgehog loss-of-function in the developing eye. We report that mnm encodes a conserved protein with zinc knuckle and RING finger domains. We show that mnm is dispensable for patterning of the eye disc, but required in the eye for normal cell proliferation and survival. We also show that mnm null mutant cells exhibit altered cell cycle profiles and contain excess nucleic acid. Moreover, mnm overexpression can induce cells to proliferate and incorporate BrdU. Thus, our data implicate mnm as a regulator of mitotic progression during the proliferative phase of eye development, possibly through the control of nucleic acid metabolism.
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Affiliation(s)
- Chonnettia Jones
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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48
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Pugh DJR, AB E, Faro A, Lutya PT, Hoffmann E, Rees DJG. DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways. BMC STRUCTURAL BIOLOGY 2006; 6:1. [PMID: 16396680 PMCID: PMC1360078 DOI: 10.1186/1472-6807-6-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Accepted: 01/05/2006] [Indexed: 02/02/2023]
Abstract
Background RBBP6 is a 250 kDa splicing-associated protein that has been identified as an E3 ligase due to the presence of a RING finger domain. In humans and mice it interacts with both p53 and Rb, and plays a role in the induction of apoptosis and regulation of the cell cycle. RBBP6 has recently been shown to be highly up-regulated in oesophageal cancer, and to be a promising target for immunotherapy against the disease. Results We show here using heteronuclear NMR that the N-terminal 81 amino acids of RBBP6 constitute a novel ubiquitin-like domain, which we have called the DWNN domain. The domain lacks conserved equivalents of K48 and K63, although the equivalents of K6 and K29 are highly, although not absolutely, conserved. The di-glycine motif that is characteristic of proteins involved in ubiquitination is found in the human and mouse form of the domain, although it is not present in all organisms. It forms part of a three-domain form of RBBP6 containing the DWNN domain, a zinc knuckle and a RING finger domain, which is found in all eukaryotic genomes so far examined, in the majority of cases at single copy number. The domain is also independently expressed in vertebrates as a single domain protein. Conclusion DWNN is a novel ubiquitin-like domain found only at the N-terminus of the RBBP6 family of splicing-associated proteins. The ubiquitin-like structure of the domain greatly increases the likelihood that RBBP6 functions through some form of ubiquitin-like modification. Furthermore, the fact that the DWNN domain is independently expressed in higher vertebrates leads us to propose that the domain may itself function as a novel ubiquitin-like modifier of other proteins.
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Affiliation(s)
- David JR Pugh
- Biotechnology Department, University of the Western Cape, Modderdam Road, Bellville 7535, South Africa
| | - Eiso AB
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Andrew Faro
- Biotechnology Department, University of the Western Cape, Modderdam Road, Bellville 7535, South Africa
| | - Portia T Lutya
- Department of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Avenue, Johannesburg 2050, South Africa
| | - Eberhard Hoffmann
- Varian Deutschland GmbH, Alsfelder Straβe 3, D-64289 Darmstadt, Germany
| | - D Jasper G Rees
- Biotechnology Department, University of the Western Cape, Modderdam Road, Bellville 7535, South Africa
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Scott RE, White-Grindley E, Ruley HE, Chesler EJ, Williams RW. P2P-R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P-R mRNA. J Cell Physiol 2005; 204:99-105. [PMID: 15617101 DOI: 10.1002/jcp.20263] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
P2P-R is a nuclear protein with potential functional roles in the control of gene expression and mitosis. The P2P-R protein also interacts with the p53 and Rb1 tumor suppressor proteins. To search for additional functional associations of P2P-R, we employed the WebQTL database that contains the results of cDNA microarray analysis on forebrain, cerebellum, and hematopoietic stem cell (HSC) specimens of multiple BXD recombinant inbred strains of mice. Using WebQTL, gene products were identified that show genetically based coexpression with P2P-R. Initial studies identified general groups of mRNAs that share common functional roles and high covariation in expression with P2P-R. These functional groups involved the regulation of transcription, nucleotide binding, translation control, and ion transport. The findings related to translational mechanisms were further evaluated. In HSCs, expression of P2P-R mRNA demonstrates an impressive expression correlation with a group of gene products associated with translation; high expression of P2P-R specifically was associated with decreased expression of 29 ribosomal protein mRNAs. In all three tissues that were screened using the WebQTL database, a strong positive expression covariance between P2P-R and the Pum2 gene product also was observed. PUM2 is a member of the highly conserved Puf family of RNA binding proteins that often function as gene-specific translation regulators. The ability of Puf proteins to repress translation is mediated by their binding to specific elements located in the 3' untranslated region (UTR) of their target mRNAs. To assess the functional significance of the strong genetic correlation in expression of P2P-R and PUM2, the 3' UTR of the P2P-R mRNA was analyzed and found to contain one perfect consensus and two near-perfect consensus PUM2 binding sequences. PUM2 pull-down methods combined with reverse transcription and RT-PCR confirmed that PUM2 does indeed bind P2P-R mRNA. These results suggest that P2P-R expression may be translationally regulated by PUM2 and that P2P-R may modulate translation by influencing ribosomal protein gene expression. This study represents the first description of a RNA target for mammalian Puf proteins and the first molecular confirmation of information obtained using the WebQTL database.
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Affiliation(s)
- Robert E Scott
- Department of Pathology, University of Tennessee Health Science Center, Memphis Tennessee, USA.
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50
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Mather A, Rakgotho M, Ntwasa M. SNAMA, a novel protein with a DWNN domain and a RING finger-like motif: a possible role in apoptosis. ACTA ACUST UNITED AC 2005; 1727:169-76. [PMID: 15733535 DOI: 10.1016/j.bbaexp.2005.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Revised: 10/14/2004] [Accepted: 01/11/2005] [Indexed: 10/25/2022]
Abstract
We have characterized SNAMA a hitherto uncharacterized Drosophila protein that appears to play a role in apoptosis. SNAMA (something that sticks like glue) is a 1231 amino acid protein with a conserved 76 residue N-terminal domain called Domain With No Name (DWNN). The DWNN domain was first identified in cytotoxic T Cell-resistant CHO cells using promoter trap mutagenesis to screen for genes involved in apoptosis. Subsequently, this domain was identified in other eukaryotic organisms including animals and plants. The SNAMA transcript is abundant early in embryogenesis but reduced in older embryos and in adult males and females. Human and mouse homologues of SNAMA are known to bind to p53 and to the retinoblastoma protein (Rb) suggesting a role in transcriptional regulation and cell cycle control. We took advantage of a P-element insertion line in which the P-element is inserted in the first intron, to investigate the biological function of the gene. These mutants are lethal when homozygous. Apoptosis appears early during embryogenesis and is observed virtually throughout the gastrula. The DWNN domain has a ubiquitin-like fold and may interact with a subset of cellular proteins. There is also a conserved RING finger-like motif along the sequence of SNAMA following a C2HC zinc finger.
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Affiliation(s)
- Arshad Mather
- School of Molecular and Cell Biology, University of the Witwatersrand. Wits. 2050, South Africa
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