1
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Tabassum S, Ghosh MK. DEAD-box RNA helicases with special reference to p68: Unwinding their biology, versatility, and therapeutic opportunity in cancer. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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2
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Transcriptome profiling in Rift Valley fever virus infected cells reveals modified transcriptional and alternative splicing programs. PLoS One 2019; 14:e0217497. [PMID: 31136639 PMCID: PMC6538246 DOI: 10.1371/journal.pone.0217497] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/13/2019] [Indexed: 12/27/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a negative-sense RNA virus belonging to the Phenuiviridae family that infects both domestic livestock and humans. The NIAID has designated RVFV as a Category A priority emerging pathogen due to the devastating public health outcomes associated with epidemic outbreaks. However, there is no licensed treatment or vaccine approved for human use. Therefore it is of great interest to understand RVFV pathogenesis in infected hosts in order to facilitate creation of targeted therapies and treatment options. Here we provide insight into the host-pathogen interface in human HEK293 cells during RVFV MP-12 strain infection using high-throughput mRNA sequencing technology. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes showed robust innate immune and cytokine-mediated inflammatory pathway activation as well as alterations in pathways associated with fatty acid metabolism and extracellular matrix receptor signaling. We also analyzed the promoter regions of DEGs for patterns in transcription factor binding sites, and found several that are known to act synergistically to impact apoptosis, immunity, metabolism, and cell growth and differentiation. Lastly, we noted dramatic changes in host alternative splicing patterns in genes associated with mRNA decay and surveillance, RNA transport, and DNA repair. This study has improved our understanding of RVFV pathogenesis and has provided novel insight into pathways and signaling modules important for RVFV diagnostics and therapeutic development.
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3
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Roles of DDX5 in the tumorigenesis, proliferation, differentiation, metastasis and pathway regulation of human malignancies. Biochim Biophys Acta Rev Cancer 2019; 1871:85-98. [DOI: 10.1016/j.bbcan.2018.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 02/07/2023]
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4
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Wang Z, Liu W, Zhou N, Wang H, Li P, Wang M, Zhang Q. Molecular characterization, origin, and evolution of teleost p68 gene family: Insights from Japanese flounder, Paralichthys olivaceus. Mar Genomics 2015; 24 Pt 3:363-70. [PMID: 26388449 DOI: 10.1016/j.margen.2015.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 11/26/2022]
Abstract
Two rounds of whole-genome duplication occurred in the common ancestor of vertebrates. Later, a third round genome duplication occurred in the teleost fishes. As a prototype member of DEAD-box RNA helicases, the function of p68 helicase in development has been well investigated in human, however, limited information is available regarding the regulatory function of this gene in the development of teleosts. In this study, being an important farmed fish in North China, Japanese flounder (Paralichthys olivaceus) was used as model fish to investigate the role of p68 gene in teleost development. Two p68 genes were first identified from Japanese flounder. Molecular characterization of them was performed by analyzing the exon-intron boundaries. Then, we confirmed that such two teleost p68 genes originated from teleost-specific genome duplication through phylogenetic and synteny analyses. Additionally, comparative analyses of amino acid sequences, variation in selective pressure, and expression profiles of p68 genes revealed probable sub-functionalization fate of teleost p68 genes after the duplication. Therefore, this study supplements the evolutionary properties of teleost p68 gene family and provides the groundwork for further studying the regulatory function of p68 genes in the development of teleosts.
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Affiliation(s)
- Zhongkai Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources of Chinese Department of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China; Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Wei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Nayu Zhou
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Huizhen Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Peizhen Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Mengxun Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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5
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The expression of RNA helicase DDX5 is transcriptionally upregulated by calcitriol through a vitamin D response element in the proximal promoter in SiHa cervical cells. Mol Cell Biochem 2015; 410:65-73. [DOI: 10.1007/s11010-015-2538-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/18/2015] [Indexed: 12/22/2022]
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6
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Guturi KKN, Sarkar M, Bhowmik A, Das N, Ghosh MK. DEAD-box protein p68 is regulated by β-catenin/transcription factor 4 to maintain a positive feedback loop in control of breast cancer progression. Breast Cancer Res 2014; 16:496. [PMID: 25499975 PMCID: PMC4308923 DOI: 10.1186/s13058-014-0496-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/04/2014] [Indexed: 01/28/2023] Open
Abstract
INTRODUCTION Nuclear accumulation of β-catenin is important for cancer development and it is found to overlap with p68 (DDX5) immunoreactivity in most breast cancers, as indicated by both clinical investigations and studies in cell lines. In this study, we aim to investigate the regulation of p68 gene expression through β-catenin/transcription factor 4 (TCF4) signaling in breast cancer. METHODS Formalin-fixed paraffin-embedded sections derived from normal human breast and breast cancer samples were used for immunohistochemical analysis. Protein and mRNA expressions were determined by immunoblotting and quantitative RT-PCR respectively. Promoter activity of p68 was checked using luciferase assay. Occupancy of several factors on the p68 promoter was evaluated using chromatin immunoprecipitation. Finally, a syngeneic mouse model of breast cancer was used to assess physiological significance. RESULTS We demonstrated that β-catenin can directly induce transcription of p68 promoter or indirectly through regulation of c-Myc in both human and mouse breast cancer cells. Moreover, by chromatin immunoprecipitation assay, we have found that both β-catenin and TCF4 occupy the endogenous p68 promoter, which is further enhanced by Wnt signaling. Furthermore, we have also established a positive feedback regulation for the expression of TCF4 by p68. To the best of our knowledge, this is the first report on β-catenin/TCF4-mediated p68 gene regulation, which plays an important role in epithelial to mesenchymal transition, as shown in vitro in breast cancer cell lines and in vivo in an animal breast tumour model. CONCLUSIONS Our findings indicate that Wnt/β-catenin signaling plays an important role in breast cancer progression through p68 upregulation.
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Affiliation(s)
- Kiran Kumar Naidu Guturi
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Moumita Sarkar
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Arijit Bhowmik
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Nilanjana Das
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Mrinal Kanti Ghosh
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
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7
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Banu SA, Huda KMK, Tuteja N. Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrobacterium-mediated transient assay. PLANT SIGNALING & BEHAVIOR 2014; 9:e28992. [PMID: 24785194 PMCID: PMC4091197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 04/23/2014] [Accepted: 04/23/2014] [Indexed: 02/28/2024]
Abstract
Helicases are molecular motor proteins that perform a variety of cellular functions including transcription, translation, DNA replication and repair, RNA maturation, ribosome synthesis, nuclear export and splicing processes. The p68 is an evolutionarily conserved protein which plays pivotal roles in all aspect RNA metabolism processes. It is well established that helicases provides abiotic stress adaptation in plants but analysis of cis-regulatory elements present in the upstream regions is still infancy. Here we report isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 in response to abiotic stress and hormonal regulation. The promoter of Psp68 was isolated by gene walking PCR from pea genomic DNA library constructed in BD genome walker kit. In silico analysis revealed that promoter of Psp68 contained a TATA, a CAAT motif and also harbors some important stress and hormone associated cis regulatory elements, including E-box, AGAAA, GATA-box, ACGT, GAAAA and GTCTC. Functional analyses were performed by Agrobacterium-mediated transient assay in tobacco leaves. Very high level of GUS activity was observed in agroinfiltrated tobacco leaves by the construct carrying the Psp68 promoter::GUS, subjected to abiotic stress and exogenous hormonal treatments. Stress-inducible nature of Psp68 promoter opens possibility for the study of the gene regulation under stress condition. Therefore, may be useful in the field of agriculture and biotechnology.
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Affiliation(s)
- Sufara Akhter Banu
- International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
| | - Kazi Md Kamrul Huda
- International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi, India
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8
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Banu SA, Huda KMK, Tuteja N. Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrobacterium-mediated transient assay. PLANT SIGNALING & BEHAVIOR 2014; 9:e28992. [PMID: 24785194 PMCID: PMC4091197 DOI: 10.4161/psb.28992] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Helicases are molecular motor proteins that perform a variety of cellular functions including transcription, translation, DNA replication and repair, RNA maturation, ribosome synthesis, nuclear export and splicing processes. The p68 is an evolutionarily conserved protein which plays pivotal roles in all aspect RNA metabolism processes. It is well established that helicases provides abiotic stress adaptation in plants but analysis of cis-regulatory elements present in the upstream regions is still infancy. Here we report isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 in response to abiotic stress and hormonal regulation. The promoter of Psp68 was isolated by gene walking PCR from pea genomic DNA library constructed in BD genome walker kit. In silico analysis revealed that promoter of Psp68 contained a TATA, a CAAT motif and also harbors some important stress and hormone associated cis regulatory elements, including E-box, AGAAA, GATA-box, ACGT, GAAAA and GTCTC. Functional analyses were performed by Agrobacterium-mediated transient assay in tobacco leaves. Very high level of GUS activity was observed in agroinfiltrated tobacco leaves by the construct carrying the Psp68 promoter::GUS, subjected to abiotic stress and exogenous hormonal treatments. Stress-inducible nature of Psp68 promoter opens possibility for the study of the gene regulation under stress condition. Therefore, may be useful in the field of agriculture and biotechnology.
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9
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Lorgeoux RP, Pan Q, Le Duff Y, Liang C. DDX17 promotes the production of infectious HIV-1 particles through modulating viral RNA packaging and translation frameshift. Virology 2013; 443:384-92. [PMID: 23769241 DOI: 10.1016/j.virol.2013.05.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/24/2013] [Accepted: 05/18/2013] [Indexed: 01/13/2023]
Abstract
RNA helicases are a large family of proteins that rearrange RNA structures and remodel ribonucleic protein complexes using energy derived from hydrolysis of nucleotide triphosphates. They have been shown to participate in every step of RNA metabolism. In the past decade, an increasing number of helicases were shown to promote or inhibit the replication of different viruses, including human immunodeficiency virus type 1. Among these helicases, the DEAD-box RNA helicase DDX17 was recently reported to modulate HIV-1 RNA stability and export. In this study, we further show that the helicase activity of DDX17 is required for the production of infectious HIV-1 particles. Over expression of the DDX17 mutant DQAD in HEK293 cells reduces the amount of packaged viral genomic RNA and diminishes HIV-1 Gag-Pol frameshift. Altogether, these data demonstrate that DDX17 promotes the production of HIV-1 infectious particles by modulating HIV-1 RNA metabolism.
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10
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Takaoka Y, Shimizu Y, Hasegawa H, Ouchi Y, Qiao S, Nagahara M, Ichihara M, Lee JD, Adachi K, Hamaguchi M, Iwamoto T. Forced expression of miR-143 represses ERK5/c-Myc and p68/p72 signaling in concert with miR-145 in gut tumors of Apc(Min) mice. PLoS One 2012; 7:e42137. [PMID: 22876303 PMCID: PMC3410903 DOI: 10.1371/journal.pone.0042137] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 07/02/2012] [Indexed: 12/28/2022] Open
Abstract
Recently, miR-143 and miR-145 have been shown to belong to a subset of microRNAs whose expression is controlled by a complex of a tumor suppressor p53 and DEAD-box RNA helicase subunits p68/p72. While accumulating studies have acknowledged that both miRNAs function as tumor suppressors and are similarly regulated, evidence of their coordinated action against tumorigenesis has been poorly presented. Herein, we establish transgenic mice that express miR-143 under the control of the CAG regulatory unit. When crossbred with Apc(Min/+) mice, the development of tumors in the small intestines is significantly attenuated. In the transgenic small intestine tumors, the endogenous miR-145 is also enhanced and the expression of c-Myc and p68/p72, both of which have been reported to be pivotal for gut tumor development, is suppressed, corresponding to the downregulation of ERK5. We demonstrate that the combination of miR-143 and miR-145 inhibits the expression of c-Myc in human colon cancer cells, whereas miR-145 retards that of p72. Moreover, we show the possibilities that miR-145 modulates p72 expression through its 3' untranslated region and that c-Myc downregulation is involved in both p68 suppression and miR-145 induction. These findings suggest that forced expression of miR-143, probably interacting with endogenous miR-145, inhibits ERK5/c-Myc and p68/p72/β-catenin signaling and hampers small intestine tumor development in Apc(Min/+) mice. This unique cascade, in turn, may prevent overproduction of a subset of tumor suppressive miRNAs by repressing their own modulators, p68/p72.
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Affiliation(s)
- Yuji Takaoka
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Yuko Shimizu
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Hitoki Hasegawa
- The Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi, Japan
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yasuo Ouchi
- The Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi, Japan
| | - Shanlou Qiao
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Miki Nagahara
- The Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi, Japan
| | - Masatoshi Ichihara
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Jiing-Dwan Lee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Koichi Adachi
- Radioisotope Research Center Medical Division, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Michinari Hamaguchi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takashi Iwamoto
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
- The Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi, Japan
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11
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Moore HC, Johnston M, Nicol SM, Bourdon JC, Thompson AM, Hutvagner G, Fuller-Pace FV. An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA. RNA (NEW YORK, N.Y.) 2011; 17:555-562. [PMID: 21346006 PMCID: PMC3062168 DOI: 10.1261/rna.2591611] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 01/28/2011] [Indexed: 05/27/2023]
Abstract
The DEAD-box RNA helicase p68 (DDX5) plays important roles in several cellular processes, including transcription, pre-mRNA processing, and microRNA (miRNA) processing. p68 expression is growth and developmentally regulated, and alterations in p68 expression and/or function have been implicated in tumor development. The p68 gene encodes an evolutionarily conserved, alternatively spliced, intron the function of which has to date remained unclear. Although the intron-containing p68 RNA does not appear to yield an alternative p68 protein, it is differentially expressed in cell lines and tissues, indicating regulation of expression. Here we show that the p68 conserved intron encodes a novel putative miRNA, suggesting a previously unknown possible regulatory function for the p68 intron. We show that this miRNA (referred to as p68 miRNA) is processed from the intron via the canonical miRNA-processing pathway and that it associates with the Argonaute protein Ago2. Finally we show that the p68 miRNA suppresses an mRNA bearing complementary target sequences, suggesting that it is functional. These findings suggest a novel mechanism by which alterations in p68 expression may impact on the cell.
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12
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Bhattacharya R, Xu Y, Rahman MA, Couraud PO, Romero IA, Weksler BB, Weidanz JA, Bickel U. A novel vascular targeting strategy for brain-derived endothelial cells using a TCR mimic antibody. J Cell Physiol 2010; 225:664-72. [PMID: 20506235 DOI: 10.1002/jcp.22256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Organ-specific vascular targeting, for example, to the blood-brain barrier, requires the identification of unique molecular addresses on a subset of endothelial cells. The present study describes a crucial step towards tapping the exquisite specificity of the peptide/HLA class I system for this goal. We utilized a novel T-cell receptor (TCR) mimic antibody of high affinity and specificity, which is restricted by HLA-A2 and has been generated to recognize a peptide epitope derived from p68 RNA helicase (YLLPAIVHI). The parent protein is highly expressed by brain endothelial cells. Flow cytometry and confocal imaging showed that the antibody binds to HLA-A2-positive human brain-derived endothelial cells, both immortalized hCMEC/D3 cells and primary cells. The TCR mimic antibody undergoes internalization into vesicles, where significant colocalization occurs with the early endosomal marker EEA-1, but barely with caveolin-1. To our knowledge internalization of neither MHC class I protein nor TCR mimics by brain endothelial cells has been previously observed. Knock down of p68 protein expression by siRNA reduced the presentation of YLLPAIVHI-peptide/HLA-A2 complexes on the cell membrane by half as measured by flow cytometry 48 h later. We also found that brain endothelial cells isolated from HLA-A2 transgenic mouse strains express the A2 transgene, and brain endothelial cells of one of these strains also present YLLPAIVHI-peptide/HLA-A2, making these mouse strains suitable models for studying TCR mimic antibodies in vivo. In conclusion, these data strongly support the notion that TCR mimic antibodies could be a new class of therapeutic targeting agents in a wide variety of diseases.
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Affiliation(s)
- Raktima Bhattacharya
- Department of Pharmaceutical Sciences, Center for Vascular Drug Research, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, USA
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13
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Janknecht R. Multi-talented DEAD-box proteins and potential tumor promoters: p68 RNA helicase (DDX5) and its paralog, p72 RNA helicase (DDX17). Am J Transl Res 2010; 2:223-234. [PMID: 20589163 PMCID: PMC2892403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Accepted: 05/01/2010] [Indexed: 05/29/2023]
Abstract
P68 (DDX5) and p72 (DDX17) are members of the DEAD-box RNA helicase family. They can unwind double-stranded RNA and also contribute to the remodeling of ribonucleoprotein complexes. These activities of p68/p72 are required for efficient RNA splicing and microRNA processing. In addition, p68/p72 perform functions that are independent of their enzymatic activity. This is especially common to their role in gene regulation, where p68/p72 coactivate various transcription factors, including the tumor suppressor p53, estrogen receptor alpha and beta-catenin. P68/p72 are posttranslationally modified by SUMO attachment and phosphorylation that regulate their coactivation potential, binding to known interactants or protein stability. Knock-out mouse models revealed that both DDX5 and DDX17 are essential genes during development. Furthermore, together with their ability to stimulate cell proliferation and prevent apoptosis, the reported overexpression of p68/p72 in three of the major human cancers (colon, breast, prostate) strongly suggests that p68/p72 promote tumorigenesis and might even represent proto-oncoproteins. If so, their inhibition holds promise as a novel way to contain or cure various carcinomas.
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Affiliation(s)
- Ralf Janknecht
- Department of Cell Biology, The University of Oklahoma Health Sciences Center, Biomedical Research Center BRC-1464 975 NE 10 Street, Oklahoma City, OK 73104, USA.
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14
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Verma B, Hawkins OE, Neethling FA, Caseltine SL, Largo SR, Hildebrand WH, Weidanz JA. Direct discovery and validation of a peptide/MHC epitope expressed in primary human breast cancer cells using a TCRm monoclonal antibody with profound antitumor properties. Cancer Immunol Immunother 2010; 59:563-73. [PMID: 19779714 PMCID: PMC11031085 DOI: 10.1007/s00262-009-0774-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
Abstract
The identification and validation of new cancer-specific T cell epitopes continues to be a major area of research interest. Nevertheless, challenges remain to develop strategies that can easily discover and validate epitopes expressed in primary cancer cells. Regarded as targets for T cells, peptides presented in the context of the major histocompatibility complex (MHC) are recognized by monoclonal antibodies (mAbs). These mAbs are of special importance as they lend themselves to the detection of epitopes expressed in primary tumor cells. Here, we use an approach that has been successfully utilized in two different infectious disease applications (WNV and influenza). A direct peptide-epitope discovery strategy involving mass spectrometric analysis led to the identification of peptide YLLPAIVHI in the context of MHC A*02 allele (YLL/A2) from human breast carcinoma cell lines. We then generated and characterized an anti-YLL/A2 mAb designated as RL6A TCRm. Subsequently, the TCRm mAb was used to directly validate YLL/A2 epitope expression in human breast cancer tissue, but not in normal control breast tissue. Moreover, mice implanted with human breast cancer cells grew tumors, yet when treated with RL6A TCRm showed a marked reduction in tumor size. These data demonstrate for the first time a coordinated direct discovery and validation strategy that identified a peptide/MHC complex on primary tumor cells for antibody targeting and provide a novel approach to cancer immunotherapy.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antigens, Neoplasm/immunology
- Blotting, Western
- Breast/metabolism
- Breast/pathology
- Breast Neoplasms/diagnosis
- Breast Neoplasms/immunology
- Breast Neoplasms/therapy
- Cancer Vaccines/therapeutic use
- DEAD-box RNA Helicases/immunology
- Enzyme-Linked Immunosorbent Assay
- Epitopes, T-Lymphocyte/immunology
- Female
- Flow Cytometry
- Histocompatibility Antigens Class I/immunology
- Humans
- Immunoenzyme Techniques
- Mice
- Mice, Nude
- Molecular Mimicry
- Peptide Fragments/immunology
- Peptide Fragments/therapeutic use
- Receptors, Antigen, T-Cell/immunology
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Surface Plasmon Resonance
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Bhavna Verma
- Department of Pharmaceutical Sciences, School of Pharmacy, Center for Immunotherapeutic Research, Texas Tech University Health Sciences Center, 1718 Pine Street, Abilene, TX 79601 USA
| | - Oriana E. Hawkins
- Department of Microbiology and Immunology, School of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | | | | | | | - William H. Hildebrand
- Department of Microbiology and Immunology, School of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | - Jon A. Weidanz
- Department of Pharmaceutical Sciences, School of Pharmacy, Center for Immunotherapeutic Research, Texas Tech University Health Sciences Center, 1718 Pine Street, Abilene, TX 79601 USA
- Receptor Logic, Inc, Abilene, TX 79601 USA
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15
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Guo J, Hong F, Loke J, Yea S, Lim CL, Lee U, Mann DA, Walsh MJ, Sninsky JJ, Friedman SL. A DDX5 S480A polymorphism is associated with increased transcription of fibrogenic genes in hepatic stellate cells. J Biol Chem 2009; 285:5428-37. [PMID: 20022962 DOI: 10.1074/jbc.m109.035295] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We recently identified a missense single nucleotide polymorphism (SNP) in DDX5 (rs1140409, p.S480A) that enhances the risk of developing cirrhosis. DDX5 is an ATP-dependent RNA helicase and transcriptional modulator. We hypothesized that the activity of DDX5 in regulating fibrogenic gene transcription in hepatic stellate cells (HSCs) is altered by the S480A SNP. To test this, we employed two approaches: 1) transient overexpression of DDX5 cDNA or siRNA knockdown of endogenous DDX5, with replacement by either DDX5 wild type (WT) or SNP cDNA, or 2) stable expression of exogenous DDX5 WT and SNP in HSC lines. WT DDX5 mRNA in HSCs was inversely correlated with gene expression for alpha2(I) collagen, tissue inhibitor of metalloproteinase-1, and transforming growth factor-beta1. Stable DDX5 SNP-expressing cells had higher basal and transforming growth factor-beta1-stimulated expression and enhanced promoter activities of fibrogenic genes. DDX5 variant-expressing cells also had higher Smad3 and AP-1-responsive reporter activities. In a one-hybrid GAL4 system, co-expression of the DDX5 SNP variant with chimeras of GAL4 DNA binding domain linked to JunD or Sp1 displayed higher transactivation of a GAL4-responsive reporter than that of DDX5 WT. Increased fibrogenic gene expression in DDX5 SNP-expressing cells was associated with reduced recruitment of DDX5 homodimers to responsive promoters, but there was no difference in the recruitment of the co-repressor HDAC1 (histone deacetylase 1). These data suggest that DDX5 is a repressor of fibrogenic genes in HSCs through interaction with transcriptional complexes. The enhanced fibrogenic activity of the DDX5 risk variant is linked to a reduced repressive function toward these target genes.
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Affiliation(s)
- Jinsheng Guo
- Division of Liver Diseases, Mount Sinai School of Medicine, New York, New York 10029, USA
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16
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Jensen ED, Niu L, Caretti G, Nicol SM, Teplyuk N, Stein GS, Sartorelli V, van Wijnen AJ, Fuller-Pace FV, Westendorf JJ. p68 (Ddx5) interacts with Runx2 and regulates osteoblast differentiation. J Cell Biochem 2008; 103:1438-51. [PMID: 17960593 DOI: 10.1002/jcb.21526] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Runx2 is an essential transcription factor for osteoblast development from mesenchymal progenitors. Runx2 regulates gene expression by interacting with numerous transcription factors and co-activators to integrate signaling events within the nucleus. In this study we used affinity purification and proteomic techniques to identify novel Runx2 interacting proteins. One of these proteins is the DEAD box RNA helicase, p68 (Ddx5). p68 regulates many aspects of RNA expression, including transcription and splicing. p68 co-localized with Runx2 in punctate foci within the nucleus. In transcription assays, p68 functioned as a co-activator of Runx2, but its helicase activity was not essential for co-activation. In accordance, Runx2 transcriptional activity was muted in p68-suppressed cells. Surprisingly, osteoblast differentiation of the multipotent progenitor C2C12 cell line was accelerated by p68 suppression and Runx2 suppressed p68 expression in calvarial progenitor cells. Together these data demonstrate that p68 is a novel co-activator for Runx2, but it inhibits osteogenic differentiation of progenitor cells. Moreover Runx2 has an active role in regulating p68 levels in osteoblast precursors. Thus, crosstalk between Runx2 and p68 controls osteoblast specification and maturation at multiple levels.
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Affiliation(s)
- Eric D Jensen
- The Cancer Center and Department of Orthopaedic Surgery, University of Minnesota, Minneapolis, Minnesota 55455, USA
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17
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Jalal C, Uhlmann-Schiffler H, Stahl H. Redundant role of DEAD box proteins p68 (Ddx5) and p72/p82 (Ddx17) in ribosome biogenesis and cell proliferation. Nucleic Acids Res 2007; 35:3590-601. [PMID: 17485482 PMCID: PMC1920232 DOI: 10.1093/nar/gkm058] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The DEAD box proteins encoded by the genes ddx5 (p68) and ddx17 (isoforms p72 and p82) are more closely related to each other than to any other member of their family. We found that p68 negatively controls p72/p82 gene expression but not vice versa. Knocking down of either gene does not affect cell proliferation, in case of p68 suppression, however, only on condition that p72/p82 overexpression was granted. In contrast, co-silencing of both genes causes perturbation of nucleolar structure and cell death. In mutant studies, the apparently redundant role(s) of p68 and p72/p82 correspond to their ability to catalyze RNA rearrangement rather than RNA unwinding reactions. In search for possible physiological targets of this RNA rearrangement activity it is shown that the nucleolytic cleavage of 32S pre-rRNA is reduced after p68 subfamily knock-down, most probably due to a failure in the structural rearrangement process within the pre-60S ribosomal subunit preceding the processing of 32S pre-rRNA.
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Affiliation(s)
| | | | - Hans Stahl
- *To whom correspondence should be addressed. +49 6841 16 26020+49 6841 16 26521
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18
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Katzenellenbogen RA, Egelkrout EM, Vliet-Gregg P, Gewin LC, Gafken PR, Galloway DA. NFX1-123 and poly(A) binding proteins synergistically augment activation of telomerase in human papillomavirus type 16 E6-expressing cells. J Virol 2007; 81:3786-96. [PMID: 17267499 PMCID: PMC1866132 DOI: 10.1128/jvi.02007-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Overcoming senescence signals in somatic cells is critical to cellular immortalization and carcinogenesis. High-risk human papillomavirus (HPV) can immortalize epithelial cells in culture through degradation of the retinoblastoma protein by HPV E7 and activation of hTERT transcription, the catalytic subunit of telomerase, by the heterodimer HPV E6/E6-associated protein (E6AP). Recent work in our laboratory identified a novel repressor of hTERT transcription, NFX1-91, which is targeted for ubiquitin-mediated degradation by HPV type 16 (HPV16) E6/E6AP. In contrast, NFX1-123, a splice variant NFX1, increased expression from an hTERT promoter that was activated by HPV16 E6/E6AP. Here, we show that HPV16 E6 bound both NFX1-91 and NFX1-123 through the common central domain of NFX1 in the absence of E6AP. NFX1-123 positively regulated hTERT expression, as its knockdown decreased hTERT mRNA levels and telomerase activity and its overexpression increased telomerase activity. We identified new protein partners of NFX1-123, including several cytoplasmic poly(A) binding proteins (PABPCs) that interacted with NFX1-123 through its N-terminal PAM2 motif, a protein domain characteristic of other PABPC protein partners. Furthermore, NFX1-123 and PABPCs together had a synergistic stimulatory effect on hTERT-regulated reporter assays. The data suggest that NFX1-123 is integral to hTERT regulation in HPV16 E6-expressing epithelial cells and that the interaction between NFX1-123 and PABPCs is critical to hTERT activity.
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Affiliation(s)
- Rachel A Katzenellenbogen
- Fred Hutchinson Cancer Research Center, and Department of Pediatrics, University of Washington, Seattle, WA 98109, USA.
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19
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Huang H, Shiffman ML, Cheung RC, Layden TJ, Friedman S, Abar OT, Yee L, Chokkalingam AP, Schrodi SJ, Chan J, Catanese JJ, Leong DU, Ross D, Hu X, Monto A, McAllister LB, Broder S, White T, Sninsky JJ, Wright TL. Identification of two gene variants associated with risk of advanced fibrosis in patients with chronic hepatitis C. Gastroenterology 2006; 130:1679-87. [PMID: 16697732 DOI: 10.1053/j.gastro.2006.02.032] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 02/08/2006] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Previously identified clinical risk factors such as sex, alcohol consumption, and age at infection do not accurately predict which patients with chronic hepatitis C (CHC) will develop advanced fibrosis (bridging fibrosis and cirrhosis). The aim of this study was to identify genetic polymorphisms that can predict the risk of advanced fibrosis in patients with CHC. METHODS A total of 916 subjects with CHC was enrolled from 2 centers. A gene-centric disease association study of 24,832 putative functional, single nucleotide polymorphisms (SNPs) was performed. Of the 1609 SNPs that were significantly associated (P </= .05) with advanced fibrosis in the discovery cohort (University of California San Francisco [UCSF], N = 433), the first batch of 100 SNPs were selected for validation in the replication cohort (Virginia Commonwealth University [VCU], N = 483). RESULTS A missense SNP in the DEAD box polypeptide 5 (DDX5) gene was significantly associated with an increased risk of advanced fibrosis in both the UCSF and the VCU cohorts (OR, 1.8 and 2.2, respectively). Two diplotype groups, carrying the haplotypes composed of the DDX5 SNP and 2 neighboring POLG2 SNPs were also significantly associated with an increased risk of advanced fibrosis and had comparable or better risk estimates. In addition, a missense SNP in the carnitine palmitoyltransferase 1A (CPT1A) gene was associated with a decreased risk of advanced fibrosis in both the UCSF and the VCU cohorts (OR, 0.3 and 0.6, respectively). CONCLUSIONS Subjects with CHC carrying DDX5 minor allele or DDX5-POLG2 haplotypes are at an increased risk of developing advanced fibrosis, whereas those carrying the CPT1A minor allele are at a decreased risk.
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20
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Uhlmann-Schiffler H, Jalal C, Stahl H. Ddx42p--a human DEAD box protein with RNA chaperone activities. Nucleic Acids Res 2006; 34:10-22. [PMID: 16397294 PMCID: PMC1325199 DOI: 10.1093/nar/gkj403] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human gene ddx42 encodes a human DEAD box protein highly homologous to the p68 subfamily of RNA helicases. In HeLa cells, two ddx42 poly(A)+ RNA species were detected both encoding the nuclear localized 938 amino acid Ddx42p polypeptide. Ddx42p has been heterologously expressed and its biochemical properties characterized. It is an RNA binding protein, and ATP and ADP modulate its RNA binding affinity. Ddx42p is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase. Interestingly, RNA unwinding by Ddx42p is promoted in the presence of a single-strand (ss) binding protein (T4gp32). Ddx42p, particularly in the ADP-bound form (the state after ATP hydrolysis), also mediates efficient annealing of complementary RNA strands thereby displacing the ss binding protein. Ddx42p therefore represents the first example of a human DEAD box protein possessing RNA helicase, protein displacement and RNA annealing activities. The adenosine nucleotide cofactor bound to Ddx42p apparently acts as a switch that controls the two opposing activities: ATP triggers RNA strand separation, whereas ADP triggers annealing of complementary RNA strands.
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Affiliation(s)
- Heike Uhlmann-Schiffler
- FR 2.3 Medical Biochemistry and Molecular Biology, Theoretical Medicine, University of the Saarland, D-66421 Homburg, Germany.
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21
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Abdelhaleem M. RNA helicases: regulators of differentiation. Clin Biochem 2005; 38:499-503. [PMID: 15885226 DOI: 10.1016/j.clinbiochem.2005.01.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 01/04/2005] [Accepted: 01/17/2005] [Indexed: 11/17/2022]
Abstract
RNA helicases are highly conserved enzymes that utilize the energy derived from NTP hydrolysis to modulate the structure of RNA. RNA helicases participate in all biological processes that involve RNA, including transcription, splicing and translation. Based on the sequence of the helicase domain, they are classified into families, such as DDX and DHX families of human RNA helicases. The specificity of RNA helicases to their targets is likely due to several factors, such as the sequence, interacting molecules, subcellular localization and the expression pattern of the helicases. There are several examples of the involvement of RNA helicases in differentiation. Human DDX3 has two closely related genes designated DDX3Y and DDX3X, which are localized to the Y and X chromosomes, respectively. DDX3Y protein is specifically expressed in germ cells and is essential for spermatogenesis. DDX25 is another RNA helicase which has been shown to be required for spermatogenesis. DDX4 shows specific expression in germ cells. The Drosophila ortholog of DDX4, known as vasa, is required for the formation of germ cells and oogenesis by a mechanism that involves regulating the translation of mRNAs essential for differentiation. Abstrakt is the Drosphila ortholog of DDX41, which has been shown to be involved in visual and CNS system development. DDX5 (p68) and its related DDX17 (p72) have also been implicated in organ/tissue differentiation. The ability of RNA helicases to modulate the structure and thus availability of critical RNA molecules for processing leading to protein expression is the likely mechanism by which RNA helicases contribute to differentiation.
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Affiliation(s)
- Mohamed Abdelhaleem
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Room 3691 Atrium, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.
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22
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Abdelhaleem M. Do human RNA helicases have a role in cancer? Biochim Biophys Acta Rev Cancer 2004; 1704:37-46. [PMID: 15238243 DOI: 10.1016/j.bbcan.2004.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Accepted: 05/06/2004] [Indexed: 11/24/2022]
Abstract
Human RNA helicases (HRH) represent a large family of enzymes that play important roles in RNA processing. The biochemical characteristics and biological functions of the majority of HRH are still to be determined. However, there are examples of dysregulation of HRH expression in various types of cancer. In addition, some HRH have been shown to be involved in the regulation of, or the molecular interaction with, molecules implicated in cancer. Other helicases take part in fusion transcripts resulting from cancer-associated chromosomal translocation. These findings raise the question of whether HRH can contribute to cancer development/progression. In this review, I summarize the cancer-related features of HRH.
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Affiliation(s)
- Mohamed Abdelhaleem
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Room 3691 Atrium, 555 University Avenue, Toronto, ON M5G 1X8, Canada.
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23
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Gendra E, Moreno A, Albà MM, Pages M. Interaction of the plant glycine-rich RNA-binding protein MA16 with a novel nucleolar DEAD box RNA helicase protein from Zea mays. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 38:875-886. [PMID: 15165181 DOI: 10.1111/j.1365-313x.2004.02095.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The maize RNA-binding MA16 protein is a developmentally and environmentally regulated nucleolar protein that interacts with RNAs through complex association with several proteins. By using yeast two-hybrid screening, we identified a DEAD box RNA helicase protein from Zea mays that interacted with MA16, which we named Z. maysDEAD box RNA helicase 1 (ZmDRH1). The sequence of ZmDRH1 includes the eight RNA helicase motifs and two glycine-rich regions with arginine-glycine-rich (RGG) boxes at the amino (N)- and carboxy (C)-termini of the protein. Both MA16 and ZmDRH1 were located in the nucleus and nucleolus, and analysis of the sequence determinants for their cellular localization revealed that the region containing the RGG motifs in both proteins was necessary for nuclear/nucleolar localization The two domains of MA16, the RNA recognition motif (RRM) and the RGG, were tested for molecular interaction with ZmDRH1. MA16 specifically interacted with ZmDRH1 through the RRM domain. A number of plant proteins and vertebrate p68/p72 RNA helicases showed evolutionary proximity to ZmDRH1. In addition, like p68, ZmDRH1 was able to interact with fibrillarin. Our data suggest that MA16, fibrillarin, and ZmDRH1 may be part of a ribonucleoprotein complex involved in ribosomal RNA (rRNA) metabolism.
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Affiliation(s)
- Elisenda Gendra
- Departament de Genetica Molecular, IBMB-CSIC, C/Jordi Girona 18, Barcelona 08034, Spain
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24
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Tsai-Morris CH, Lei S, Jiang Q, Sheng Y, Dufau ML. Genomic organization and transcriptional analysis of gonadotropin-regulated testicular RNA helicase—GRTH/DDX25 gene. Gene 2004; 331:83-94. [PMID: 15094194 DOI: 10.1016/j.gene.2004.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/07/2004] [Accepted: 02/04/2004] [Indexed: 10/26/2022]
Abstract
The gonadotropin-regulated testicular RNA helicase (GRTH/DDX25) is a new member of the DEAD-box protein family. Phylogenetic analysis revealed that GRTH is distantly related to other members of the family. GRTH is transcriptionally up-regulated by gonadotropin, displays ATPase and RNA helicase activities, and participates in germ cell development. To understand the regulation of GRTH gene expression, we investigated its structural organization and aspects of basal transcriptional regulation at the promoter domain. The 20-kb mouse GRTH gene contains 12 coding exons and all but one of its conserved helicase motifs are contained within single exons. GRTH is a TATA-less gene with multiple transcriptional start sites (TSS), GC-rich sequences and a promoter located within -205/+63 bp of the gene. Sequences -852/-354 and -501/-354 bp caused 40-60% and >80% inhibition of transcription in expressing and non-expressing cells, respectively. Transcriptional activity was recovered only in expressing cells by the addition of upstream sequences (-1085/-852 bp). Sp1/Sp3 supported basal transcriptional activity in all cell types, while E-box was an activator-binding site only in non-expressing cells. These findings indicate that a differential pattern of transcriptional regulation may be involved in the control of GRTH gene expression in a cell-specific manner.
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Affiliation(s)
- Chon-Hwa Tsai-Morris
- Section on Molecular Endocrinology, ERRB, National Institute of Child Health and Human Development, National Institutes of Health, Building 49-6A36, 49 Convent Dr., Bethesda, MD 20892-4510, USA.
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25
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Valdez BC, Perlaky L, Henning D. Expression, cellular localization, and enzymatic activities of RNA helicase II/Gu(beta). Exp Cell Res 2002; 276:249-63. [PMID: 12027455 DOI: 10.1006/excr.2002.5538] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA helicase II/Gu (RH-II/Gu) is a nucleolar DEAD-box protein that unwinds double-stranded RNA and introduces secondary structure to a single-stranded RNA. We recently identified its paralogue, RH-II/Gu(beta), in contrast to the original RH-II/Gu(alpha). Their similar intron-exon structures on chromosome 10 suggest gene duplication. To determine functional differences, their expression, localization, and enzymatic activities were compared. RH-II/Gu(alpha) is expressed two- to threefold more than RH-II/Gu(beta) in most tissues. Both proteins localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gu(beta) also localizes to nuclear speckles containing splicing factor SC35, suggesting possible involvement in pre-mRNA splicing. The C-terminus responsible for nuclear speckle localization of RH-II/Gu(beta) contains an arginine-serine-rich domain present in some RNA splicing proteins. In vitro assays show weaker ATPase and RNA helicase activities of RH-II/Gu(beta). RH-II/Gu(alpha) unwinds RNA substrate with a 21- or 34-nt duplex and 5' overhangs, but RH-II/Gu(beta) unwinds only the shorter duplex. Although RH-II/Gu(beta) has no RNA folding activity, it catalyzes formation of an RNA complex with unidentified structure, which is not observed when assayed with a mixture of the two enzymes. Instead, the presence of RH-II/Gu(beta) stimulates RH-II/Gu(alpha) unwinding activity. Our data suggest distinct and complex regulation of expression of the two paralogues with nonredundant gene products.
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MESH Headings
- Active Transport, Cell Nucleus/drug effects
- Active Transport, Cell Nucleus/genetics
- Amino Acid Sequence
- Animals
- Cell Compartmentation/genetics
- Cell Nucleolus/enzymology
- Cell Nucleolus/genetics
- Cell Nucleus/enzymology
- Cells, Cultured
- DEAD-box RNA Helicases
- Dactinomycin/pharmacology
- Eukaryotic Cells/enzymology
- Gene Expression Regulation, Enzymologic/genetics
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Molecular Sequence Data
- Nuclear Matrix/enzymology
- Nuclear Matrix/genetics
- Nucleic Acid Synthesis Inhibitors/pharmacology
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Splicing/genetics
- RNA, Double-Stranded/drug effects
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- Tumor Cells, Cultured/enzymology
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Affiliation(s)
- Benigno C Valdez
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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26
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Godbout R, Packer M, Katyal S, Bléoo S. Cloning and expression analysis of the chicken DEAD box gene DDX1. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1574:63-71. [PMID: 11955614 DOI: 10.1016/s0167-4781(01)00346-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DEAD box proteins are putative RNA unwinding proteins found in organisms ranging from mammals to bacteria. While some DEAD box genes expressed in higher eukaryotes are ubiquitous, others have distribution profiles that suggest a cell-, tissue-, or developmental-specific role. The DEAD box gene, DDX1, was identified by differential screening of a subtracted retinoblastoma cDNA library. A limited survey of human fetal tissues indicated that DDX1 mRNA has a widespread distribution but is not uniformly expressed in all tissues. To further document the spatial and temporal distribution of DDX1 during embryonic development, we cloned the chicken DDX1 cDNA. The predicted amino acid sequence of chicken DDX1 was 93% identical to that of human DDX1. All DEAD box motifs, as well as a SPRY domain, were present in chicken DDX1. Northern and Western blot analyses showed highest levels of DDX1 at early stages of development. Tissue maturation was generally accompanied by a decrease in expression, although DDX1 levels remained elevated in late embryonic retina and brain. In situ hybridization of retinal tissue sections revealed widespread distribution of DDX1 mRNA at early developmental stages with preferential expression in amacrine and ganglion cells of the differentiated tissue. Preferential expression of DDX1 was also observed in specific areas of the brain in older embryos, such as the external granule layer of the cerebellum. These results suggest a specific role for DDX1 in subsets of differentiated cells as well as a more general role in undifferentiated cells.
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Affiliation(s)
- Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, T6G 1Z2, Edmonton, AB, Canada.
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27
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Valdez BC, Yang H, Hong E, Sequitin AM. Genomic structure of newly identified paralogue of RNA helicase II/Gu: detection of pseudogenes and multiple alternatively spliced mRNAs. Gene 2002; 284:53-61. [PMID: 11891046 DOI: 10.1016/s0378-1119(01)00888-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
RNA helicase II/Gu (RH-II/Gu or DDX21) is a DEAD-box enzyme that localizes to the nucleoli and may be involved in ribosomal RNA synthesis or processing. It has two paralogues, RH-II/Gualpha and RH-II/Gubeta, both genes of which are on chromosome 10. Their similar genomic structures suggest the two genes arose by gene duplication. Both genes are expressed at higher levels in some normal human tissues compared to matching tumor tissues. Pseudogenes for RH-II/Gubeta exist on chromosomes 2, 3 and 4. No pseudogene was identified for RH-II/Gualpha. Both exon inclusion and exon skipping were found to post-transcriptionally regulate RH-II/Gubeta gene expression. No alternative splicing was identified for RH-II/Gualpha. Overall, the results suggest that the two paralogues of RH-II/Gu arose by gene duplication but the resulting genes are differentially regulated.
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Affiliation(s)
- Benigno C Valdez
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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28
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Uhlmann-Schiffler H, Rössler OG, Stahl H. The mRNA of DEAD box protein p72 is alternatively translated into an 82-kDa RNA helicase. J Biol Chem 2002; 277:1066-75. [PMID: 11675387 DOI: 10.1074/jbc.m107535200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p68 and p72 are two highly related DEAD box proteins with similar biochemical activities in the nucleus of vertebrate cells; it is unknown whether they have redundant or differential in vivo functions. We report on a third member of this subfamily that is alternatively expressed from p72 mRNA. A detailed analysis of HeLa p72 mRNA was performed. It has an overall length of more than 5 kb and contains a 0.75-kb 5'-untranslated region and a 3'-untranslated region of 2.5 kb. Its open reading frame extends to nucleotide -243 upstream of the first in-frame AUG (A in the AUG triplet is +1) which serves as the p72 translation initiator codon. We provide evidence that alternative translation at a non-AUG within the extra coding region of this mRNA yields an 82-kDa protein (p82). Immunological studies substantiate that p82 is a naturally existing p72 variant and that both proteins are expressed at similar concentrations. p82 purified from HeLa cells is an ATP-dependent RNA helicase with biochemical properties almost identical to those of p72.
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Affiliation(s)
- Heike Uhlmann-Schiffler
- Fachbereich Medizinische Biochemie und Molekularbiologie, Fachrichtung Theoretische Medizin, Universität des Saarlandes, D-66421 Homburg, Germany
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29
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Hirst M, Ho C, Sabourin L, Rudnicki M, Penn L, Sadowski I. A two-hybrid system for transactivator bait proteins. Proc Natl Acad Sci U S A 2001; 98:8726-31. [PMID: 11447261 PMCID: PMC37503 DOI: 10.1073/pnas.141413598] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We describe a two-hybrid strategy for detection of interactions with transactivator proteins. This repressed transactivator (RTA) system employs the N-terminal repression domain of the yeast general repressor TUP1. TUP1-GAL80 fusion proteins, when coexpressed with GAL4, are shown to inhibit transcription of GAL4-dependent reporter genes. This effect requires the C-terminal 30 residues of GAL4, which are required for interaction with GAL80 in vitro. Furthermore, repression of GAL transcription by TUP1-GAL80 requires SRB10, demonstrating that the TUP1 repression domain, in the context of a two-hybrid interaction, functions by the same mechanism as endogenous TUP1. Using this strategy, we demonstrate interactions between the mammalian basic helix-loop-helix proteins MyoD and E12, and between c-Myc and Bin-1. We have also identified interacting clones from a TUP1-cDNA fusion expression library by using GAL4-VP16 as a bait fusion. These results demonstrate that RTA is generally applicable for identifying and characterizing interactions with transactivator proteins in vivo.
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Affiliation(s)
- M Hirst
- Department of Biochemistry and Molecular Biology; University of British Columbia Vancouver, BC, Canada V6T 1Z3
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Rössler OG, Straka A, Stahl H. Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72. Nucleic Acids Res 2001; 29:2088-96. [PMID: 11353078 PMCID: PMC55448 DOI: 10.1093/nar/29.10.2088] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA helicases, like their DNA-specific counterparts, can function as processive enzymes, unwinding RNA with a defined step size in a unidirectional fashion. Recombinant nuclear DEAD-box protein p68 and its close relative p72 are reported here to function in a similar fashion, though the processivity of both RNA helicases appears to be limited to only a few consecutive catalytic steps. The two proteins resemble each other also with regard to other biochemical properties. We have found that both proteins exhibit an RNA annealing in addition to their helicase activity. By using both these activities the enzymes are able in vitro to catalyse rearrangements of RNA secondary structures that otherwise are too stable to be resolved by their low processive helicase activities. RNA rearrangement proceeds via protein induced formation and subsequent resolution of RNA branch migration structures, whereby the latter step is dependent on ATP hydrolysis. The analysed DEAD-box proteins are reminiscent of certain DNA helicases, for example those found in bacteriophages T4 and T7, that catalyse homologous DNA strand exchange in cooperation with the annealing activity of specific single strand binding proteins.
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Affiliation(s)
- O G Rössler
- Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, D-66421 Homburg, Germany
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