1
|
Fujita KI, Ito M, Irie M, Harada K, Fujiwara N, Ikeda Y, Yoshioka H, Yamazaki T, Kojima M, Mikami B, Mayeda A, Masuda S. Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes. Nat Commun 2024; 15:455. [PMID: 38225262 PMCID: PMC10789772 DOI: 10.1038/s41467-023-44217-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
mRNA export is an essential pathway for the regulation of gene expression. In humans, closely related RNA helicases, UAP56 and URH49, shape selective mRNA export pathways through the formation of distinct complexes, known as apo-TREX and apo-AREX complexes, and their subsequent remodeling into similar ATP-bound complexes. Therefore, defining the unidentified components of the apo-AREX complex and elucidating the molecular mechanisms underlying the formation of distinct apo-complexes is key to understanding their functional divergence. In this study, we identify additional apo-AREX components physically and functionally associated with URH49. Furthermore, by comparing the structures of UAP56 and URH49 and performing an integrated analysis of their chimeric mutants, we exhibit unique structural features that would contribute to the formation of their respective complexes. This study provides insights into the specific structural and functional diversification of these two helicases that diverged from the common ancestral gene Sub2.
Collapse
Affiliation(s)
- Ken-Ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
- Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Misa Ito
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Midori Irie
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Kotaro Harada
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Naoko Fujiwara
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Yuya Ikeda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Hanae Yoshioka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Tomohiro Yamazaki
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Masaki Kojima
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, 611-0011, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
- Department of Food Science and Nutrition, Faculty of Agriculture Kindai University, Nara, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Nara, 631-8505, Japan.
- Antiaging Center, Kindai University, Higashiosaka, Osaka, 577-8502, Japan.
| |
Collapse
|
2
|
Xie Y, Gao S, Zhang K, Bhat P, Clarke BP, Batten K, Mei M, Gazzara M, Shay JW, Lynch KW, Angelos AE, Hill PS, Ivey AL, Fontoura BMA, Ren Y. Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Cell Rep 2023; 42:112988. [PMID: 37578863 PMCID: PMC10508174 DOI: 10.1016/j.celrep.2023.112988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/10/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
mRNA in eukaryotic cells is packaged into highly compacted ribonucleoprotein particles (mRNPs) in the nucleus and exported to the cytoplasm for translation. mRNP packaging and export require the evolutionarily conserved transcription-export (TREX) complex. TREX facilitates loading of various RNA-binding proteins on mRNA through the action of its DDX39B subunit. SARNP (Tho1 [transcriptional defect of Hpr1 by overexpression 1] in yeast) is shown to interact with DDX39B and affect mRNA export. The molecular mechanism of how SARNP recognizes DDX39B and functions in mRNP assembly is unclear. Here, we determine the crystal structure of a Tho1/DDX39B/RNA complex, revealing a multivalent interaction mediated by tandem DDX39B interacting motifs in SARNP/Tho1. The high-order complex of SARNP and DDX39B is evolutionarily conserved, and human SARNP can engage with five DDX39B molecules. RNA sequencing (RNA-seq) from SARNP knockdown cells shows the most affected RNAs in export are GC rich. Our work suggests the role of the high-order SARNP/DDX39B/RNA complex in mRNP assembly and export.
Collapse
Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Austin L Ivey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA.
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
| |
Collapse
|
3
|
Kang GJ, Park MK, Byun HJ, Kim HJ, Kim EJ, Yu L, Kim B, Shim JG, Lee H, Lee CH. SARNP, a participant in mRNA splicing and export, negatively regulates E-cadherin expression via interaction with pinin. J Cell Physiol 2019; 235:1543-1555. [PMID: 31313837 DOI: 10.1002/jcp.29073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/18/2019] [Indexed: 12/17/2022]
Abstract
Triple-negative breast cancer (TNBC) is associated with a high mortality rate, which is related to the insufficient number of appropriate biomarkers and targets. Therefore, there is an urgent need to discover appropriate biomarkers and targets for TNBC. SARNP (Hcc-1 and CIP29) is highly expressed in several cancers. It binds to UAP56, an RNA helicase component of the TREX complex in messenger RNA (mRNA) splicing and export. However, the role of SARNP in mRNA splicing and export and in the progression of breast cancer, especially of TNBC, remains unknown. Therefore, we examined the role of SARNP in mRNA splicing and export and progression of TNBC. We confirmed that SARNP binds to UAP56 and Aly and that SARNP overexpression enhances mRNA splicing, whereas its knockdown suppressed mRNA export. The SARNP overexpression induced the proliferation of MCF7 cells, whereas its knockdown induced E-cadherin expression and downregulated vimentin and N-cadherin expressions in SK-BR-3 and MDA-MB-231 cells. SARNP downregulates E-cadherin expression by interaction with pinin. Mice injected with MDA-MB-231shSARNP cells exhibited a significant reduction in tumor growth and lung metastasis compared with those injected with MDA-MB-231shCon cells in vivo. These findings suggested that SARNP is involved in mRNA splicing and export. SARNP maintains mesenchymal phenotype by escaping from inhibitory interaction with pinin leading to the downregulation of E-cadherin expression.
Collapse
Affiliation(s)
| | - Mi Kyung Park
- Division of Cancer Biology, National Cancer Center, Goyang, Korea
| | | | - Hyun Ji Kim
- College of Pharmacy, Dongguk University, Seoul, Korea
| | - Eun Ji Kim
- College of Pharmacy, Dongguk University, Seoul, Korea
| | - Lu Yu
- College of Pharmacy, Dongguk University, Seoul, Korea
| | - Boram Kim
- College of Pharmacy, Dongguk University, Seoul, Korea
| | - Jae Gal Shim
- Division of Cancer Biology, National Cancer Center, Goyang, Korea
| | - Ho Lee
- Division of Cancer Biology, National Cancer Center, Goyang, Korea
| | | |
Collapse
|
4
|
Mechanism and Regulation of Co-transcriptional mRNP Assembly and Nuclear mRNA Export. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:1-31. [DOI: 10.1007/978-3-030-31434-7_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
5
|
Abstract
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.
Collapse
|
6
|
Jacobsen JOB, Allen MD, Freund SMV, Bycroft M. High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1. Acta Crystallogr F Struct Biol Commun 2016; 72:500-6. [PMID: 27303905 PMCID: PMC4909252 DOI: 10.1107/s2053230x16007597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/06/2016] [Indexed: 11/10/2022] Open
Abstract
THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.
Collapse
Affiliation(s)
| | - Mark D. Allen
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England
| | | | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England
| |
Collapse
|
7
|
Mo XB, Lu X, Zhang YH, Zhang ZL, Deng FY, Lei SF. Gene-based association analysis identified novel genes associated with bone mineral density. PLoS One 2015; 10:e0121811. [PMID: 25811989 PMCID: PMC4374695 DOI: 10.1371/journal.pone.0121811] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/04/2015] [Indexed: 12/31/2022] Open
Abstract
Genetic factors contribute to the variation of bone mineral density (BMD), which is a major risk factor of osteoporosis. The aim of this study was to identify more “novel” genes for BMD. Based on the publicly available SNP-based P values, we performed an initial gene-based analysis in a total of 32,961 individuals. Furthermore, we performed differential expression, pathway and protein-protein interaction analyses to find supplementary evidence to support the significance of the identified genes. About 21,695 genes for femoral neck (FN)-BMD and 21,683 genes for lumbar spine (LS)-BMD were analyzed using gene-based association analysis. A total of 35 FN-BMD associated genes and 53 LS-BMD associated genes were identified (P < 2.3×10-6) after Bonferroni correction. Among them, 64 genes have not been reported in previous SNP-based genome-wide association studies. Differential expression analysis further supported the significant associations of 14 genes with FN-BMD and 19 genes with LS-BMD. Especially, WNT3 and WNT9B in the Wnt signaling pathway for FN-BMD were further supported by pathway analysis and protein-protein interaction analysis. The present study took the advantage of gene-based association method to perform a supplementary analysis of the GWAS dataset and found some BMD-associated genes. The evidence taken together supported the importance of Wnt signaling pathway genes in determining osteoporosis. Our findings provided more insights into the genetic basis of osteoporosis.
Collapse
Affiliation(s)
- Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yong-Hong Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Zeng-Li Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- * E-mail:
| |
Collapse
|
8
|
Walker A, Mrózek K, Kohlschmidt J, Rao KW, Pettenati MJ, Sterling LJ, Marcucci G, Carroll AJ, Bloomfield CD. New recurrent balanced translocations in acute myeloid leukemia and myelodysplastic syndromes: cancer and leukemia group B 8461. Genes Chromosomes Cancer 2013; 52:385-401. [PMID: 23225546 PMCID: PMC3874732 DOI: 10.1002/gcc.22036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 10/31/2012] [Indexed: 12/16/2022] Open
Abstract
Acquired chromosome abnormalities in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are among the most valuable determinants of diagnosis and prognosis. In search of new recurrent balanced translocations, we reviewed the Cancer and Leukemia Group B (CALGB) cytogenetics database containing pretreatment and relapse karyotypes of 4,701 adults with AML and 565 with MDS who were treated on CALGB trials. We identified all cases with balanced structural rearrangements occurring as a sole abnormality or in addition to one other abnormality, excluded abnormalities known to be recurrent, and then reviewed the literature to determine whether any of what we considered unique, previously unknown abnormalities had been reported. As a result, we identified seven new recurrent balanced translocations in AML or MDS: t(7;11)(q22;p15.5), t(10;11)(q23;p15), t(2;12)(p13;p13), t(12;17)(p13;q12), t(2;3)(p21;p21), t(5;21)(q31;q22), and t(8;14)(q24.1;q32.2), and additionally, t(10;12)(p11;q15), a new translocation in AML previously reported in a case of acute lymphoblastic leukemia. Herein, we report hematologic and clinical characteristics and treatment outcomes of patients with these newly recognized recurrent translocations. We also report 52 unique balanced translocations, together with the clinical data of patients harboring them, which to our knowledge have not been previously published. We hope that once the awareness of their existence is increased, some of these translocations may become recognized as novel recurring abnormalities. Identification of additional cases with both the new recurrent and the unique balanced translocations will enable determination of their prognostic significance and help to provide insights into the mechanisms of disease pathogenesis in patients with these rare abnormalities.
Collapse
Affiliation(s)
- Alison Walker
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | - Krzysztof Mrózek
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | - Jessica Kohlschmidt
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN
| | - Kathleen W. Rao
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mark J. Pettenati
- Comprehensive Cancer Center Wake Forest University, Winston-Salem, NC
| | - Lisa J. Sterling
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | - Guido Marcucci
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | | | - Clara D. Bloomfield
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| |
Collapse
|
9
|
Kelsey JS, Blumberg DD. A SAP domain-containing protein shuttles between the nucleus and cell membranes and plays a role in adhesion and migration in D. discoideum. Biol Open 2013; 2:396-406. [PMID: 23616924 PMCID: PMC3625868 DOI: 10.1242/bio.20133889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 01/10/2013] [Indexed: 12/30/2022] Open
Abstract
The AmpA protein reduces cell adhesion, thereby influencing cell migration in Dictyostelium. To understand how ampA influences cell migration, second site suppressors of an AmpA overexpressing cell line were created by REMI mutagenesis. Mutant candidates were identified by their ability to suppress the large plaques that the AmpA overexpressing cells form on bacterial lawns as a result of their increased rate of migration. One suppressor gene, sma, encodes an uncharacterized protein, which contains a SAP DNA-binding domain and a PTEN-like domain. Using sma gene knockouts and Sma-mRFP expressing cell lines, a role for sma in influencing cell migration was uncovered. Knockouts of the sma gene in a wild-type background enhanced chemotaxis. An additional role for Sma in influencing cell–cell adhesion was also demonstrated. Sma protein transitions between cytosolic and nuclear localizations as a function of cell density. In growing cells migrating to folic acid it is localized to regions of actin polymerization and absent from the nucleus. A role for Sma in influencing ampA mRNA levels is also demonstrated. Sma additionally appears to be involved in ampA pathways regulating cell size, actin polymerization, and cell substrate adhesion. We present insights to the SAP domain-containing group of proteins in Dictyostelium and provide evidence of a role for a SAP domain-containing protein shuttling from the nucleus to sites of actin polymerization during chemotaxis to folic acid and influencing the efficiency of migration.
Collapse
Affiliation(s)
- Jessica S Kelsey
- Department of Biological Sciences, University of Maryland Baltimore County , 1000 Hilltop Circle, Baltimore, MD 21250 , USA
| | | |
Collapse
|
10
|
Dufu K, Livingstone MJ, Seebacher J, Gygi SP, Wilson SA, Reed R. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes Dev 2010; 24:2043-53. [PMID: 20844015 DOI: 10.1101/gad.1898610] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The conserved TREX mRNA export complex is known to contain UAP56, Aly, Tex1, and the THO complex. Here, we carried out proteomic analysis of immunopurified human TREX complex and identified the protein CIP29 as the only new component with a clear yeast relative (known as Tho1). Tho1 is known to function in mRNA export, and we provide evidence that CIP29 likewise functions in this process. Like the known TREX components, a portion of CIP29 localizes in nuclear speckle domains, and its efficient recruitment to mRNA is both splicing- and cap-dependent. We show that UAP56 mediates an ATP-dependent interaction between the THO complex and both CIP29 and Aly, indicating that TREX assembly is ATP-dependent. Using recombinant proteins expressed in Escherichia coli, we show that UAP56, Aly, and CIP29 form an ATP-dependent trimeric complex, and UAP56 bridges the interaction between CIP29 and Aly. We conclude that the interaction of two conserved export proteins, CIP29 and Aly, with UAP56 is strictly regulated by ATP during assembly of the TREX complex.
Collapse
Affiliation(s)
- Kobina Dufu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
PURPOSE OF REVIEW Recurring chromosomal abnormalities are considered the primary genetic change in oncogenesis as well as an important indicator for tumor phenotype and clinical outcome. This review highlights recent findings regarding the genes associated with chromosomal translocations. RECENT FINDINGS A great number of novel fusion genes associated with chromosomal translocations have been cloned. These novel fusion genes are found in the smaller part of various malignancies, and it can be expected that the significance of novel fusion gene occurrence for oncogenesis will be clarified in the not too distant future. Observation of high frequencies of mutations in NOTCH1, NPM and JAK2 in T-cell acute lymphoblastic leukemia, acute myeloid leukemia with normal karyotype and myeloproliferative disorders (polycythemia vera, essential thrombocythemia and idiopathic myelofibrosis) have provided important suggestions for a better understanding of chromosomal translocations. This is because all these genes had already been identified as genes associated with chromosomal translocations in a small subset of specific phenotypes of hematologic malignancies. SUMMARY This review summarizes recent findings associated with chromosomal translocations including newly identified fusion genes, a novel mechanism of fusion gene formation and their relevance for novel targeted therapies. Continuing attempts to identify genes associated with chromosomal translocations can be expected to provide further insights into the significance of various gene alterations in cancer and the development of novel targeted therapies.
Collapse
Affiliation(s)
- Tomohiko Taki
- Department of Molecular Laboratory Medicine, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | | |
Collapse
|
12
|
Dirksen EHC, Cloos J, Braakhuis BJM, Brakenhoff RH, Heck AJR, Slijper M. Human Lymphoblastoid Proteome Analysis Reveals a Role for the Inhibitor of Acetyltransferases Complex in DNA Double-Strand Break Response. Cancer Res 2006; 66:1473-80. [PMID: 16452203 DOI: 10.1158/0008-5472.can-05-2129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A DNA double-strand break (DSB) is highly cytotoxic; it emerges as the type of DNA damage that most severely affects the genomic integrity of the cell. It is essential that DNA DSBs are recognized and repaired efficiently, in particular, prior to mitosis, to prevent genomic instability and eventually, the development of cancer. To assess the pathways that are induced on DNA DSBs, 14 human lymphoblastoid cell lines were challenged with bleomycin for 30 and 240 minutes to establish the fast and more prolonged response, respectively. The proteomes of 14 lymphoblastoid cell lines were investigated to account for the variation among individuals. The primary DNA DSB response was expected to occur within the nucleus; therefore, the nuclear extracts were considered. Differential analysis was done using two-dimensional difference in gel electrophoresis; paired ANOVA statistics were used to recognize significant changes in time. Many proteins whose nuclear levels changed statistically significantly showed a fast response, i.e., within 30 minutes after bleomycin challenge. A significant number of these proteins could be assigned to known DNA DSB response processes, such as sensing DSBs (Ku70), DNA repair through effectors (high-mobility group protein 1), or cell cycle arrest at the G(2)-M phase checkpoint (14-3-3 zeta). Interestingly, the nuclear levels of all three proteins in the INHAT complex were reduced after 30 minutes of bleomycin challenge, suggesting that this complex may have a role in changing the chromatin structure, allowing the DNA repair enzymes to gain access to the DNA lesions.
Collapse
Affiliation(s)
- Eef H C Dirksen
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 15, 3584 CA Utrecht, the Netherlands
| | | | | | | | | | | |
Collapse
|
13
|
Abstract
In all organisms, cell proliferation is orchestrated by coordinated patterns of gene expression. Transcription results from the activity of the RNA polymerase machinery and depends on the ability of transcription activators and repressors to access chromatin at specific promoters. During the last decades, increasing evidence supports aberrant transcription regulation as contributing to the development of human cancers. In fact, transcription regulatory proteins are often identified in oncogenic chromosomal rearrangements and are overexpressed in a variety of malignancies. Most transcription regulators are large proteins, containing multiple structural and functional domains some with enzymatic activity. These activities modify the structure of the chromatin, occluding certain DNA regions and exposing others for interaction with the transcription machinery. Thus, chromatin modifiers represent an additional level of transcription regulation. In this review we focus on several families of transcription activators and repressors that catalyse histone post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination and SUMOylation); and how these enzymatic activities might alter the correct cell proliferation program, leading to cancer.
Collapse
Affiliation(s)
- Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
| | | |
Collapse
|