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Papini C, Wang Z, Kudalkar SN, Schrank TP, Tang S, Sasaki T, Wu C, Tejada B, Ziegler SJ, Xiong Y, Issaeva N, Yarbrough WG, Anderson KS. Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer. iScience 2022; 25:105077. [PMID: 36164654 PMCID: PMC9508485 DOI: 10.1016/j.isci.2022.105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 12/03/2022] Open
Abstract
APOBEC3 family members are cytidine deaminases catalyzing conversion of cytidine to uracil. Many studies have established a link between APOBEC3 expression and cancer development and progression, especially APOBEC3A (A3A) and APOBEC3B (A3B). Preclinical studies with human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) and clinical trial specimens revealed induction of A3B, but not A3A expression after demethylation. We examined the kinetic features of the cytidine deaminase activity for full length A3B and found that longer substrates and a purine at −2 position favored by A3B, whereas A3A prefers shorter substrates and an adenine or thymine at −2 position. The importance and biological significance of A3B catalytic activity rather than A3A and a preference for purine at the −2 position was also established in HPV+ HNSCCs. Our study explored factors influencing formation of A3A and A3B-related cancer mutations that are essential for understanding APOBEC3-related carcinogenesis and facilitating drug discovery. A3B is upregulated after 5-AzaC treatment and related to 5-AzaC sensitivity in HPV+ HNSCC Full-length A3B prefers longer substrates and a purine at −2 site biochemically A3B also prefers a purine at −2 site in both HPV+ and HPV− HNSCC cells A3B signature at -2 site linked to poor patient survival in HPV+ HNSCC low smokers
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Affiliation(s)
- Christina Papini
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Zechen Wang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Shalley N Kudalkar
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Travis Parke Schrank
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Su Tang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Tomoaki Sasaki
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Cory Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Brandon Tejada
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Samantha J Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Lab Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Wendell G Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Lab Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Shi M, Tan L, Zhang Y, Meng C, Wang W, Sun Y, Song C, Liu W, Liao Y, Yu S, Ren T, Ding Z, Liu X, Qiu X, Ding C. Characterization and functional analysis of chicken APOBEC4. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 106:103631. [PMID: 31991164 DOI: 10.1016/j.dci.2020.103631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The APOBEC proteins play significant roles in the innate and adaptive immune system, probably due to their deaminase activities. Because APOBEC1 (A1) and APOBEC3 (A3) are absent in the chicken genome, we were interested in determining whether chicken APOBEC4 (A4) possessed more complex functions than its mammalian homologs. In this study, chicken A4 (chA4) mRNA was identified and cloned for the first time. Based on bioinformatics analyses, the conserved zinc-coordinating motif (HXE … PC(X)2-6C) was identified on the surface of chA4 and contained highly conserved His97, Glu99, Pro130, Cys131 and Cys138 active sites. The highest expression levels of constitutive chA4 were detected in primary lymphocytes and bursa of Fabricius. Newcastle Disease (ND) is one of the most serious infectious diseases in birds, causing major economic losses to the poultry industry. In vitro, Newcastle Disease Virus (NDV) early infection induced significant increases in chA4 expression in the chicken B cell line, DT40, the macrophage cell line, HD11 and the CD4+ T cell line, MSB-1, but not the fibroblast cell line, DF-1. In vivo, the expression levels of chA4 were up-regulated in several tissues from NDV-infected chickens, especially the thymus, testicles, duodenum and kidney. The high level expression of exogenous chA4 displayed inhibitory effects on NDV and reduced viral RNA in infected cells. Taken together, these data demonstrate that chA4 is involved in the chicken immune system and may play important roles in host anti-viral responses.
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Affiliation(s)
- Mengyu Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Yaodan Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Wei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Shengqing Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Tao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, People's Republic of China.
| | - Zhuang Ding
- Laboratory of Infectious Diseases, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Xiufan Liu
- Key Laboratory of Animal Infectious Diseases, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China.
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China.
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China.
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Abstract
Background: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade. Host cytidine deaminases (
e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis. By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity. To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation. The model plant
Arabidopsis thaliana genome encodes nine cytidine deaminases (
AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Methods: Here we tested the effects of expression of
AtCDAs on the pararetrovirus Cauliflower mosaic virus (CaMV). Two different experiments were carried out. First, we transiently overexpressed each one of the nine
A. thalianaAtCDA genes in
Nicotianabigelovii plants infected with CaMV, and characterized the resulting mutational spectra, comparing them with those generated under normal conditions. Secondly, we created
A. thaliana transgenic plants expressing an artificial microRNA designed to knock-out the expression of up to six
AtCDA genes. This and control plants were then infected with CaMV. Virus accumulation and mutational spectra where characterized in both types of plants. Results: We have shown that the
A. thalianaAtCDA1 gene product exerts a mutagenic activity, significantly increasing the number of G to A mutations
in vivo, with a concomitant reduction in the amount of CaMV genomes accumulated. Furthermore, the magnitude of this mutagenic effect on CaMV accumulation is positively correlated with the level of
AtCDA1 mRNA expression in the plant. Conclusions: Our results suggest that deamination of viral genomes may also work as an antiviral mechanism in plants.
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Affiliation(s)
- Susana Martín
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de València, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de València, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", CSIC-Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain.,Área de Genética, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de València, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain.,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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Banerjee Y, Santos RD, Al-Rasadi K, Rizzo M. Targeting PCSK9 for therapeutic gains: Have we addressed all the concerns? Atherosclerosis 2016; 248:62-75. [PMID: 26987067 DOI: 10.1016/j.atherosclerosis.2016.02.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 01/28/2016] [Accepted: 02/16/2016] [Indexed: 02/08/2023]
Abstract
Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) regulates the expression of low-density lipoprotein (LDL)-receptors, through reducing their recycling by binding to the receptor along with LDL and targeting it for lysosomal destruction. PCSK9 also enhances the degradation of very-low-density-lipoprotein receptor (VLDLR) and lipoprotein receptor-related protein 1 (LRP-1) in a LDL-receptor independent manner. This role in lipid homeostasis presents PCSK9 as an attractive target for the therapeutic management of familial hypercholesterolemia as well as other refractory dyslipidaemias. However, PCSK9 mediates multifarious functions independent of its role in lipid homeostasis, which can be grouped under "pleiotropic functions" of the protein. This includes PCSK9's role in: trafficking of epithelial sodium channel; hepatic regeneration; pancreatic integrity and glucose homeostasis; antiviral activity; antimalarial activity; regulation of different cell signalling pathways; cortical neural differentiation; neuronal apoptosis and Alzheimer's disease. The question that needs to be investigated in depth is "How will the pleotropic functions of PCSK9, be affected by the therapeutic intervention of the protease's LDL-receptor lowering activity?" In this review, we appraise the different lipid lowering strategies targeting PCSK9 in light of the protein's different pleiotropic functions. Additionally, we delineate the key areas that require further examination, to ensure the long-term safety of the above lipid-lowering strategies.
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Affiliation(s)
- Yajnavalka Banerjee
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.
| | - Raul D Santos
- Lipid Clinic Heart Institute (InCor), University of Sao Paulo Medical School Hospital, Sao Paulo, Brazil
| | - Khalid Al-Rasadi
- Department of Clinical Biochemistry, Sultan Qaboos University Hospital, Muscat, Oman
| | - Manfredi Rizzo
- Department of Internal Medicine and Medical Specialties, University of Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, Italy
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Xu Y, Li L, Li J, Liu Q. Structural and biological function of NYD-SP15 as a new member of cytidine deaminases. Gene 2016; 583:36-47. [PMID: 26945630 DOI: 10.1016/j.gene.2016.02.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 02/16/2016] [Accepted: 02/21/2016] [Indexed: 11/26/2022]
Abstract
Recent studies were mainly focus on the cytidine deaminase family genes, which contained a lot of members that varied on the function of catalytic deamination in RNA or DNA and were involved in the process of growth maintenance, host immunity, retroviral infection, tumorigenesis, and drug resistance with a feature of C-U deamination. In this study, we identified a new member of cytidine deaminase family, NYD-SP15. Previous work showed that the deduced structure of the protein contained two dCMP_cyt_deam domains, which were involved in zinc ion binding. NYD-SP15 was expressed variably in a wide range of tissues, indicating its worthy biological function and creative significances. Sequence analysis, RT-PCR, western blot, flow cytometry, direct-site mutation and GST pull-down assay were performed to analyze the construction and function of NYD-SP15. The results in our studies showed that NYD-SP15 was closely related to deoxycytidylate deaminase and cytidine deaminase, with authentic cytidine deaminase activity in vivo and vitro as well as homo dimerization effects. NYD-SP15 contained nuclear localization sequence (NLS) and nuclear export-signal (NES) and could dynamically shuttle between the nucleus and cytoplasm. Furthermore, NYD-SP15 gene over-expression reduced the cells growth and blocked G1 to S phase, which implied a potential inhibition effect on cell growth.
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Affiliation(s)
- Yidan Xu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lei Li
- Department of Pharmacology, Basic Medical Sciences of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jianmin Li
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Minkah N, Chavez K, Shah P, Maccarthy T, Chen H, Landau N, Krug LT. Host restriction of murine gammaherpesvirus 68 replication by human APOBEC3 cytidine deaminases but not murine APOBEC3. Virology 2014; 454-455:215-26. [PMID: 24725948 PMCID: PMC4036618 DOI: 10.1016/j.virol.2014.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/27/2013] [Accepted: 02/20/2014] [Indexed: 11/28/2022]
Abstract
Humans encode seven APOBEC3 (A3A-A3H) cytidine deaminase proteins that differ in their expression profiles, preferred nucleotide recognition sequence and capacity for restriction of RNA and DNA viruses. We identified APOBEC3 hotspots in numerous herpesvirus genomes. To determine the impact of host APOBEC3 on herpesvirus biology in vivo, we examined whether murine APOBEC3 (mA3) restricts murine gammaherpesvirus 68 (MHV68). Viral replication was impaired by several human APOBEC3 proteins, but not mA3, upon transfection of the viral genome. The restriction was abrogated upon mutation of the A3A and A3B active sites. Interestingly, virus restriction by A3A, A3B, A3C, and A3DE was lost if the infectious DNA was delivered by the virion. MHV68 pathogenesis, including lung replication and splenic latency, was not altered in mice lacking mA3. We infer that mA3 does not restrict wild type MHV68 and restriction by human A3s may be limited in the herpesvirus replication process.
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Affiliation(s)
- Nana Minkah
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kevin Chavez
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Parth Shah
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Thomas Maccarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hui Chen
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA; Infectious Disease Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Nathaniel Landau
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016, USA; Infectious Disease Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Laurie T Krug
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA.
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APOBEC1-mediated editing and attenuation of herpes simplex virus 1 DNA indicate that neurons have an antiviral role during herpes simplex encephalitis. J Virol 2011; 85:9726-36. [PMID: 21775448 DOI: 10.1128/jvi.05288-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
APOBEC1 (A1) is a cytidine deaminase involved in the regulation of lipids in the small intestine. Herpes simplex virus 1 (HSV-1) is a ubiquitous pathogen that is capable of infecting neurons in the brain, causing encephalitis. Here, we show that A1 is induced during encephalitis in neurons of rats infected with HSV-1. In cells stably expressing A1, HSV-1 infection resulted in significantly reduced virus replication compared to that in control cells. Infectivity could be restored to levels comparable to those observed for control cells if A1 expression was silenced by specific A1 short hairpin RNAs (shRNA). Moreover, cytidine deaminase activity appeared to be essential for this inhibition and led to an impaired accumulation of viral mRNA transcripts and DNA copy numbers. The sequencing of viral gene UL54 DNA, extracted from infected A1-expressing cells, revealed G-to-A and C-to-T transitions, indicating that A1 associates with HSV-1 DNA. Taken together, our results demonstrate a model in which A1 induction during encephalitis in neurons may aid in thwarting HSV-1 infection.
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Matsumoto T, Marusawa H, Endo Y, Ueda Y, Matsumoto Y, Chiba T. Expression of APOBEC2 is transcriptionally regulated by NF-kappaB in human hepatocytes. FEBS Lett 2006; 580:731-5. [PMID: 16427049 DOI: 10.1016/j.febslet.2005.12.081] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 12/21/2005] [Accepted: 12/27/2005] [Indexed: 10/25/2022]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic subunit 2 (APOBEC2) is a member of the nucleic-acid-editing enzymes. However, the physiological function of APOBEC2 remains unclear. We demonstrate that APOBEC2 expression is strongly enhanced in response to both tumour necrosis factor-alpha (TNF-alpha) and interleukin-1beta. Inhibition of NF-kappaB activation invariably blocks TNF-alpha-induced APOBEC2 expression. The promoter region of APOBEC2 contains functional NF-kappaB response elements in the 5' untranslated region of the gene at -625/-616. These results show that APOBEC2 expression is regulated by pro-inflammatory cytokines via NF-kappaB activation and suggest a possible role of APOBEC2 in the pathophysiology of hepatic inflammation.
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Affiliation(s)
- Tomonori Matsumoto
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Shogoin, Kyoto 606-8507, Japan
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Maris C, Masse J, Chester A, Navaratnam N, Allain FHT. NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor. RNA (NEW YORK, N.Y.) 2005; 11:173-86. [PMID: 15659357 PMCID: PMC1370706 DOI: 10.1261/rna.7190705] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Accepted: 11/19/2004] [Indexed: 05/20/2023]
Abstract
We have solved the NMR structure of the 31-nucleotide (nt) apoB mRNA stem-loop, a substrate of the cytidine deaminase APOBEC1. We found that the edited base located at the 5' end of the octa-loop is stacked between two adenosines in both the unedited (cytidine 6666) and the edited (uridine 6666) forms and that the rest of the loop is unstructured. The 11-nt "mooring" sequence essential for editing is partially flexible although it is mostly in the stem of the RNA. The octa-loop and the internal loop in the middle of the stem confer this flexibility. These findings shed light on why APOBEC1 alone cannot edit efficiently the cytidine 6666 under physiological conditions, the editing base being buried in the loop and not directly accessible. We also show that APOBEC1 does not specifically bind apoB mRNA and requires the auxiliary factor, APOBEC1 complementary factor (ACF), to edit specifically cytidine 6666. The binding of ACF to both the mooring sequence and APOBEC1 explains the specificity of the reaction. Our NMR study lead us to propose a mechanism in which ACF recognizes first the flexible nucleotides of the mooring sequence (the internal loop and the 3' end octa-loop) and subsequently melts the stem-loop, exposing the amino group of the cytidine 6666 to APOBEC1. Thus, the flexibility of the mooring sequence plays a central role in the RNA recognition by ACF.
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Affiliation(s)
- Christophe Maris
- Institute for Molecular Biology and Biophysics, ETH Hönggerberg HPK D11.2, CH-8093 Zürich, Switzerland
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Chester A, Scott J, Anant S, Navaratnam N. RNA editing: cytidine to uridine conversion in apolipoprotein B mRNA. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1494:1-13. [PMID: 11072063 DOI: 10.1016/s0167-4781(00)00219-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA editing is a post-transcriptional process that changes the informational capacity within the RNA. These processes include alterations made by nucleotide deletion, insertion and base conversion. A to I and C to U conversion occurs in mammals and these editing events are catalysed by RNA binding deaminases. C to U editing of apoB mRNA was the first mammalian editing event to be identified. The minimal protein complex necessary for apoB mRNA editing has been determined and consists of APOBEC-1 and ACF. Overexpression of APOBEC-1 in transgenic animals caused liver dysplasia and APOBEC-1 has been identified in neurofibromatosis type 1 tumours, suggesting that RNA editing may be another mechanism for tumourigenesis. Several APOBEC-1-like proteins have been identified, including a family of APOBEC-1-related proteins with unknown function on chromosome 22. This review summarises the different types of RNA editing and discusses the current status of C to U apoB mRNA editing. This knowledge is very important in understanding the structure and function of these related proteins and their role in biology.
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Affiliation(s)
- A Chester
- MRC Molecular Medicine, Clinical Science Centre, Imperial College School of Medicine, Hammersmith Hospital, London, UK
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Lellek H, Kirsten R, Diehl I, Apostel F, Buck F, Greeve J. Purification and molecular cloning of a novel essential component of the apolipoprotein B mRNA editing enzyme-complex. J Biol Chem 2000; 275:19848-56. [PMID: 10781591 DOI: 10.1074/jbc.m001786200] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Editing of apolipoprotein B (apoB) mRNA requires the catalytic component APOBEC-1 together with "auxiliary" proteins that have not been conclusively characterized so far. Here we report the purification of these additional components of the apoB mRNA editing enzyme-complex from rat liver and the cDNA cloning of the novel APOBEC-1-stimulating protein (ASP). Two proteins copurified into the final active fraction and were characterized by peptide sequencing and mass spectrometry: KSRP, a 75-kDa protein originally described as a splicing regulating factor, and ASP, a hitherto unknown 65-kDa protein. Separation of these two proteins resulted in a reduction of APOBEC-1-stimulating activity. ASP represents a novel type of RNA-binding protein and contains three single-stranded RNA-binding domains in the amino-terminal half and a putative double-stranded RNA-binding domain at the carboxyl terminus. Purified recombinant glutathione S-transferase (GST)-ASP, but not recombinant GST-KSRP, stimulated recombinant GST-APOBEC-1 to edit apoB RNA in vitro. These data demonstrate that ASP is the second essential component of the apoB mRNA editing enzyme-complex. In rat liver, ASP is apparently associated with KSRP, which may confer stability to the editing enzyme-complex with its substrate apoB RNA serving as an additional auxiliary component.
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Affiliation(s)
- H Lellek
- Medizinische Kernklinik und Poliklinik and the Institut für Zellbiochemie und Klinische Neurobiologie, Universitäts-Krankenhaus Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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Mehta A, Kinter MT, Sherman NE, Driscoll DM. Molecular cloning of apobec-1 complementation factor, a novel RNA-binding protein involved in the editing of apolipoprotein B mRNA. Mol Cell Biol 2000; 20:1846-54. [PMID: 10669759 PMCID: PMC85365 DOI: 10.1128/mcb.20.5.1846-1854.2000] [Citation(s) in RCA: 213] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C-to-U editing of apolipoprotein B (apo-B) mRNA is catalyzed by a multiprotein complex that recognizes an 11-nucleotide mooring sequence downstream of the editing site. The catalytic subunit of the editing enzyme, apobec-1, has cytidine deaminase activity but requires additional unidentified proteins to edit apo-B mRNA. We purified a 65-kDa protein that functionally complements apobec-1 and obtained peptide sequence information which was used in molecular cloning experiments. The apobec-1 complementation factor (ACF) cDNA encodes a novel 64.3-kDa protein that contains three nonidentical RNA recognition motifs. ACF and apobec-1 comprise the minimal protein requirements for apo-B mRNA editing in vitro. By UV cross-linking and immunoprecipitation, we show that ACF binds to apo-B mRNA in vitro and in vivo. Cross-linking of ACF is not competed by RNAs with mutations in the mooring sequence. Coimmunoprecipitation experiments identified an ACF-apobec-1 complex in transfected cells. Immunodepletion of ACF from rat liver extracts abolished editing activity. The immunoprecipitated complexes contained a functional holoenzyme. Our results support a model of the editing enzyme in which ACF binds to the mooring sequence in apo-B mRNA and docks apobec-1 to deaminate its target cytidine. The fact that ACF is widely expressed in human tissues that lack apobec-1 and apo-B mRNA suggests that ACF may be involved in other RNA editing or RNA processing events.
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Affiliation(s)
- A Mehta
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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Hersberger M, Patarroyo-White S, Arnold KS, Innerarity TL. Phylogenetic analysis of the apolipoprotein B mRNA-editing region. Evidence for a secondary structure between the mooring sequence and the 3' efficiency element. J Biol Chem 1999; 274:34590-7. [PMID: 10574922 DOI: 10.1074/jbc.274.49.34590] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein (apo) B mRNA editing is the deamination of C(6666) to uridine, which changes the codon at position 2153 from a genomically encoded glutamine (CAA) to an in-frame stop codon (UAA). The apoB mRNA-editing enzyme complex recognizes the editing region of the apoB pre-mRNA with exquisite precision. Four sequence elements spanning 139 nucleotides (nt) on the apoB mRNA have been identified that specify this precision. In cooperation with the indispensable mooring sequence and spacer element, a 5' efficiency element and a 3' efficiency element enhance editing in vitro. A phylogenetic comparison of 32 species showed minor differences in the apoB mRNA sequence, and the apoB mRNA from 31 species was robustly edited in vitro. However, guinea pig mRNA was poorly edited. Compared with the consensus sequences of these 31 species, guinea pig apoB mRNA has three variations in the 3' efficiency element, and the conversion of these to the consensus sequence increased editing to the levels in the other species. From this information, a model for the secondary structure was formulated in which the mooring sequence and the 3' efficiency element form a double-stranded stem. Thirty-one mammalian apoB mRNA sequences are predicted to form this stem positioning C(6666) two nucleotides upstream of the stem. However, the guinea pig apoB mRNA has a mutation in the 3' efficiency element (C(6743) to U) that predicts an extension of the stem and hence the lower editing efficiency. A test of this model demonstrated that a single substitution at 6743 (U to C) in the guinea pig apoB mRNA, that should reduce the stem, enhanced editing, and mutations in the 3' efficiency element that extended the stem for three base pairs dramatically reduced editing. Furthermore, the addition of a 20-nucleotide 3' efficiency element RNA, to a 58-nucleotide guinea pig apoB mRNA lacking the 3' efficiency element more than doubled the in vitro editing activity. Based on these results, a model is proposed in which the mooring sequence and the 3' efficiency element form a double-stranded stem, thus suggesting a mechanism of how the 3' efficiency element enhances editing.
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Affiliation(s)
- M Hersberger
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, California 94141-9100, USA
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14
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Siddiqui JF, Van Mater D, Sowden MP, Smith HC. Disproportionate relationship between APOBEC-1 expression and apolipoprotein B mRNA editing activity. Exp Cell Res 1999; 252:154-64. [PMID: 10502408 DOI: 10.1006/excr.1999.4598] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Apolipoprotein B (apoB) mRNA editing is a site-specific (nucleotide 6666) cytidine to uridine transition catalyzed by a cytidine deaminase, APOBEC-1, in the context of a multiprotein complex referred to as the C/U editosome. This report quantifies for the first time the effect of altering APOBEC-1 protein abundance on the proportion of edited apoB mRNAs using transfected McArdle rat hepatoma cells which had been sorted by flow cytometry into populations expressing different levels of green fluorescent protein-APOBEC-1 chimera, GFP-APOBEC. A correlation was observed in which increased expression of GFP-APOBEC protein resulted in a higher proportion of edited apoB mRNA. The number of enzyme molecules required to increase the proportion of edited apoB RNAs was disproportionately high relative to that which might have been predicted from a typical catalytic relationship. Moreover, editing of apoB mRNA at inappropriate sites (promiscuous editing) occurred in response to overexpressing GFP-APOBEC. The data suggest that experimental manipulation of APOBEC-1 abundance in the absence of other regulatory considerations will always result in some level of promiscuous editing. Coordinate expression of APOBEC-1 and the auxiliary proteins and/or regulation of their interactions may be required to increase editing activity without losing editing-site fidelity.
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Affiliation(s)
- J F Siddiqui
- Department of Biochemistry and Biophysics, Health Science, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, New York 14642, USA
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15
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Steinburg MF, Schock D, Backus JW, Smith HC. Tissue-specific differences in the role of RNA 3' of the apolipoprotein B mRNA mooring sequence in editosome assembly. Biochem Biophys Res Commun 1999; 263:81-6. [PMID: 10486257 DOI: 10.1006/bbrc.1999.1329] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Site-specific editing of apolipoprotein B (apoB) mRNA by the cytidine deaminase, APOBEC-1 is proposed to require interactions of auxiliary protein(s) with an eleven nucleotide element, the mooring sequence, located 3' of the C --> U editing site. An analysis of the RNA sequence dependence for protein-RNA interactions and editosome assembly in rat liver and the small intestine demonstrated that the mooring sequence was a minimal requirement for these interactions. Sequences 3' of the mooring sequence either interacted with 66 kDa and 44 kDa proteins or enhanced the interactions of these proteins with the mooring sequence. The data also suggested tissue-specific differences in the relative importance of the 3' cis-acting 'enhancer' elements in the efficiency or stability of editosome assembly. We propose that the previously demonstrated differences in apoB mRNA editing efficiency and its regulation in liver and intestine may in part be due to differences in auxiliary protein interactions with apoB mRNA 3' of the mooring sequence.
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Affiliation(s)
- M F Steinburg
- Department of Biochemistry and Biophysics, Department of Pathology, Environmental Health Sciences Center, 601 Elmwood Avenue, Rochester, New York 14642, USA
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16
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Mutational analysis of apolipoprotein B mRNA editing enzyme (APOBEC1): structure–function relationships of RNA editing and dimerization. J Lipid Res 1999. [DOI: 10.1016/s0022-2275(20)32141-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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Nakamuta M, Tsai A, Chan L, Davidson NO, Teng BB. Sequence elements required for apolipoprotein B mRNA editing enhancement activity from chicken enterocytes. Biochem Biophys Res Commun 1999; 254:744-50. [PMID: 9920812 DOI: 10.1006/bbrc.1998.9963] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mammalian intestinal apolipoprotein B (apoB) mRNA edits codon 2153 from CAA in apoB100 mRNA to a stop codon (UAA) in apoB48 mRNA. By contrast, chicken intestinal apoB mRNA contains a CAA codon at the corresponding site, but is not edited. Chicken enterocyte S100 extracts fail to edit mammalian apoB RNA, but contain factor(s) which enhance the mammalian enterocytes editing activity. By converting the chicken apoB mooring sequences to the conserved mammalian sequences, the study confirmed that this 11-nucleotide stretch was necessary and sufficient for minimal RNA editing. Using rat and chicken apoB chimeric constructs, the study revealed that mammalian apoB sequences were required for editing enhancement. In concert with the 29-nucleotide conserved cassette, the 5' rat apoB element (nucleotides 6615-6629) increased editing at C-6666, and was necessary for editing enhancement of chicken enterocyte S100 extracts. Similarly, the 3' rat apoB element (nucleotides 6726-6752) was required for editing enhancement of chicken enterocyte S100 extracts, but to a lesser extent in efficiency, compared to the 5' region. In conclusion, this study identified the sequences required for editing enhancement activity from chicken enterocyte S100 extracts.
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Affiliation(s)
- M Nakamuta
- Institute of Molecular Medicine, University of Texas-Houston, Houston, Texas, 77030, USA
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18
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Scott J, Navaratnam N, Carter C. Molecular modelling and the biosynthesis of apolipoprotein B containing lipoproteins. Atherosclerosis 1998; 141 Suppl 1:S17-24. [PMID: 9888637 DOI: 10.1016/s0021-9150(98)00213-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
APOBEC-1 is the cytidine deaminase. We show by sequence alignment, molecular modelling and mutagenesis, that it is related in crystal structure to the cytidine deaminase of Escherichia coli (ECCDA). The two enzymes are both homodimers with composite active sites formed with loops from each monomer. In the sequence of APOBEC-1, three gaps compared to ECCDA match the size and contour of the minimal RNA substrate. We propose a model in which the asymmetric binding of one active site to the substrate cytidine which is positioned by the downstream binding of the product uridine and that this helps to target the other active site for deamination.
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Affiliation(s)
- J Scott
- National Heart and Lung Institute, Imperial College School of Medicine, Hammersmith Hospital, London, UK.
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19
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Richardson N, Navaratnam N, Scott J. Secondary structure for the apolipoprotein B mRNA editing site. Au-binding proteins interact with a stem loop. J Biol Chem 1998; 273:31707-17. [PMID: 9822632 DOI: 10.1074/jbc.273.48.31707] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C to U editing of apolipoprotein B (apoB) mRNA converts a glutamine codon in apoB100 mRNA into a stop translation codon thereby generating apoB48. The catalytic subunit of the editing enzyme, APOBEC-1, is an RNA-binding cytidine deaminase that requires auxiliary factors for the editing of apoB mRNA. Computer modeling and ribonuclease probing of the wild-type and mutant apoB RNA substrates reveal a stem loop at the editing site. This structure incorporates the essential sequence motifs required for editing. The localization of the edited cytidine within the loop suggests how it could be presented to the active site of APOBEC-1 for deamination. We have identified 43/45 kDa proteins from chick enterocytes and show evidence for their involvement in auxiliary editing activity. p43/45 demonstrates preferential binding to AU-rich RNA and to the Caauuug motif that forms the loop and proximal stem of the apoB mRNA.
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Affiliation(s)
- N Richardson
- MRC Molecular Medicine Group, Clinical Science Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom
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20
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Van Mater D, Sowden MP, Cianci J, Sparks JD, Sparks CE, Ballatori N, Smith HC. Ethanol increases apolipoprotein B mRNA editing in rat primary hepatocytes and McArdle cells. Biochem Biophys Res Commun 1998; 252:334-9. [PMID: 9826530 DOI: 10.1006/bbrc.1998.9647] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Apolipoprotein B (apoB) mRNA editing involves a site-specific cytidine to uridine transition catalyzed by the cytidine deaminase, APOBEC-1, in the context of and regulated by a multi-protein-containing editosome. ApoB mRNA editing in vivo is subject to tissue specific, developmental and metabolic regulation. We demonstrate for the first time that the amount of edited apoB mRNA in rat primary hepatocytes is markedly increased subsequent to transient treatment with ethanol in vitro. The apparent change in editing efficiency was dose-dependent (from 0.1%-2.4% initial ethanol dose) and occurred with rapid onset. The proportion of edited apoB mRNA was also markedly enhanced in a rat hepatoma cell line, McArdle RH7777 cells and in a stable McArdle cell line over-expressing APOBEC-1 by transient treatment with 2.5 % ethanol. In contrast, the apoB mRNA editing in a human hepatoma cell line, HepG2 cells and a stable HepG2 cell line over-expressing APOBEC-1 did not respond to ethanol treatment. The data support the possibility that editing activity is ethanol-responsive but suggest that this change is cell type-specific.
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Affiliation(s)
- D Van Mater
- Departments of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, 14642, USA
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21
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Mehta A, Driscoll DM. A sequence-specific RNA-binding protein complements apobec-1 To edit apolipoprotein B mRNA. Mol Cell Biol 1998; 18:4426-32. [PMID: 9671452 PMCID: PMC109028 DOI: 10.1128/mcb.18.8.4426] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/1998] [Accepted: 05/08/1998] [Indexed: 02/08/2023] Open
Abstract
The editing of apolipoprotein B (apo-B) mRNA involves the site-specific deamination of cytidine to uracil. The specificity of editing is conferred by an 11-nucleotide mooring sequence located downstream from the editing site. Apobec-1, the catalytic subunit of the editing enzyme, requires additional proteins to edit apo-B mRNA in vitro, but the function of these additional factors, known as complementing activity, is not known. Using RNA affinity chromatography, we show that the complementing activity binds to a 280-nucleotide apo-B RNA in the absence of apobec-1. The activity did not bind to the antisense strand or to an RNA with three mutations in the mooring sequence. The eluate from the wild-type RNA column contained a 65-kDa protein that UV cross-linked to apo-B mRNA but not to the triple-mutant RNA. This protein was not detected in the eluates from the mutant or the antisense RNA columns. Introduction of the mooring sequence into luciferase RNA induced cross-linking of the 65-kDa protein. A 65-kDa protein that interacted with apobec-1 was also detected by far-Western analysis in the eluate from the wild-type RNA column but not from the mutant RNA column. For purification, proteins were precleared on the mutant RNA column prior to chromatography on the wild-type RNA column. Silver staining of the affinity-purified fraction detected a single prominent protein of 65 kDa. Our results suggest that the complementing activity may function as the RNA-binding subunit of the holoenzyme.
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Affiliation(s)
- A Mehta
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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22
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Greeve J, Lellek H, Rautenberg P, Greten H. Inhibition of the apolipoprotein B mRNA editing enzyme-complex by hnRNP C1 protein and 40S hnRNP complexes. Biol Chem 1998; 379:1063-73. [PMID: 9792439 DOI: 10.1515/bchm.1998.379.8-9.1063] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The apolipoprotein (apo) B mRNA can be modified by a posttranscriptional base change from cytidine to uridine at nucleotide position 6666. This editing of apo B mRNA is mediated by a specific enzyme-complex of which only the catalytic subunit APOBEC-1 (apo B mRNA editing enzyme component 1) has been cloned and extensively characterized. In this study, two-hybrid selection in yeast identified hnRNP C1 protein to interact with APOBEC-1. Recombinant hnRNP C1 protein inhibited partially purified apo B mRNA editing activity from rat small intestine and bound specifically to apo B sense RNA around the editing site. The inhibition of apo B mRNA editing by hnRNP C1 protein was not due to masking of the RNA substrate as the mutant protein M104 spanning the RNA-binding domain of hnRNP C1 protein bound strongly to the apo B RNA, but did not inhibit the editing reaction. The apo B mRNA editing enzyme-complex of rat liver nuclear extracts sedimented in sucrose density gradients around 22-27S, but did not contain hnRNP C1 protein that was found exclusively within 40S hnRNP complexes. The removal of 40S hnRNP complexes increased the activity of the 22-27S editing enzyme-complex. Adding back 40S hnRNP complexes with hnRNP C1 protein resulted in an inhibition of the 22-27S apo B mRNA editing enzyme-complex, while addition of 18S fractions had no effect. In conclusion, hnRNP C1 protein identified by two-hybrid selection in yeast is a potent inhibitor of the apo B mRNA editing enzyme-complex. The abundant hnRNP C1 protein, which is contiguously deposited on nascent pre-mRNA during transcription and is involved in spliceosome assembly and mRNA splicing, is a likely regulator of the editing of apo B mRNA which restricts the activity of APOBEC-1 to limited and specific editing events.
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Affiliation(s)
- J Greeve
- Medizinische Klinik, Universitäts-Krankenhaus Eppendorf, Hamburg, Germany
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23
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Greeve J, Axelos D, Welker S, Schipper M, Greten H. Distinct promoters induce APOBEC-1 expression in rat liver and intestine. Arterioscler Thromb Vasc Biol 1998; 18:1079-92. [PMID: 9672068 DOI: 10.1161/01.atv.18.7.1079] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The expression of apolipoprotein (apo) B can be modulated by mRNA editing, a unique posttranscriptional base change in the apo B mRNA. Apo B-48, the translation product of edited apo B mRNA, is not a precursor of the atherogenic low density lipoproteins and lipoprotein(a). In humans and various other mammals, the apo B mRNA is edited in the intestine but not in the liver, which exclusively secretes apo B-100-containing lipoproteins as precursors for low density lipoprotein formation. In species such as the rat, mouse, dog, and horse, apo B mRNA is also edited in the liver, resulting in low plasma levels of low density lipoprotein. Editing of the apo B mRNA is mediated by the apo B mRNA-editing enzyme complex, of which the catalytic subunit APOBEC-1 is not expressed in the liver of species without hepatic editing. To understand the molecular basis for liver-specific expression of APOBEC-1 and the editing of hepatic apo B mRNA, the expression pattern and genomic organization of the rat APOBEC-1 gene have been characterized. The rat APOBEC-1 gene contains 6 exons and 2 promoters with distinct activities. The expression of APOBEC-1 in the rat liver is the result of a promoter located upstream, with tissue-specific exon use and alternate splicing within the 5'-untranslated region of APOBEC-1 mRNA encoded by exon 2. In addition to the liver, this promoter also induces APOBEC-1 expression in the spleen, lung, kidney, heart, and skeletal muscle. The promoter located downstream belongs to a new class of TATA-less promoters and is responsible for the abundant expression of APOBEC-1 in the intestine. Mapping of the transcriptional start sites and deletion analysis of the promoter regions by using luciferase as the reporter gene have defined the regulatory elements of both promoters. The downstream, intestine-specific promoter contains a negative regulatory element between -1100 and -500, which appears to restrict its activity to the intestine. The upstream, liver-specific promoter of the rat APOBEC-1 gene induces APOBEC-1 expression and editing of apo B mRNA in human hepatoma HuH-7 and Hep G2 cells. Understanding the molecular basis for the liver-specific expression of APOBEC-1 in the rat promises new strategies to induce APOBEC-1 expression in the human liver for the reduction of atherogenic lipoprotein levels by hepatic apo B mRNA editing.
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Affiliation(s)
- J Greeve
- Medizinische Kernklinik und Poliklinik, Universitäts-Krankenhaus Eppendorf, Hamburg, Germany
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24
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Smith HC. Analysis of protein complexes assembled on apolipoprotein B mRNA for mooring sequence-dependent RNA editing. Methods 1998; 15:27-39. [PMID: 9614650 DOI: 10.1006/meth.1998.0603] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Apolipoprotein B (apoB) mRNA editing involves a cytidine-to-uridine transition at a select site catalyzed by a cytidine deaminase known as APOBEC-1. This enzyme cannot edit RNA alone but acquires site-specific editing capacity in the context of additional protein factors (auxiliary proteins). These proteins are currently hypothesized to assemble with APBEC-1 as a holoenzyme complex or editosome. Auxiliary proteins are the focus of ongoing research as they presumably serve important structural and regulatory roles in the editosome. The abilities of auxiliary proteins to interact with APOBEC-1 and apoB RNA and to promote RNA editing activity are important endpoints used as proof that proteins are functionally involved in apoB RNA editing. This article reviews the discovery of the editosome and provides detailed protocols for its isolation and subfractionation.
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Affiliation(s)
- H C Smith
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, New York 14642, USA
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25
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Hersberger M, Innerarity TL. Two efficiency elements flanking the editing site of cytidine 6666 in the apolipoprotein B mRNA support mooring-dependent editing. J Biol Chem 1998; 273:9435-42. [PMID: 9545269 DOI: 10.1074/jbc.273.16.9435] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Normally, apolipoprotein B (apoB) mRNA editing deaminates a single cytidine (C6666) in apoB mRNA. However, when the catalytic subunit of the editing enzyme complex, APOBEC-1, was overexpressed in transgenic mice and rabbits, numerous cytidines in the apoB mRNA and in a novel mRNA, NAT1, were aberrantly hyperedited, and the animals developed liver dysplasia and hepatocellular carcinomas. To identify the RNA motifs in the apoB mRNA that support physiological editing and those that support aberrant hyperediting, we constructed rabbit apoB RNA substrates and tested them in vitro for physiological editing and hyperediting. Three previously unrecognized RNA elements that are critical for efficient physiological editing at C6666 were identified. In concert with the mooring sequence (6671-6681), the 5' efficiency element (6609-6628), an A-rich region (6629-6640), and the 3' efficiency element (6717-6747) increased editing at C6666. The 5' efficiency element was the most potent, elevating physiological editing to wild-type levels in combination with the mooring sequence. The 3' efficiency element was somewhat less important but increased physiological editing to levels approaching wild type. These elements encompass 139 nucleotides on the apoB RNA transcript and are sufficient for editing with the efficiency of full-length apoB mRNA. Furthermore, a distal downstream apoB region (6747-6824) may function as a recognition element in the apoB mRNA. Hyperediting at C6802 in the rabbit apoB mRNA is mediated by RNA elements similar to those required for normal physiological editing at C6666. Similarly sized upstream and downstream flanking regions of C6802 are necessary for hyperediting in combination with a degenerate mooring sequence.
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Affiliation(s)
- M Hersberger
- Gladstone Institute of Cardiovascular Disease, Cardiovascular Research Institute, University of California, San Francisco, California 94141-9100, USA.
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26
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Sowden MP, Eagleton MJ, Smith HC. Apolipoprotein B RNA sequence 3' of the mooring sequence and cellular sources of auxiliary factors determine the location and extent of promiscuous editing. Nucleic Acids Res 1998; 26:1644-52. [PMID: 9512534 PMCID: PMC147457 DOI: 10.1093/nar/26.7.1644] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Apolipoprotein B (apoB) RNA editing involves a cytidine to uridine transition at nucleotide 6666 (C6666) 5' of an essential cis -acting 11 nucleotide motif known as the mooring sequence. APOBEC-1 (apoB editing catalytic sub-unit 1) serves as the site-specific cytidine deaminase in the context of a multiprotein assembly, the editosome. Experimental over-expression of APOBEC-1 resulted in an increased proportion of apoB mRNAs edited at C6666, as well as editing of sites that would otherwise not be recognized (promiscuous editing). In the rat hepatoma McArdle cell line, these sites occurred predominantly 5' of the mooring sequence on either rat or human apoB mRNA expressed from transfected cDNA. In comparison, over-expression of APOBEC-1 in HepG2 (HepG2-APOBEC) human hepatoma cells, induced promiscuous editing primarily 5' of the mooring sequence, but sites 3' of the C6666 were also used more efficiently. The capacity for promiscuous editing was common to rat, rabbit and human sources of APOBEC-1. The data suggested that differences in the distribution of promiscuous editing sites and in the efficiency of their utilization may reflect cell-type-specific differences in auxiliary proteins. Deletion of the mooring sequence abolished editing at the wild type site and markedly reduced, but did not eliminate, promiscuous editing. In contrast, deletion of a pair of tandem UGAU motifs 3' of the mooring sequence in human apoB mRNA selectively reduced promiscuous editing, leaving the efficiency of editing at the wild type site essentially unaffected. ApoB RNA constructs and naturally occurring mRNAs such as NAT-1 (novel APOBEC-1 target-1) that lack this downstream element were not promiscuously edited in McArdle or HepG2 cells. These findings underscore the importance of RNA sequences and the cellular context of auxiliary factors in regulating editing site utilization.
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Affiliation(s)
- M P Sowden
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Box 712, 601 Elmwood Avenue, Rochester, NY 14642, USA
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27
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Navaratnam N, Fujino T, Bayliss J, Jarmuz A, How A, Richardson N, Somasekaram A, Bhattacharya S, Carter C, Scott J. Escherichia coli cytidine deaminase provides a molecular model for ApoB RNA editing and a mechanism for RNA substrate recognition. J Mol Biol 1998; 275:695-714. [PMID: 9466941 DOI: 10.1006/jmbi.1997.1506] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ApoB RNA-editing enzyme (APOBEC-1) is a cytidine deaminase. Molecular modeling and mutagenesis show that APOBEC-1 is related in quaternary and tertiary structure to Escherichia coli cytidine deaminase (ECCDA). Both enzymes form a homodimer with composite active sites constructed with contributions from each monomer. Significant gaps are present in the APOBEC-1 sequence, compared to ECCDA. The combined mass of the gaps (10 kDa) matches that for the minimal RNA substrate. Their location in ECCDA suggests how APOBEC-1 can be reshaped to accommodate an RNA substrate. In this model, the asymmetrical binding to one active site of a downstream U (equivalent to the deamination product) helps target the other active site for deamination of the upstream C substrate.
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Affiliation(s)
- N Navaratnam
- MRC Molecular Medicine Group, Imperial College School of Medicine, Hammersmith Hospital, London, UK
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28
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Yang Y, Yang Y, Smith HC. Multiple protein domains determine the cell type-specific nuclear distribution of the catalytic subunit required for apolipoprotein B mRNA editing. Proc Natl Acad Sci U S A 1997; 94:13075-80. [PMID: 9371802 PMCID: PMC24265 DOI: 10.1073/pnas.94.24.13075] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/1997] [Accepted: 10/03/1997] [Indexed: 02/05/2023] Open
Abstract
Apolipoprotein B (apoB) mRNA editing catalyzed by apoB mRNA editing catalytic subunit 1 (APOBEC-1) has been proposed to be a nuclear process. To test this hypothesis, the subcellular distribution of hemagglutinin- (HA) tagged APOBEC-1 expressed in transiently transfected hepatoma cells was determined by indirect immunofluorescence microscopy. HA-APOBEC-1 was detected in both the nucleus and cytoplasm of rat and human hepatoma cells. Mutagenesis of APOBEC-1 demonstrated that the N-terminal 56 amino acids (1-56) were necessary for the nuclear distribution of APOBEC-1, but this region did not contain a functional nuclear localization signal (NLS). However, we identified a 24-amino acid domain in the C terminus of APOBEC-1 with characteristics of a cytoplasmic retention signal (CRS) or a nuclear export signal (NES). These data suggest, therefore, that the nuclear import of APOBEC-1 may not be mediated by a positive NLS; rather, it may be achieved by overcoming the effect of a CRS/NES. We also demonstrated that the nuclear distribution of APOBEC-1 occurred only in cell lines that were capable of editing apoB RNA. We propose that the cellular distribution of APOBEC-1 is determined by multiple domains within this protein, and a nuclear localization of the enzyme may be regulated by cell type-specific factors that render these cells uniquely editing competent.
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Affiliation(s)
- Y Yang
- Department of Biochemistry, University of Rochester, NY 14642, USA
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29
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Yang Y, Yang Y, Kovalski K, Smith HC. Partial characterization of the auxiliary factors involved in apolipoprotein B mRNA editing through APOBEC-1 affinity chromatography. J Biol Chem 1997; 272:27700-6. [PMID: 9346911 DOI: 10.1074/jbc.272.44.27700] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
APOBEC-1-catalyzed apolipoprotein B (apoB) mRNA editing requires auxiliary factors, but the number and functions of these factors are unknown. We have partially purified the editing activity from extracts of a McArdle cell line overexpressing His6-hemagglutinin-tagged, rat APOBEC-1 using metal-chelating affinity chromatography. The 1,200-fold purification achieved by this approach was partially dependent on exogenously added RNA containing a mooring sequence for editosome assembly. Affinity-purified editing activity could be separated by 300 mM NaCl extraction into two fractions, a salt-resistant fraction (editing fraction 1; EF1) and a salt-soluble fraction (EF2). Neither EF1 nor EF2 alone could edit apoB RNA, but when added together they reconstituted full editing activity. Previously identified candidate auxiliary factors including the p66/p44 apoB RNA binding proteins and the presumptive editosome assembly factor p240 were all present in the affinity-purified editing complex. Moreover, virtually all of p66, p240, and APOBEC-1 were present in EF1, whereas p44 was quantitatively recovered in EF2. This is the first demonstration that p66 and p44 can bind to apoB RNA independently of one another. In addition, 100- and 55-kDa apoB RNA cross-linking proteins have been identified in the APOBEC-1 affinity-purified material. RNA competition studies demonstrated that p100, p66, and p55 bound selectively to apoB RNA, whereas p44 had general RNA cross-linking characteristics. The data underscore the multiplicity of auxiliary factors potentially involved in apoB RNA editing and suggest an editosome far more complicated than may have been previously appreciated.
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Affiliation(s)
- Y Yang
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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Hirano K, Min J, Funahashi T, Davidson NO. Cloning and characterization of the rat apobec-1 gene: a comparative analysis of gene structure and promoter usage in rat and mouse. J Lipid Res 1997. [DOI: 10.1016/s0022-2275(20)37193-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Yamanaka S, Poksay KS, Arnold KS, Innerarity TL. A novel translational repressor mRNA is edited extensively in livers containing tumors caused by the transgene expression of the apoB mRNA-editing enzyme. Genes Dev 1997; 11:321-33. [PMID: 9030685 DOI: 10.1101/gad.11.3.321] [Citation(s) in RCA: 175] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transgene expression of the apolipoprotein B mRNA-editing enzyme (APOBEC-1) causes dysplasia and carcinoma in mouse and rabbit livers. Using a modified differential display technique, we identified a novel mRNA (NAT1 for novel APOBEC-1 target no. 1) that is extensively edited at multiple sites in these livers. The aberrant editing alters encoded amino acids, creates stop codons, and results in markedly reduced levels of the NAT1 protein in transgenic mouse livers. NAT1 is expressed ubiquitously and is extraordinarily conserved among species. It has homology to the carboxy-terminal portion of the eukaryotic translation initiation factor (eIF) 4G that binds eIF4A and eIF4E to form eIF4F. NAT1 binds eIF4A but not eIF4E and inhibits both cap-dependent and cap-independent translation. NAT1 is likely to be a fundamental translational repressor, and its aberrant editing could contribute to the potent oncogenesis induced by overexpression of APOBEC-1.
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Affiliation(s)
- S Yamanaka
- University of California, San Francisco 94141-9100, USA
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Lau PP, Zhu HJ, Nakamuta M, Chan L. Cloning of an Apobec-1-binding protein that also interacts with apolipoprotein B mRNA and evidence for its involvement in RNA editing. J Biol Chem 1997; 272:1452-5. [PMID: 8999813 DOI: 10.1074/jbc.272.3.1452] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Apolipoprotein (apo)B mRNA editing is mediated by a multiprotein editosome complex. Apobec-1 is the catalytic component of this complex, but other proteins involved in editing have not been identified. We used the yeast two-hybrid system to identify an apobec-1-interacting protein, ABBP-1. ABBP-1 contains 331 amino acid residues and is identical to a previously reported human type A/B hnRNP except for a 47-residue insertion at its C-terminal region. It contains typical RNP motifs at its N-terminal half and glycine-rich motifs in the C-terminal region. Northern blot analysis indicates that ABBP-1 mRNA is distributed in multiple human tissues. By deletion analysis, we mapped the apobec-1-binding region to the glycine-rich domain. ABBP-1 also binds to apoB mRNA transcripts around the editing site and can be UV-cross-linked to them in vitro. Immnodepletion of ABBP-1 from an active apoB mRNA editing tissue extract inhibits its editing activity. Down-regulation of ABBP-1 in an apobec-1-expressing HepG2 cell line by transfection with an antisense ABBP-1 cDNA construct leads to inhibition of endogenous apoB mRNA editing. We conclude that ABBP-1 is an apobec-1-interacting protein that may play an important role in apoB mRNA editing.
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Affiliation(s)
- P P Lau
- Departments of Cell Biology and Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
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Oka K, Kobayashi K, Sullivan M, Martinez J, Teng BB, Ishimura-Oka K, Chan L. Tissue-specific inhibition of apolipoprotein B mRNA editing in the liver by adenovirus-mediated transfer of a dominant negative mutant APOBEC-1 leads to increased low density lipoprotein in mice. J Biol Chem 1997; 272:1456-60. [PMID: 8999814 DOI: 10.1074/jbc.272.3.1456] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
APOBEC-1 is a catalytic subunit of an apolipoprotein B (apoB) mRNA editing enzyme complex. In humans it is expressed only in the intestine, whereas in mice it is expressed in both the liver and intestine. APOBEC-1 exists as a spontaneous homodimer (Lau, P. P., Zhu, H.-J., Baldini, A., Charnsangavej, C., and Chan, L. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8522-8526). We tested the editing activity and dimerization potential of three different mouse APOBEC-1 mutants using in vitro editing activity assay and immunoprecipitation in the presence of epitope-tagged APOBEC-1. One catalytically inactive mutant, mu1 (H61K/C93S/C96S), that retains its capacity to dimerize with wild-type APOBEC-1 was found to inhibit the editing activity of the latter and was thus a dominant negative mutant. Two other inactive mutants that dimerized poorly with APOBEC-1 failed to inhibit its activity. Intravenous injection of a mu1 adenovirus, Admu1, in C57BL/6J mice in vivo resulted in liver-specific expression of mu1 mRNA. On days 4 and 9 after virus injection, endogenous hepatic apoB mRNA editing was 23.3 +/- 5.0 and 36.8 +/- 5.7%, respectively, compared with 65.3 +/- 11 and 71.3 +/- 5.2%, respectively, for luciferase adenovirus-treated animals. Plasma apoB-100 accounted for 95 and 93% of total plasma apoB in Admu1 animals on days 4 and 9, respectively, compared with 78 and 72% in luciferase adenovirus animals. Plasma cholesterol on day 9 was 98 +/- 17 mg/dl in the mu1-treated animals, substantially higher than phosphate-buffered saline-treated (57 +/- 9 mg/dl) or luciferase-treated (71 +/- 12 mg/dl) controls. Fast protein liquid chromatography analysis of mouse plasma showed that the intermediate density/low density lipoprotein fractions in the animals treated with the dominant negative mutant adenovirus were much higher than those in controls. We conclude that active APOBEC-1 functions as a dimer and its activity is inhibited by a dominant negative mutant. Furthermore, apoB mRNA editing determines the availability of apoB-100, which in turn limits the amount of intermediate density/low density lipoprotein that can be formed in mice. Liver-specific inhibition of apoB mRNA editing is an important component of any strategy to enhance the value of mice as a model for human lipoprotein metabolism.
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Affiliation(s)
- K Oka
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030-3498, USA
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Mehta A, Banerjee S, Driscoll DM. Apobec-1 interacts with a 65-kDa complementing protein to edit apolipoprotein-B mRNA in vitro. J Biol Chem 1996; 271:28294-9. [PMID: 8910449 DOI: 10.1074/jbc.271.45.28294] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The editing of apolipoprotein-B (apoB) mRNA involves the deamination of cytidine at nucleotide 6666 to uridine. The catalytic subunit of the editing enzyme, apobec-1, is a cytidine deaminase that requires other unidentified proteins to edit apoB mRNA in vitro. We partially purified an activity from baboon kidney that functionally complements apobec-1. The complementing activity was protease-sensitive and micrococcal nuclease-resistant, had a native molecular mass of 65 +/- 10 kDa on size exclusion chromatography, and sedimented at 4.5 S in glycerol gradients. Purified recombinant His6-tagged apobec-1 immobilized on beads depleted >90% of the complementing activity from partially purified extracts. These beads edited apoB mRNA in vitro in the absence of exogenous apobec-1 or complementing activity. A functional holoenzyme containing apobec-1 and the complementing activity was eluted from the apobec-1-affinity resin using 0.5 M imidazole, whereas buffer containing 0.4 M KCl eluted only the complementing activity. The carboxyl-terminal 59 amino acids of apobec-1 were not required for interaction with the complementing activity in vitro. Our results demonstrate that the complementing protein interacts directly with apobec-1 in the absence of apoB mRNA.
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Affiliation(s)
- A Mehta
- Department of Cell Biology, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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Nakamuta M, Chang BH, Zsigmond E, Kobayashi K, Lei H, Ishida BY, Oka K, Li E, Chan L. Complete phenotypic characterization of apobec-1 knockout mice with a wild-type genetic background and a human apolipoprotein B transgenic background, and restoration of apolipoprotein B mRNA editing by somatic gene transfer of Apobec-1. J Biol Chem 1996; 271:25981-8. [PMID: 8824235 DOI: 10.1074/jbc.271.42.25981] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have produced gene knockout mice by targeted disruption of the apobec-1 gene. As recently reported by Hirano et al. (Hirano, K.-I., Young, S. G., Farese, R. V., Jr., Ng, J., Sande, E., Warburton, C., Powell-Braxton, L. M., and Davidson, N. O. (1996) J. Biol. Chem. 271, 9887-9890), these animals do not edit apolipoprotein (apo) B mRNA or produce apoB-48. In this study we have performed a detailed analysis of the lipoprotein phenotypic effects of apobec-1 gene disruption that were not examined in the previous study. We first analyzed the plasma lipoproteins in knockout animals with a wild-type genetic background. Although there was no difference in plasma cholesterol between apobec-1(-/-), +/-, or +/+ mice, there was a marked (176%) increase in plasma apoB-100, from 1.8 +/- 1.2 mg/dl in apobec-1(+/+) mice to 2.7 +/- 0.6 mg/dl in apobec-1(+/-) and 5.0 +/- 1.4 mg/dl in apobec-1(-/-) mice. Plasma apoE was similar in these animals. By fast protein liquid chromatography (FPLC) analysis, there was a significant decrease in plasma high density lipoprotein (HDL) cholesterol in apobec-1(-/-) mice. We further fractionated the plasma lipoproteins into d < 1.006, 1.006-1.02, 1.02-1.05, 1.05-1.08, 1.08-1.10, and 1.10-1.21 g/ml classes, and found a marked (30-40%) reduction in the cholesterol and protein content in the (d 1.08-1.10 and 1.10-1.21) HDL fractions, corroborating the FPLC data. SDS-gel analysis revealed an absence of apoB-48, an increase in apoB-100 in the very low density lipoprotein (VLDL) and low density lipoprotein (LDL) fractions, and a small decrease in apoA-I in the HDL fractions in the apobec-1(-/-) samples. We next raised the basal plasma apoB levels in the apobec-1(-/-) animals by cross-breeding them with human apoB transgenic (TgB) mice. The plasma apoB-100 was 3-fold higher in apobec-1(-/-)/TgB+/- mice (26.6 +/- 18.3 mg/dl) than in apobec-1(+/+)/TgB+/- mice (9.8 +/- 3.9 mg/dl, p < 0.05). The apobec-1(-/-)/TgB+/- mice had a plasma cholesterol levels of 170 +/- 28 mg/dl and triglyceride levels of 106 +/- 31 mg/dl, which are 80% and 58% higher, respectively, than the corresponding values of 94 +/- 21 mg/dl and 67 +/- 11 mg/dl in apobec+/+/TgB+/- mice. By FPLC, the apobec-1(-/-)/TgB+/- animals developed markedly elevated plasma LDL cholesterol (518.5 +/- 329.5 microg/ml) that is 373% that of apobec1(+/+)/TgB+/- mice (139.0 +/- 87.0 microg/ml) (p < 0.05). The elevated plasma triglyceride was accounted for mainly by a 97% increase in VLDL triglyceride in the apobec1(-/-)/TgB+/- mice. We conclude that apobec-1(-/-) animals have a distinctive lipoprotein phenotype characterized by significant hyperapoB-100 and HDL deficiency in mice with a wild-type genetic background. Furthermore, the abolition of apoB mRNA editing elevates plasma total cholesterol and LDL cholesterol in apobec-1(-/-) animals with a TgB background. Finally, to exclude the possibility that absence of apoB mRNA editing was a secondary effect of chronic Apobec-1 deficiency, we treated apobec-1(-/-) mice with a replication-defective mouse Apobec-1 adenoviral vector and found that we could acutely restore apoB mRNA editing in the liver. These experiments indicate that Apobec-1 is an essential component of the apoB mRNA editing machinery and absence of editing in the knockout animals is a direct consequence of the absence of functional Apobec-1.
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Affiliation(s)
- M Nakamuta
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030-3498, USA
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36
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Greeve J, Jona VK, Chowdhury NR, Horwitz MS, Chowdhury JR. Hepatic gene transfer of the catalytic subunit of the apolipoprotein B mRNA editing enzyme results in a reduction of plasma LDL levels in normal and watanabe heritable hyperlipidemic rabbits. J Lipid Res 1996. [DOI: 10.1016/s0022-2275(20)37565-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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37
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Hussain MM, Kancha RK, Zhou Z, Luchoomun J, Zu H, Bakillah A. Chylomicron assembly and catabolism: role of apolipoproteins and receptors. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1300:151-70. [PMID: 8679680 DOI: 10.1016/0005-2760(96)00041-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Chylomicrons are lipoproteins synthesized exclusively by the intestine to transport dietary fat and fat-soluble vitamins. Synthesis of apoB48, a translational product of the apob gene, is required for the assembly of chylomicrons. The apob gene transcription in the intestine results in 14 and 7 kb mRNAs. These mRNAs are post-transcriptionally edited creating a stop codon. The edited mRNAs chylomicrons from the shorter apoB48 peptide remains to be elucidated. In addition, the roles of proteins involved in the assembly pathway, e.g. apobec-1, MTP and apoA-IV, needs to be studied. Cloning of enzymes involved in the intestinal biosynthesis of triglycerides will be crucial to fully appreciate the assembly of chylomicrons. There is a need for cell culture and transgenic animal models that can be used for intestinal lipoprotein assembly. The catabolism of chylomicrons is far more complex and efficient than the catabolism of VLDL. Even though the major steps involved in the catabolism of chylomicrons are now known, the determinants for apolipoprotein exchange, processing of remnants in the space of Disse, as well as the mechanism of uptake of these particles by extra-hepatic tissue needs further exploration.
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Affiliation(s)
- M M Hussain
- Department of Pathology, Medical College of Pennsylvania, Philadelphia 19129, USA. hussain@medcolpa. edu
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38
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Yamanaka S, Poksay KS, Driscoll DM, Innerarity TL. Hyperediting of multiple cytidines of apolipoprotein B mRNA by APOBEC-1 requires auxiliary protein(s) but not a mooring sequence motif. J Biol Chem 1996; 271:11506-10. [PMID: 8626710 DOI: 10.1074/jbc.271.19.11506] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
An RNA-binding cytidine deaminase (APOBEC-1) and unidentified auxiliary protein(s) are required for apolipoprotein (apo) B mRNA editing. A sequence motif on apoB mRNA ("mooring sequence," nucleotides 6671-6681) is obligatory for the editing of cytidine 6666 (C6666), the only cytidine on apoB mRNA converted to uridine in normal animals. Transgenic animals with hepatic overexpression of APOBEC-1 develop liver tumors, and other non-apoB mRNAs are edited, suggesting a loss of the normally precise specificity. In this study, we examined apoB mRNA from these transgenic animals to determine if cytidines aside from C6666 are edited. Multiple cytidines downstream from C6666 in apoB mRNA were edited extensively by the overexpressed APOBEC-1. This pathophysiological "hyperediting" could be mimicked in vitro by incubating a synthetic apoB RNA substrate with the transgenic mouse liver extracts. Multiple cytidines in the synthetic apoB RNA were edited by recombinant APOBEC-1 but only with supplementation of the auxiliary protein(s). Mutations in the mooring sequence markedly decreased the normal editing of C6666 but, surprisingly, increased the hyperediting of downstream cytidines. Furthermore, cytidines in an apoB RNA substrate lacking the mooring sequence were also edited in vitro. These results indicate that the hyperediting of apoB mRNA by overexpressed APOBEC-1 depends upon auxiliary protein(s) but is independent of the mooring sequence motif. These results suggest that hyperediting may represent the first step in a two-step recognition model for normal apoB mRNA editing.
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Affiliation(s)
- S Yamanaka
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco 94141-9100, USA
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39
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Abstract
Considerable progress has been made in unraveling the mechanistic features of RNA editing processes in a number of genetic systems. Recent highlights include the identification of the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme as a zinc-dependent cytidine deaminase that binds to RNA, the demonstration that adenosines in brain glutamate receptor pre-mRNAs are converted into inosines and that double-stranded RNA A deaminase (dsRAD), the candidate enzyme, is another zinc-dependent RNA nucleotide deaminase, and a mounting body of evidence for a cleavage-ligation mechanism for U insertion/deletion editing in kinetoplastid protozoa.
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Affiliation(s)
- R Benne
- Department of Biochemistry, Faculty of Medicine, University of Amsterdam, Academic Medical Centre, The Netherlands.
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40
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Sowden M, Hamm JK, Smith HC. Overexpression of APOBEC-1 results in mooring sequence-dependent promiscuous RNA editing. J Biol Chem 1996; 271:3011-7. [PMID: 8621694 DOI: 10.1074/jbc.271.6.3011] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Apolipoprotein B (apoB) RNA editing involves site-specific deamination of a cytidine to a uridine. A mooring sequence, a spacer region, and a regulator region are components of the apoB RNA editing motif of which only the mooring sequence is both necessary and sufficient for editosome assembly and editing. The catalytic component of the editosome is APOBEC-1. In rat hepatoma, stable cell lines, overexpression of APOBEC-1 resulted in 3 6-fold stimulation of the editing efficiency on either rat endogenous apoB RNA or transiently expressed human apoB RNA. In these cell lines, cytidines in addition to the one at the wild type site were edited. The occurrence and efficiency of this "promiscuous" editing increased with increasing expression of APOBEC-1. Promiscuous editing was restricted to cytidines 5' of the mooring sequence and only occurred on RNAs that had been edited at the wild type site. Moreover, RNAs with mutant editing motifs supported high efficiency but low fidelity editing in the presence of high levels of APOBEC-1. This study demonstrates that overexpression of APOBEC-1 can increase the efficiency of site-specific editing but can also result in promiscuous editing.
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Affiliation(s)
- M Sowden
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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Innerarity TL, Borén J, Yamanaka S, Olofsson SO. Biosynthesis of apolipoprotein B48-containing lipoproteins. Regulation by novel post-transcriptional mechanisms. J Biol Chem 1996; 271:2353-6. [PMID: 8576187 DOI: 10.1074/jbc.271.5.2353] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- T L Innerarity
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94141-9100, USA
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Skuse GR, Cappione AJ, Sowden M, Metheny LJ, Smith HC. The neurofibromatosis type I messenger RNA undergoes base-modification RNA editing. Nucleic Acids Res 1996; 24:478-85. [PMID: 8602361 PMCID: PMC145654 DOI: 10.1093/nar/24.3.478] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A functional mooring sequence, known to be required for apolipoprotein B (apoB) mRNA editing, exists in the mRNA encoding the neurofibromatosis type I (NF1) tumor suppressor. Editing of NF1 mRNA modifies cytidine in an arginine codon (CGA) at nucleotide 2914 to a uridine (UGA), creating an in frame translation stop codon. NF1 editing occurs in normal tissue but was several-fold higher in tumors. In vitro editing and transfection assays demonstrated that apoB and NF1 RNA editing will take place in both neural tumor and hepatoma cells. Unlike apoB, NF1 editing did not demonstrate dependence on rate-limiting quantities of APOBEC-1 (the apoB editing catalytic subunit) suggesting that different trans-acting factors may be involved in the two editing processes.
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Affiliation(s)
- G R Skuse
- Department of Medicine, University of Rochester School of Medicine and Dentistry, NY 14642, USA
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43
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Affiliation(s)
- J Scott
- Department of Medicine Royal Postgraduate Medical School Hammersmith Hospital, London, England
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Nakamuta M, Oka K, Krushkal J, Kobayashi K, Yamamoto M, Li WH, Chan L. Alternative mRNA splicing and differential promoter utilization determine tissue-specific expression of the apolipoprotein B mRNA-editing protein (Apobec1) gene in mice. Structure and evolution of Apobec1 and related nucleoside/nucleotide deaminases. J Biol Chem 1995; 270:13042-56. [PMID: 7768898 DOI: 10.1074/jbc.270.22.13042] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Apolipoprotein (apo) B mRNA editing consists of a C-->U conversion involving the first base of the codon CAA, encoding Gln 2153, to UAA, a stop codon. Editing occurs in the intestine only in most mammals, and in both the liver and intestine in a few mammalian species including mouse. We have cloned the cDNA for the mouse apoB mRNA editing protein, apobec1. Expression of mouse apobec1 cDNA in HepG2 cells results in the editing of the intracellular apoB mRNA. The cDNA predicts a 229-amino acid protein showing 92, 66, and 70% identity to the rat, rabbit, and human proteins, respectively. Based on the estimated values of divergence of apobec1 sequences in terms of the numbers of synonymous and non-synonymous suhstitutions per site, we found that apobec1 is a fairly rapidly evolving protein. Sequence comparison among mammalian apobec1 sequences has permitted the identification of seven conserved regions that may be functionally important for editing activity. We present a phylogenetic tree relating apobec1 sequences to double-stranded RNA adenosine deaminase and other nucleotide/nucleoside deaminases. Northern blot analysis indicates that apobec1 mRNA exists in two different sizes, a approximately 2.2-kilobase (kb) form in small intestine and a approximately 2.4-kb form in liver, spleen, kidney, lung, muscle, and heart. To study the molecular basis for the different sized apobec1 mRNAs, we cloned the apobec1 gene and characterized its exon-intron organization together with the sequences expressed in the hepatic and intestinal mRNA. The mouse apobec1 gene contains 8 exons and spans approximately 25 kb, and is located in chromosome 6. The major hepatic mRNA contains all 8 exons, whereas the major small intestinal mRNA misses the first 3 exons and its transcription is initiated in exon 4. The intestinal mRNA also contains at its 5' end a unique 102-nucleotide piece that is absent in the liver mRNA. We also identified two alternatively spliced hepatic apobec1 mRNAs with different acceptor sites in exon 4. Transient expression studies using promoter-reporter gene constructs in HeLa, Hepa, and Caco-2 cells indicate that the 5'-flanking sequences of the liver mRNA (i.e. upstream of exon 1) have predominantly hepatic promoter activity and the 5'-flanking sequences of the major small intestine mRNA (i.e. upstream of exon 4) have preferential intestinal promoter activity.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- M Nakamuta
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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45
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MacGinnitie AJ, Anant S, Davidson NO. Mutagenesis of apobec-1, the Catalytic Subunit of the Mammalian Apolipoprotein B mRNA Editing Enzyme, Reveals Distinct Domains That Mediate Cytosine Nucleoside Deaminase, RNA Binding, and RNA Editing Activity. J Biol Chem 1995. [DOI: 10.1074/jbc.270.24.14768] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Affiliation(s)
- F J Field
- Department of Internal Medicine, University of Iowa, Iowa City 52242, USA
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