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Efficient Translation of Epstein-Barr Virus (EBV) DNA Polymerase Contributes to the Enhanced Lytic Replication Phenotype of M81 EBV. J Virol 2018; 92:JVI.01794-17. [PMID: 29263273 DOI: 10.1128/jvi.01794-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/17/2017] [Indexed: 11/20/2022] Open
Abstract
Epstein-Barr virus (EBV) is linked to the development of both lymphoid and epithelial malignancies worldwide. The M81 strain of EBV, isolated from a Chinese patient with nasopharyngeal carcinoma (NPC), demonstrates spontaneous lytic replication and high-titer virus production in comparison to the prototype B95-8 EBV strain. Genetic comparisons of M81 and B95-8 EBVs were previously been performed in order to determine if the hyperlytic property of M81 is associated with sequence differences in essential lytic genes. EBV SM is an RNA-binding protein expressed during early lytic replication that is essential for virus production. We compared the functions of M81 SM and B95-8 SM and demonstrate that polymorphisms in SM do not contribute to the lytic phenotype of M81 EBV. However, the expression level of the EBV DNA polymerase protein was much higher in M81- than in B95-8-infected cells. The relative deficiency in the expression of B95-8 DNA polymerase was related to the B95-8 genome deletion, which truncates the BALF5 3' untranslated region (UTR). Similarly, the insertion of bacmid DNA into the widely used recombinant B95-8 bacmid creates an inefficient BALF5 3' UTR. We further showed that the while SM is required for and facilitates the efficient expression of both M81 and B95-8 mRNAs regardless of the 3' UTR, the BALF5 3' UTR sequence is important for BALF5 protein translation. These data indicate that the enhanced lytic replication and virus production of M81 compared to those of B95-8 are partly due to the robust translation of EBV DNA polymerase required for viral DNA replication due to a more efficient BALF5 3' UTR in M81.IMPORTANCE Epstein-Barr virus (EBV) infects more than 90% of the human population, but the incidence of EBV-associated tumors varies greatly in different parts of the world. Thus, understanding the connection between genetic polymorphisms from patient isolates of EBV, gene expression phenotypes, and disease is important and may help in developing antiviral therapy. This study examines potential causes of the enhanced lytic replicative properties of M81 EBV isolated from a nasopharyngeal carcinoma (NPC) patient and provides new evidence for the role of the BALF5 gene 3' UTR sequence in DNA polymerase protein expression during lytic replication. Variation in the gene structure of the DNA polymerase gene may therefore contribute to lytic virus reactivation and pathogenesis.
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Nazim M, Masuda A, Rahman MA, Nasrin F, Takeda JI, Ohe K, Ohkawara B, Ito M, Ohno K. Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms. Nucleic Acids Res 2017; 45:1455-1468. [PMID: 28180311 PMCID: PMC5388418 DOI: 10.1093/nar/gkw823] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/11/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022] Open
Abstract
Acetylcholinesterase (AChE), encoded by the ACHE gene, hydrolyzes the neurotransmitter acetylcholine to terminate synaptic transmission. Alternative splicing close to the 3΄ end generates three distinct isoforms of AChET, AChEH and AChER. We found that hnRNP H binds to two specific G-runs in exon 5a of human ACHE and activates the distal alternative 3΄ splice site (ss) between exons 5a and 5b to generate AChET. Specific effect of hnRNP H was corroborated by siRNA-mediated knockdown and artificial tethering of hnRNP H. Furthermore, hnRNP H competes for binding of CstF64 to the overlapping binding sites in exon 5a, and suppresses the selection of a cryptic polyadenylation site (PAS), which additionally ensures transcription of the distal 3΄ ss required for the generation of AChET. Expression levels of hnRNP H were positively correlated with the proportions of the AChET isoform in three different cell lines. HnRNP H thus critically generates AChET by enhancing the distal 3΄ ss and by suppressing the cryptic PAS. Global analysis of CLIP-seq and RNA-seq also revealed that hnRNP H competitively regulates alternative 3΄ ss and alternative PAS in other genes. We propose that hnRNP H is an essential factor that competitively regulates alternative splicing and alternative polyadenylation.
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Affiliation(s)
- Mohammad Nazim
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mohammad Alinoor Rahman
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Farhana Nasrin
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kenji Ohe
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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Cao XL, Chen JJ, Cao Y, Nie GX, Wan QY, Wang LF, Su JG. Identification and expression of the laboratory of genetics and physiology 2 gene in common carp Cyprinus carpio. JOURNAL OF FISH BIOLOGY 2015; 86:74-91. [PMID: 25359511 DOI: 10.1111/jfb.12541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/09/2014] [Indexed: 06/04/2023]
Abstract
In this study, a laboratory of genetics and physiology 2 gene (lgp2) from common carp Cyprinus carpio was isolated and characterized. The full-length complementary (c)DNA of lgp2 was 3061 bp and encoded a polypeptide of 680 amino acids, with an estimated molecular mass of 77 341·2 Da and a predicted isoelectric point of 6·53. The predicted protein included four main overlapping structural domains: a conserved restriction domain of bacterial type III restriction enzyme, a DEAD-DEAH box helicase domain, a helicase super family C-terminal domain and a regulatory domain. Real-time quantitative polymerase chain reaction (PCR) showed widespread expression of lgp2, mitochondrial antiviral signalling protein (mavs) and interferon transcription factor 3 (irf3) in tissues of nine organs. lgp2, mavs and irf3 expression levels were significantly induced in all examined organs by infection with koi herpesvirus (KHV). lgp2, mavs and irf3 messenger (m)RNA levels were significantly up-regulated in vivo after KHV infection, and lgp2 transcripts were also significantly enhanced in vitro after stimulation with synthetic, double-stranded RNA polyinosinic polycytidylic [poly(I:C)]. These findings suggest that lgp2 is an inducible protein involved in the innate immune defence against KHV in C. carpio. These results provide the basis for further research into the role and mechanisms of lgp2 in fishes.
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Affiliation(s)
- X L Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China; College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China
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Li W, Zhang Y, Zhang C, Pei X, Wang Z, Jia S. Presence of poly(A) and poly(A)-rich tails in a positive-strand RNA virus known to lack 3׳ poly(A) tails. Virology 2014; 454-455:1-10. [PMID: 24725926 DOI: 10.1016/j.virol.2014.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/08/2013] [Accepted: 02/01/2014] [Indexed: 01/08/2023]
Abstract
Here we show that Tobacco mosaic virus (TMV), a positive-strand RNA virus known to end with 3׳ tRNA-like structures, does possess a small fraction of gRNA bearing polyadenylate tails. Particularly, many tails are at sites corresponding to the 3׳ end of near full length gRNA, and are composed of poly(A)-rich sequences containing the other nucleotides in addition to adenosine, resembling the degradation-stimulating poly(A) tails observed in all biological kingdoms. Further investigations demonstrate that these polyadenylated RNA species are not enriched in chloroplasts. Silencing of cpPNPase, a chloroplast-localized polynucleotide polymerase known to not only polymerize the poly(A)-rich tails but act as a 3׳ to 5׳ exoribonuclease, does not change the profile of polyadenylate tails associated with TMV RNA. Nevertheless, because similar tails were also detected in other phylogenetically distinct positive-strand RNA viruses lacking poly(A) tails, such kind of polyadenylation may reflect a common but as-yet-unknown interface between hosts and viruses.
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Affiliation(s)
- Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yongqiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Jia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Yang L, Liu J, Liu M, Qian M, Zhang M, Hu H. Identification of fatty acid synthase from the Pacific white shrimp, Litopenaeus vannamei and its specific expression profiles during white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2011; 30:744-749. [PMID: 21199673 DOI: 10.1016/j.fsi.2010.12.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/24/2010] [Accepted: 12/24/2010] [Indexed: 05/30/2023]
Abstract
Fatty acid synthase (FAS) in animal tissues consists of two identical monomers and is known to be a complex multi-functional enzyme that plays an important role in energy homeostasis. However, there are few reports of studies focused on the relationship between FAS and virus infection in invertebrates. In the present study, we cloned the FAS gene from an economically important invertebrate, the Pacific white shrimp Litopenaeus vannamei. The full-length FAS cDNA is 8268 bp, including a 5'-terminal untranslated region of 137 bp, a 3'-terminal untranslated region of 601 bp and an open reading frame of 7530 bp. FAS cDNA encodes a polypeptide of 2509 amino acid residues that contains a typical β-ketoacyl synthase (KS) domain at the N-terminus, next to a malonyl/acetyltransferase (MAT) domain, a dehydrase domain, an enoyl reductase domain, a ketoacyl reductase domain, a phosphopantetheine attachment site domain and a thioesterase domain at the C-terminus. Quantitative real-time RT-PCR revealed the up-regulated expression of FAS in L. vannamei hepatopancreas and muscle after white spot syndrome virus (WSSV) infection. The expression of FAS in muscle was 13.03-fold greater than that in the control (p<0.05) and 2.93-fold greater in hepatopancreas (p>0.05). Meanwhile, expression of the fatty acid-binding protein (FABP), another important factor in lipid metabolism, was increased in muscle to 19.20-fold greater than that in the control (p<0.05) but only 0.76-fold in hepatopancreas (p>0.05). These results implied that WSSV infected body surface tissues, but there was very little infection of internal organs. We suggest that the increase of FAS expression is induced in WSSV-infected shrimps, and the virus changes the lipid metabolism of the host, which directly affects virus assembly or defense against virus infection.
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Affiliation(s)
- Ling Yang
- College of Life Sciences, China Jiliang University, 258 Xueyuan Street, Xiasha, HangZhou, ZheJiang, China
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Prediction of non-canonical polyadenylation signals in human genomic sequences based on a novel algorithm using a fuzzy membership function. J Biosci Bioeng 2009; 107:569-78. [DOI: 10.1016/j.jbiosc.2009.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2008] [Revised: 01/05/2009] [Accepted: 01/05/2009] [Indexed: 11/23/2022]
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Salem TZ, Garcia-Maruniak A, Lietze VU, Maruniak JE, Boucias DG. Analysis of transcripts from predicted open reading frames of Musca domestica salivary gland hypertrophy virus. J Gen Virol 2009; 90:1270-1280. [PMID: 19264592 DOI: 10.1099/vir.0.009613-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Musca domestica salivary gland hypertrophy virus (MdSGHV) is a large dsDNA virus that infects and sterilizes adult houseflies. The transcriptome of this newly described virus was analysed by rapid amplification of cDNA 3'-ends (3'-RACE) and RT-PCR. Direct sequencing of 3'-RACE products revealed 78 poly(A) transcripts containing 95 of the 108 putative ORFs. An additional six ORFs not amplified by 3'-RACE were detected by RT-PCR. Only seven of the 108 putative ORFs were not amplified by either 3'-RACE or RT-PCR. A series of 5'-RACE reactions were conducted on selected ORFs that were identified by 3'-RACE to be transcribed in tandem (tandem transcripts). In the majority of cases, the downstream ORFs were detected as single transcripts as well as components of the tandem transcripts, whereas the upstream ORFs were found only in tandem transcripts. The only exception was the upstream ORF MdSGHV084, which was differentially transcribed as a single transcript at 1 and 2 days post-infection (days p.i.) and as a tandem transcript (MdSGHV084/085) at 2 days p.i. Transcriptome analysis of MdSGHV detected splicing in the 3' untranslated region (3'-UTR) and extensive heterogeneity in the polyadenylation signals and cleavage sites. In addition, 23 overlapping antisense transcripts were found. In conclusion, sequencing the 3'-RACE products without cloning served as an alternative approach to detect both 3'-UTRs and transcript variants of this large DNA virus.
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Affiliation(s)
- Tamer Z Salem
- Department of Microbial Molecular Biology, AGERI, Agricultural Research Center, 9 Gamaa Street, Giza 12619, Egypt.,Department of Entomology and Nematology, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
| | - Alejandra Garcia-Maruniak
- Department of Entomology and Nematology, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
| | - Verena-U Lietze
- Department of Entomology and Nematology, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
| | - James E Maruniak
- Department of Entomology and Nematology, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
| | - Drion G Boucias
- Department of Entomology and Nematology, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
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Barth S, Pfuhl T, Mamiani A, Ehses C, Roemer K, Kremmer E, Jäker C, Höck J, Meister G, Grässer FA. Epstein-Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5. Nucleic Acids Res 2007; 36:666-75. [PMID: 18073197 PMCID: PMC2241876 DOI: 10.1093/nar/gkm1080] [Citation(s) in RCA: 259] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) have been implicated in sequence-specific cleavage, translational repression or deadenylation of specific target mRNAs resulting in post-transcriptional gene silencing. Epstein–Barr virus (EBV) encodes 23 miRNAs of unknown function. Here we show that the EBV-encoded miRNA miR-BART2 down-regulates the viral DNA polymerase BALF5. MiR-BART2 guides cleavage within the 3′-untranslated region (3′UTR) of BALF5 by virtue of its complete complementarity to its target. Induction of the lytic viral replication cycle results in a reduction of the level of miR-BART2 with a strong concomitant decrease of cleavage of the BALF5 3′UTR. Expression of miR-BART2 down-regulates the activity of a luciferase reporter gene containing the BALF5 3′UTR. Forced expression of miR-BART2 during lytic replication resulted in a 40–50% reduction of the level of BALF5 protein and a 20% reduction of the amount of virus released from EBV-infected cells. Our results are compatible with the notion that EBV-miR-BART2 inhibits transition from latent to lytic viral replication.
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Affiliation(s)
- Stephanie Barth
- Institute of Virology, University of Saarland Medical School, 66424 Homburg, Germany
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Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E. Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 2007; 104:7606-11. [PMID: 17446270 PMCID: PMC1863443 DOI: 10.1073/pnas.0702332104] [Citation(s) in RCA: 294] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A comprehensive mapping of interactions among Epstein-Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on EBV strategies for replication and persistence. Interactions of EBV proteins with each other and with human proteins were assessed by using a stringent high-throughput yeast two-hybrid system. Overall, 43 interactions between EBV proteins and 173 interactions between EBV and human proteins were identified. EBV-EBV and EBV-human protein interaction, or "interactome" maps provided a framework for hypotheses of protein function. For example, LF2, an EBV protein of unknown function interacted with the EBV immediate early R transactivator (Rta) and was found to inhibit Rta transactivation. From a broader perspective, EBV genes can be divided into two evolutionary classes, "core" genes, which are conserved across all herpesviruses and subfamily specific, or "noncore" genes. Our EBV-EBV interactome map is enriched for interactions among proteins in the same evolutionary class. Furthermore, human proteins targeted by EBV proteins were enriched for highly connected or "hub" proteins and for proteins with relatively short paths to all other proteins in the human interactome network. Targeting of hubs might be an efficient mechanism for EBV reorganization of cellular processes.
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Affiliation(s)
- Michael A. Calderwood
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Kavitha Venkatesan
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115; and
| | - Li Xing
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Michael R. Chase
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Alexei Vazquez
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115; and
- The Simons Center for Systems Biology, Institute for Advanced Studies, Princeton, NJ 08540
| | - Amy M. Holthaus
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Alexandra E. Ewence
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Ning Li
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115; and
| | - Tomoko Hirozane-Kishikawa
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115; and
| | - David E. Hill
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115; and
| | - Marc Vidal
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115; and
- To whom correspondence may be addressed. E-mail: and
| | - Elliott Kieff
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
- To whom correspondence may be addressed. E-mail: and
| | - Eric Johannsen
- *Program in Virology, Departments of Medicine and Microbiology and Molecular Genetics, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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Poirier R, Lemaire I, Lemaire S. Characterization, localization and possible anti-inflammatory function of rat histone H4 mRNA variants. FEBS J 2006; 273:4360-73. [PMID: 16939626 DOI: 10.1111/j.1742-4658.2006.05444.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two histone H4 mRNA variants, H4-v.1 and histogranin mRNAs, were detected in the rat genome and measured in various tissues and isolated alveolar macrophages. Medium to high levels of both mRNAs were present in the liver, adrenal glands, thymus, bone marrow and alveolar macrophages. H4-v.1 cDNA contained an open reading frame that coded for unmodified whole histone H4, whereas histogranin cDNA lacked the first ATG codon and contained an open reading frame that coded for modified (Thr89) H4-(84-102). The two genes displayed a sequence homologous (> 80%) to the open reading frame of core H4 somatic (H4s) and H4 germinal (H4g) and their variant nature was supported by the absence of histone consensus palindromic and purine-rich sequences in the proximal 3'UTR, and the presence of a polyadenylation signal in the distal 3'UTR and of specific upstream transcription factor-binding sites. H4-v.1 and histogranin transcripts, but not H4s transcript, were selectively induced by lipopolysaccharide and/or interferon gamma in alveolar macrophages. In vitro transcription/translation experiments with H4-v.1 and histogranin cDNA pCMV constructs produced peptides with the molecular mass (2 kDa) of the alternative histone H4 translation product which, like synthetic H4-(86-100) and [Thr89]H4-(86-100) or rat histogranin, inhibited lipopolysaccharide-induced prostaglandin E(2) release from rat alveolar macrophages. The synthetic peptides also inhibited the secretion of the CXC chemokine interleukin-8 (GRO/CINC-1) in response to lipopolysaccharide. The presence of H4-v.1 and histogranin mRNAs in tissues wherein immune reactions take place and the inhibitory effects of their translation products on prostaglandin E(2) and interkeukin-8 secretion by activated alveolar macrophages suggest an anti-inflammatory function.
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Affiliation(s)
- René Poirier
- Department of Cellular and Molecular Medicine, University of Ottawa, Canada
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11
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Praml C, Savelyeva L, Schwab M. Aflatoxin B1 aldehyde reductase (AFAR) genes cluster at 1p35-1p36.1 in a region frequently altered in human tumour cells. Oncogene 2003; 22:4765-73. [PMID: 12879023 DOI: 10.1038/sj.onc.1206684] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alterations of the distal portion of the short arm of chromosome 1 (1p) are among the earliest abnormalities of human colorectal tumours. Recently, we have cloned the Aflatoxin B1 aldehyde reductase (AFAR) gene from a smallest region of overlapping deletion that is frequently (48%) hemizygously deleted in sporadic colorectal cancer. AFAR is expressed in a broad range of tissues. Its closely related rat protein is the major factor conferring resistance of rats towards aflatoxin B1-induced liver carcinogenesis. Here, we have identified cDNAs covering two additional human AFAR-related genes localized in close proximity to the previously described AFAR at 1p35-36. We have analysed their structure and tissue-related expression. One of them, AFAR3, carries a Selenocysteine-Insertion Element (SECIS)-like structure that during translation may recode an in-frame TGA-stop codon to a selenocysteine. Two additional AFAR-pseudogenes are localized at Xq25 and 1p12, respectively. AFAR exon sequences share an identity of DNA and amino acids of more than 78%. Also large blocks of intronic sequences can be up to 98.6% identical. Knowledge of the AFAR genes and their structure will be essential in genetic and functional studies, where discrimination of the genes and proteins is a prerequisite for evaluating their individual functions.
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Affiliation(s)
- Christian Praml
- Division of Tumour Genetics B030, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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12
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Auxiliary elements of mammalian pre-mRNAs polyadenylation signals. ACTA ACUST UNITED AC 2002. [DOI: 10.7124/bc.00062e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - D. M. Hovorun
- Institute of Molecular Biology and Genetics, NAS of Ukraine
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13
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Scorilas A. Polyadenylate polymerase (PAP) and 3' end pre-mRNA processing: function, assays, and association with disease. Crit Rev Clin Lab Sci 2002; 39:193-224. [PMID: 12120781 DOI: 10.1080/10408360290795510] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polyadenylate polymerase (PAP) is one of the enzymes involved in the formation of the polyadenylate tail of the 3' end of mRNA. Poly (A) tail formation is a significant component of 3' processing, a link in the chain of events, including transcription, splicing, and cleavage/polyadenylation of pre-mRNA. Transcription, capping, splicing, polyadenylation, and transport take place as coupled processes that can regulate one another. The poly(A) tail is found in almost all eukaryotic mRNA and is important in enhancing translation initiation and determining mRNA stability. Control of poly(A) tail synthesis could possibly be a key regulatory step in gene expression. PAP-specific activity values are measured by a highly sensitive assays and immunocytochemical methods. High levels of PAP activity are associated with rapidly proliferating cells, it also prevents apoptosis. Changes of PAP activity may cause a decrease in the rate of polyadenylation in the brain during epileptic seizures. Testis-specific PAP may play an important role in spermiogenesis. PAP was found to be an unfavorable prognostic factor in leukemia and breast cancer. Furthermore, measurements of PAP activity may contribute to the definition of the biological profile of tumor cells. It is crucial to know the specific target causing the elevation of serum PAP, for it to be used as a marker for disease. This review summarizes the recently accumulated knowledge on PAP including its function, assays, and association with various human diseases, and proposes future avenues for research.
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Affiliation(s)
- Andreas Scorilas
- National Center for Scientific Research Demokritos, IPC, Athens, Greece.
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14
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Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res 2000; 10:1001-10. [PMID: 10899149 PMCID: PMC310884 DOI: 10.1101/gr.10.7.1001] [Citation(s) in RCA: 494] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequences to 157,775 polyadenylated expressed sequence tags (ESTs), used as markers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known polyadenylation signals were found in only 73% of the 3' fragments. Ten single-base variants of the AAUAAA sequence were identified with a highly significant occurrence rate, potentially representing 14.9% of the actual polyadenylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence tend to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal type suggests that variant signals (including the common AUUAAA) are processed less efficiently than the canonical signal and could therefore be selected for regulatory purposes. However, the position of the site in the untranslated region may also play a role in polyadenylation rate.
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Affiliation(s)
- E Beaudoing
- Structural and Genetic Information Laboratory, Marseille, France
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15
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Abstract
A variant polyadenylation signal, which is conserved and employed by mammalian hepadnaviruses, has a sequence resembling that of the TATA box. We report here that this composite box manifests all the promoter characteristics. It binds effectively TATA-binding protein with TFIIB and TFIIA in a synergistic manner. This capacity, however, is lost when the box is converted to a canonical and simple poly(A) signal. Furthermore, we show that it has promoter activity and supports transcription of reporter genes preferentially in liver-derived cells, a characteristic behavior of the hepatitis B virus (HBV) promoters. In addition, we show that the HBV noncanonical poly(A) signal supports transcription initiation from the viral genome, suggesting that it is a genuine promoter, possibly of the polymerase/reverse transcriptase gene. Finally, we found that this deviant poly(A) signal is crucial for HBV replication since a viral mutant with a canonical poly(A) box is impaired in replication. Our data, therefore, raise the interesting and novel possibility that a composite poly(A) box might have a dual function. At the level of DNA it functions as a promoter to initiate transcription, whereas at the level of RNA it serves as a poly(A) signal to process RNA. An interesting outcome of this strategy of gene expression is that it provides a novel mechanism for the synthesis of an approximately genome length transcript.
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Affiliation(s)
- N Paran
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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Zhao J, Hyman L, Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999; 63:405-45. [PMID: 10357856 PMCID: PMC98971 DOI: 10.1128/mmbr.63.2.405-445.1999] [Citation(s) in RCA: 808] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.
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Affiliation(s)
- J Zhao
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, Massachusetts 02111, USA
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17
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Key SC, Yoshizaki T, Pagano JS. The Epstein-Barr virus (EBV) SM protein enhances pre-mRNA processing of the EBV DNA polymerase transcript. J Virol 1998; 72:8485-92. [PMID: 9765385 PMCID: PMC110257 DOI: 10.1128/jvi.72.11.8485-8492.1998] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Epstein-Barr virus (EBV) DNA polymerase (pol) mRNA, which contains a noncanonical polyadenylation signal, UAUAAA, is cleaved and polyadenylated inefficiently (S. C. S. Key and J. S. Pagano, Virology 234:147-159, 1997). We postulated that the EBV early proteins SM and M, which appear to act posttranscriptionally and are homologs of herpes simplex virus (HSV) ICP27, might compensate for the inefficient processing of pol pre-mRNA. Here we show that the SM and M proteins interact with each other in vitro. In addition, glutathione S-transferase-SM/M fusion proteins precipitate the heterogeneous ribonucleoprotein (hnRNP) C1 splicing protein. Further, the SM protein is coimmunoprecipitated from SM-expressing cell extracts with an antibody to the hnRNP A1/A2 proteins, which are splicing and nuclear shuttling proteins. Finally, the amount of processed EBV DNA polymerase mRNA was increased three- to fourfold in a HeLa cell line expressing SM; this increase was not due to enhanced transcription. Thus, inefficient processing of EBV pol RNA by cellular cleavage and polyadenylation factors appears to be compensated for and may be regulated by the early EBV protein, SM, perhaps via RNA 3'-end formation.
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Affiliation(s)
- S C Key
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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