101
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Cencic R, Robert F, Pelletier J. Identifying small molecule inhibitors of eukaryotic translation initiation. Methods Enzymol 2007; 431:269-302. [PMID: 17923239 DOI: 10.1016/s0076-6879(07)31013-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotes, translation initiation is rate-limiting with much regulation exerted at the ribosome recruitment and ternary complex (eIF2.GTP.Met-tRNA(i)(Met)) formation steps. Although small molecule inhibitors have been extremely useful for chemically dissecting translation, there is a dearth of compounds available to study the initiation phase in vitro and in vivo. In this chapter, we describe reverse and forward chemical genetic screens developed to identify new inhibitors of translation. The ability to manipulate cell extracts biochemically, and to compare the activity of small molecules on translation of mRNA templates that differ in their factor requirements for ribosome recruitment, facilitates identification of the relevant target.
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Affiliation(s)
- Regina Cencic
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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102
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Park JM, Intine RV, Maraia RJ. Mouse and human La proteins differ in kinase substrate activity and activation mechanism for tRNA processing. Gene Expr 2007; 14:71-81. [PMID: 18257391 PMCID: PMC6042041 DOI: 10.3727/105221607783417619] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The La protein interacts with a variety of small RNAs as well as certain growth-associated mRNAs such as Mdm2 mRNA. Human La (hLa) phosphoprotein is so highly conserved that it can replace the tRNA processing function of the fission yeast La protein in vivo. We used this system, which is based on tRNA-mediated suppression (TMS) of ade6-704 in S. pombe, to compare the activities of mouse and human La proteins. Prior studies indicate that hLa is activated by phosphorylation of serine-366 by protein kinase CK2, neutralizing a negative effect of a short basic motif (SBM). First, we report the sequence mapping of the UGA stop codon that requires suppressor tRNA for TMS, to an unexpected site in S. pombe ade6-704. Next, we show that, unlike hLa, native mLa is unexpectedly inactive for TMS, although its intrinsic activity is revealed by deletion of its SBM. We then show that mLa is not phosphorylated by CK2, accounting for the mechanistic difference between mLa and hLa. We found a PKA/PKG target sequence in mLa (S199) that is not present in hLa, and show that PKA/PKG efficiently phosphorylates mLa S199 in vitro. A noteworthy conclusion that comes from this work is that this fission yeast system can be used to gain insight into differences in control mechanisms used by La proteins of different mammalian species. Finally, RNA binding assays indicate that while mutation of mLa S199 has little effect on pre-tRNA binding, it substantially decreases binding to a probe derived from Mdm2 mRNA. In closing, we note that species-specific signaling through La may be relevant to the La-dependent Mdm2 pathways of p53 metabolism and cancer progression in mice and humans.
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Affiliation(s)
- Jung-Min Park
- Intramural Research Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert V. Intine
- Intramural Research Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J. Maraia
- Intramural Research Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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103
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Abstract
The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 5'-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 5'-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.
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Affiliation(s)
- Stephen D Baird
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
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104
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Curry S, Conte MR. A terminal affair: 3'-end recognition by the human La protein. Trends Biochem Sci 2006; 31:303-5. [PMID: 16679019 DOI: 10.1016/j.tibs.2006.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 03/15/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
The La protein, an autoantigen in rheumatic disease, orchestrates several aspects of the metabolism of noncoding RNA molecules. More than 20 years ago it was shown that La primarily binds the 3' UUU-OH tails of nascent transcripts of RNA polymerase III. A recent study now reveals how the structure of the amino-terminal domain of the human La protein achieves specific 3'-end recognition.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Faculty of Natural Sciences, Imperial College, Exhibition Road, London SW7 2AZ, UK
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105
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Han F, Zhang X. Internal initiation of mRNA translation in insect cell mediated by an internal ribosome entry site (IRES) from shrimp white spot syndrome virus (WSSV). Biochem Biophys Res Commun 2006; 344:893-9. [PMID: 16631622 DOI: 10.1016/j.bbrc.2006.03.229] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 03/30/2006] [Indexed: 11/26/2022]
Abstract
Internal initiation of mRNA translation can be mediated by internal ribosome entry site (IRES) elements which are located mainly in RNA viruses as well as certain mammalian and insect mRNA molecules. Thus far, only one DNA virus has been discovered to contain IRES element. In this investigation, an IRES element from white spot syndrome virus (WSSV), a DNA virus of marine shrimp, was demonstrated to direct the efficient translation of dicistronic mRNA in Trichoplusia ni insect cells. The IRES was inserted between glutathione S-transferase (GST) and green fluorescent protein (GFP) genes to construct a dicistronic cassette (GST-IRES-GFP). After transfection of this dicistronic cassette in insect cell, the Northern blot indicated that only one transcript corresponding to the mRNA of GST-IRES-GFP could be detected. However, the GST and GFP genes were simultaneously translated as revealed by Western blot and fluorescent microscopy, respectively. Based on sequence orientation and deletion analyses, the IRES element was 180 nucleotides (nt) in length and orientation-dependent. By comparison with that of cap-dependent initiation, the translation efficiency mediated by IRES was 98.77%. This finding promises that the WSSV IRES could be very useful to co-express two or more proteins due to its shorter length and higher translation efficiency.
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Affiliation(s)
- Fang Han
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen 361005, PR China
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106
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107
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Colón-Ramos DA, Shenvi CL, Weitzel DH, Gan EC, Matts R, Cate J, Kornbluth S. Direct ribosomal binding by a cellular inhibitor of translation. Nat Struct Mol Biol 2006; 13:103-11. [PMID: 16429152 PMCID: PMC2741086 DOI: 10.1038/nsmb1052] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 12/12/2005] [Indexed: 02/05/2023]
Abstract
During apoptosis and under conditions of cellular stress, several signaling pathways promote inhibition of cap-dependent translation while allowing continued translation of specific messenger RNAs encoding regulatory and stress-response proteins. We report here that the apoptotic regulator Reaper inhibits protein synthesis by binding directly to the 40S ribosomal subunit. This interaction does not affect either ribosomal association of initiation factors or formation of 43S or 48S complexes. Rather, it interferes with late initiation events upstream of 60S subunit joining, apparently modulating start-codon recognition during scanning. CrPV IRES-driven translation, involving direct ribosomal recruitment to the start site, is relatively insensitive to Reaper. Thus, Reaper is the first known cellular ribosomal binding factor with the potential to allow selective translation of mRNAs initiating at alternative start codons or from certain IRES elements. This function of Reaper may modulate gene expression programs to affect cell fate.
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Affiliation(s)
- Daniel A Colón-Ramos
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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108
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Teplova M, Yuan YR, Phan AT, Malinina L, Ilin S, Teplov A, Patel DJ. Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen. Mol Cell 2006; 21:75-85. [PMID: 16387655 PMCID: PMC4689297 DOI: 10.1016/j.molcel.2005.10.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Revised: 09/24/2005] [Accepted: 10/25/2005] [Indexed: 11/25/2022]
Abstract
The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUU(OH) 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the beta sheet edge, rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUU(OH) 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events.
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Affiliation(s)
- Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
| | - Yu-Ren Yuan
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
| | - Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
| | - Lucy Malinina
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
| | - Serge Ilin
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
| | - Alexei Teplov
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer
Center, New York, New York 10021
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109
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Spriggs KA, Bushell M, Mitchell SA, Willis AE. Internal ribosome entry segment-mediated translation during apoptosis: the role of IRES-trans-acting factors. Cell Death Differ 2005; 12:585-91. [PMID: 15900315 DOI: 10.1038/sj.cdd.4401642] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
During apoptosis, there is a reduction in translation initiation caused by caspase cleavage of several of the factors required for the cap-dependent scanning mechanism. Under these circumstances, many proteins that are required for apoptosis are instead translated by the alternative method of internal ribosome entry. This mechanism requires the formation of a complex RNA structural element and in the presence of internal ribosome entry segment (IRES)-trans-acting factors (ITAFs), the ribosome is recruited to the RNA. The interactions of several ITAFs with IRESs have been investigated in detail, and several mechanisms of action have been noted, including acting as chaperones, stabilising and remodelling the RNA structure. Structural remodelling by PTB in particular will be discussed, and how this protein is able to facilitate recruitment of the ribosome to several IRESs by causing previously occluded sites to become more accessible.
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Affiliation(s)
- K A Spriggs
- School of Pharmacy, University of Nottingham, University Park, Nottingham, UK
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110
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Brenet F, Dussault N, Borch J, Ferracci G, Delfino C, Roepstorff P, Miquelis R, Ouafik L. Mammalian peptidylglycine alpha-amidating monooxygenase mRNA expression can be modulated by the La autoantigen. Mol Cell Biol 2005; 25:7505-21. [PMID: 16107699 PMCID: PMC1190315 DOI: 10.1128/mcb.25.17.7505-7521.2005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 01/17/2005] [Accepted: 05/17/2005] [Indexed: 11/20/2022] Open
Abstract
Peptidylglycine alpha-amidating monooxygenase (PAM; EC 1.14.17.3) catalyzes the COOH-terminal alpha-amidation of peptidylglycine substrates, yielding amidated products. We have previously reported a putative regulatory RNA binding protein (PAM mRNA-BP) that binds specifically to the 3' untranslated region (UTR) of PAM-mRNA. Here, the PAM mRNA-BP was isolated and revealed to be La protein using affinity purification onto a 3' UTR PAM RNA, followed by tandem mass spectrometry identification. We determined that the core binding sequence is approximately 15-nucleotides (nt) long and is located 471 nt downstream of the stop codon. Moreover, we identified the La autoantigen as a protein that specifically binds the 3' UTR of PAM mRNA in vivo and in vitro. Furthermore, La protein overexpression caused a nuclear retention of PAM mRNAs and resulted in the down-regulation of endogenous PAM activity. Most interestingly, the nuclear retention of PAM mRNA is lost upon expressing the La proteins that lack a conserved nuclear retention element, suggesting a direct association between PAM mRNA and La protein in vivo. Reporter assays using a chimeric mRNA that combined luciferase and the 3' UTR of PAM mRNA demonstrated a decrease of the reporter activity due to an increase in the nuclear localization of reporter mRNAs, while the deletion of the 15-nt La binding site led to their clear-cut cytoplasmic relocalization. The results suggest an important role for the La protein in the modulation of PAM expression, possibly by mechanisms that involve a nuclear retention and perhaps a processing of pre-PAM mRNA molecules.
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Affiliation(s)
- Fabienne Brenet
- Université de la Méditerranée, Aix-Marseille II, Laboratoire de Cancérologie Expérimentale, Inserm EMI 0359, Faculté de Médecine Secteur Nord, IFR Jean Roche, Marseille, France
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111
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Konishi T, Sasaki S, Watanabe T, Kitayama J, Nagawa H. Overexpression of hRFI (human ring finger homologous to inhibitor of apoptosis protein type) inhibits death receptor-mediated apoptosis in colorectal cancer cells. Mol Cancer Ther 2005; 4:743-50. [PMID: 15897238 DOI: 10.1158/1535-7163.mct-05-0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The acquisition of antiapoptotic properties is one of the essential mechanistic steps in colorectal carcinogenesis and is closely correlated with a loss of chemosensitivity and radiosensitivity. Human ring finger homologous to inhibitor of apoptosis protein type (hRFI) is a newly discovered gene encoding a ring finger domain highly homologous to that of X chromosome-linked inhibitor of apoptosis protein. Immunohistochemistry has revealed that the expression of hRFI increased in transition from normal colorectal mucosas to adenomas and from adenomas to carcinomas, suggesting an essential role in the early stage of colorectal carcinogenesis. However, the function role of hRFI in colorectal carcinoma has not been elucidated. To determine whether hRFI possesses an antiapoptotic function in colorectal cancer cells, HCT116 colorectal cancer cells stably overexpressing hRFI were established. The hRFI transfectant exhibited significant resistance to apoptosis induced by tumor necrosis factor-alpha or tumor necrosis factor-related apoptosis-inducing ligand compared with control. This antiapoptotic response was associated with decreased activity of caspase-3, -8, and -9. We also established an antisense down-regulation of hRFI, which effectively reversed the antiapoptotic activity of the hRFI transfectant. This confirmed that the antiapoptotic property of the hRFI transfectant was not due to the clonal effect but in fact dependent on hRFI function. In conclusion, hRFI possesses an antiapoptotic function in HCT116 colorectal cancer cells. Considering the progressive increase of hRFI expression in the advance of the colorectal adenoma-carcinoma sequence, hRFI is one of the important players in colorectal carcinogenesis through its effect on apoptosis regulation.
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Affiliation(s)
- Tsuyoshi Konishi
- Department of Surgical Oncology, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
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112
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Miura P, Thompson J, Chakkalakal JV, Holcik M, Jasmin BJ. The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J Biol Chem 2005; 280:32997-3005. [PMID: 16061482 DOI: 10.1074/jbc.m503994200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Utrophin up-regulation in muscle fibers of Duchenne muscular dystrophy patients represents a potential therapeutic strategy. It is thus important to delineate the regulatory events presiding over utrophin in muscle in attempts to develop pharmacological interventions aimed at increasing utrophin expression. A number of studies have now shown that under several experimental conditions, the abundance of utrophin is increased without a corresponding elevation in its mRNA. Here, we examine whether utrophin expression is regulated at the translational level in regenerating muscle fibers. Treatment of mouse tibialis anterior muscles with cardiotoxin to induce muscle degeneration/regeneration led to a large (approximately 14-fold) increase in the levels of utrophin A with a modest change in expression of its transcript (40%). Isolation of the mouse utrophin A 5'-untranslated region (UTR) revealed that it is relatively long with a predicted high degree of secondary structure. In control muscles, the 5'-UTR of utrophin A caused an inhibition upon translation of a reporter protein. Strikingly, this inhibition was removed during regeneration, indicating that expression of utrophin A in regenerating muscles is translationally regulated via its 5'-UTR. Using bicistronic reporter vectors, we observed that this translational effect involves an internal ribosome entry site in the utrophin A 5'-UTR. Thus, internal ribosome entry site-mediated translation of utrophin A can, at least partially, account for the discordant expression of utrophin A protein and transcript in regenerating muscle. These findings provide a novel target for up-regulating levels of utrophin A in Duchenne muscular dystrophy muscle fibers via pharmacological interventions.
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MESH Headings
- 5' Untranslated Regions
- Animals
- Binding Sites
- Blotting, Northern
- Blotting, Western
- Cells, Cultured
- Cobra Cardiotoxin Proteins/metabolism
- Gene Expression Regulation
- Genes, Reporter
- Genetic Vectors
- Mice
- Mice, Inbred C57BL
- Microscopy, Fluorescence
- Models, Genetic
- Muscle Fibers, Skeletal/metabolism
- Muscle, Skeletal/metabolism
- Muscles/metabolism
- Plasmids/metabolism
- Protein Biosynthesis
- Protein Structure, Secondary
- RNA/metabolism
- RNA, Messenger/metabolism
- Regeneration
- Reverse Transcriptase Polymerase Chain Reaction
- Ribosomes/metabolism
- Up-Regulation
- Utrophin/chemistry
- Utrophin/genetics
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Affiliation(s)
- Pedro Miura
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
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113
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Oltean S, Banerjee R. A B12-responsive internal ribosome entry site (IRES) element in human methionine synthase. J Biol Chem 2005; 280:32662-8. [PMID: 16051610 DOI: 10.1074/jbc.m501964200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Regulation of homocysteine, a sulfur-containing amino acid that is a risk factor for cardiovascular diseases, is poorly understood. Methionine synthase (MS) is a key enzyme that clears intracellular homocysteine, and its activity is induced by its cofactor, vitamin B12, at a translational level. In this study, we demonstrate that translation of MS, which has a long and highly structured 5'-untranslated region, is initiated from an internal ribosome entry site (IRES), which is modulated by B12. The minimal IRES element spans 71 bases immediately upstream of the initiation codon. Electrophoretic mobility shift analysis reveals the presence of a B12 -dependent protein-RNA complex and suggests the possibility that B12-dependent increase of IRES efficiency is mediated via a protein. Modulation of the IRES-dependent translation of an essential gene by the cofactor of the encoded enzyme represents a novel example of a gene-nutrient interaction.
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Affiliation(s)
- Sebastian Oltean
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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114
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Cornelis S, Tinton SA, Schepens B, Bruynooghe Y, Beyaert R. UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein. Nucleic Acids Res 2005; 33:3095-108. [PMID: 15928332 PMCID: PMC1142345 DOI: 10.1093/nar/gki611] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Upstream of N-ras (Unr) has been described as an internal initiation trans-acting factor (ITAF) in the cap-independent translation of some particular viral and cellular mRNAs. Two factors led us to hypothesize that the UNR 5′-untranslated region (5′-UTR) may contain an internal ribosome entry site (IRES). The first was the requirement for persisting Unr expression under conditions that correlate with cap-independent translation. The other was the observation that the primary UNR transcript contains a 447 nt long 5′-UTR including two upstream AUGs that may restrict translation initiation via cap-dependent ribosome scanning. Here we report that the UNR 5′-UTR allows IRES-dependent translation, as revealed by a dicistronic reporter assay. Various controls ruled out the contribution of leaky scanning, cryptic promoter sequences or RNA processing events to the ability of the UNR 5′-UTR to mediate internal initiation of translation. Ultraviolet cross-linking analysis and RNA affinity chromatography revealed the binding of polypyrimidine tract binding protein (PTB) to the UNR IRES, requiring a pyrimidine-rich region (nucleotides 335–355). Whereas overexpression of PTB in several cell lines inhibited UNR IRES activity and UNR protein expression, depletion of endogenous PTB using RNAi increased UNR IRES activity. Moreover, a mutant version of the UNR IRES lacking the PTB binding site was more efficient at directing IRES-mediated translation. In conclusion, our results demonstrate that translation of the ITAF Unr can itself be regulated by an IRES that is downregulated by PTB.
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Affiliation(s)
- Sigrid Cornelis
- Department for Molecular Biomedical Research, VIB-Ghent University, Unit of Molecular Signal Transduction in Inflammation B-9052 Gent-Zwijnaarde, Belgium.
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115
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Kim TD, Kim JS, Kim JH, Myung J, Chae HD, Woo KC, Jang SK, Koh DS, Kim KT. Rhythmic serotonin N-acetyltransferase mRNA degradation is essential for the maintenance of its circadian oscillation. Mol Cell Biol 2005; 25:3232-46. [PMID: 15798208 PMCID: PMC1069600 DOI: 10.1128/mcb.25.8.3232-3246.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase [AANAT]) is the key enzyme in melatonin synthesis regulated by circadian rhythm. To date, our understanding of the oscillatory mechanism of melatonin has been limited to autoregulatory transcriptional and posttranslational regulations of AANAT mRNA. In this study, we identify three proteins from pineal glands that associate with cis-acting elements within species-specific AANAT 3' untranslated regions to mediate mRNA degradation. These proteins include heterogeneous nuclear ribonucleoprotein R (hnRNP R), hnRNP Q, and hnRNP L. Their RNA-destabilizing function was determined by RNA interference and overexpression approaches. Expression patterns of these factors in pineal glands display robust circadian rhythm. The enhanced levels detected after midnight correlate with an abrupt decline in AANAT mRNA level. A mathematical model for the AANAT mRNA profile and its experimental evidence with rat pinealocytes indicates that rhythmic AANAT mRNA degradation mediated by hnRNP R, hnRNP Q, and hnRNP L is a key process in the regulation of its circadian oscillation.
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Affiliation(s)
- Tae-Don Kim
- National Research Laboratory, Department of Life Science, Pohang University of Science and Technology, San 31 Hyoja-Dong, Pohang, Kyung-Buk 790-784, Republic of Korea
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116
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Abstract
Cells respond to stress stimuli through coordinated changes in gene expression. The regulation of translation is often used under these circumstances because it allows immediate and selective changes in protein levels. There are many examples of translational control in response to stress. Here we examine two representative models, the regulation of eukaryotic initiation factor-2alpha by phosphorylation and internal ribosome initiation through the internal ribosome-entry site, which illustrate the importance of translational control in the cellular stress response and apoptosis.
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Affiliation(s)
- Martin Holcik
- Apoptosis Research Center, Room R3116, Children's Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada.
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117
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Vazquez-Pianzola P, Urlaub H, Rivera-Pomar R. Proteomic analysis of reaper 5' untranslated region-interacting factors isolated by tobramycin affinity-selection reveals a role for La antigen in reaper mRNA translation. Proteomics 2005; 5:1645-55. [PMID: 15789343 DOI: 10.1002/pmic.200401045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Translational control is a key step in gene expression regulation during apoptosis. To understand the mechanisms of mRNA translation of a pro-apoptotic gene, reaper (rpr), we adapted the tobramycin-aptamer technique described by Hartmuth et al. (Proc. Natl. Acad. Sci. USA 2002, 99, 16719-16724) for the analysis of proteins interacting with rpr 5' untranslated region (UTR). We assembled ribonucleoprotein complexes in vitro using translation extracts derived from Drosophila embryos and purified the RNA-protein complexes for mas spectrometry analysis. We identified the proteins bound to the 5' UTR of rpr. One of them, the La antigen, was validated by RNA-crosslinking experiments using recombinant protein and by the translation efficiency of reporter mRNAs in Drosophila cells after RNAinterference experiments. Our data provide evidence of the involvement of La antigen in the translation of rpr and set a protocol for purification of tagged-RNA-protein complexes from cytoplasmic extracts.
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Affiliation(s)
- Paula Vazquez-Pianzola
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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118
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Fukamiya N, Lee KH, Muhammad I, Murakami C, Okano M, Harvey I, Pelletier J. Structure–activity relationships of quassinoids for eukaryotic protein synthesis. Cancer Lett 2005; 220:37-48. [PMID: 15737686 DOI: 10.1016/j.canlet.2004.04.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Accepted: 04/27/2004] [Indexed: 12/30/2022]
Abstract
The effect of 63 quassinoids on eukaryotic protein synthesis has been investigated. Seventeen of the tested compounds showed potent in vitro activity, with IC50s below 2 microM for inhibition in Krebs ascites translation extracts. Sixteen of these quassinoids were also potent inhibitors of in vivo protein synthesis when exposed to Hela cells for 1 h. Our results led to the following structure-activity relationships for quassinoids regarding translation inhibition. Activity is influenced by (i) the nature of the C-15 side chain, (ii) the nature of A ring modifications, (iii) the presence or absence of a sugar moiety, and (iv) the presence of an epoxymethano bridge.
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Affiliation(s)
- Narihiko Fukamiya
- Faculty of Integrated Arts and Sciences, Hiroshima University, Kagamiyama 1-7-1, Higashi, Hiroshima 739-8521, Japan
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119
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Tinton S, Schepens B, Bruynooghe Y, Beyaert R, Cornelis S. Regulation of the cell-cycle-dependent internal ribosome entry site of the PITSLRE protein kinase: roles of Unr (upstream of N-ras) protein and phosphorylated translation initiation factor eIF-2alpha. Biochem J 2005; 385:155-63. [PMID: 15330758 PMCID: PMC1134683 DOI: 10.1042/bj20040963] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 08/10/2004] [Accepted: 08/26/2004] [Indexed: 12/19/2022]
Abstract
The PITSLRE kinases belong to the large family of cyclin-dependent protein kinases. Their function has been related to cell-cycle regulation, splicing and apoptosis. We have previously shown that the open reading frame of the p110(PITSLRE) transcript contains an IRES (internal ribosome entry site) that allows the expression of a smaller p58(PITSLRE) isoform during the G2/M stage of the cell cycle. In the present study we investigated further the role of cis- and trans-acting factors in the regulation of the PITSLRE IRES. Progressive deletion analysis showed that both a purine-rich sequence and a Unr (upstream of N-ras) consensus binding site are essential for PITSLRE IRES activity. In line with these observations, we demonstrate that the PITSLRE IRES interacts with the Unr protein, which is more prominently expressed at the G2/M stage of the cell cycle. We also show that phosphorylation of the alpha-subunit of the canonical initiation factor eIF-2 is increased at G2/M. Interestingly, phosphorylation of eIF-2alpha has a permissive effect on the efficiency of both the PITSLRE IRES and the ornithine decarboxylase IRES, two cell cycle-dependent IRESs, in mediating internal initiation of translation, whereas this was not observed with the viral EMCV (encephalomyocarditis virus) and HRV (human rhinovirus) IRESs.
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Key Words
- cap-independent translation
- α-subunit of eukaryotic initiation factor 2 (eif-2α)
- g2/m cell-cycle stage
- internal ribosome-entry-site (ires)-specific trans-acting factor (itaf)
- p58pitslre protein kinase
- upstream of n-ras
- apaf-1, apoptotic-protease-activating factor 1
- cat-1, cationic amino acid transporter protein 1
- dtt, dithiothreitol
- eifs, eukaryotic initiation factors
- eif-2α, α-subunit of eukaryotic initiation factor 2
- emcv, encephalomyocarditis virus
- fcs, fetal-calf serum
- fluc, firefly luciferase
- hnrnp, heterogeneous nuclear ribonucleoprotein
- il-3, interleukin-3
- itaf, ires-specific trans-acting factor
- hrv, human rhinovirus
- ires, internal ribosome entry site
- odc, ornithine decarboxylase
- pars, polypurine (a)-rich sequence
- pdgf, platelet-derived growth factor
- pkr, double-stranded-rna-activated protein kinase
- pkr-k296r, death mutant [lys296→arginine]kpr
- ptb, polypyrimidine-tract-binding protein
- 5′-race, rapid amplification of cdna ends
- rluc, renilla luciferase
- rrl, rabbit reticulocyte lysate
- sv40, simian virus 40
- unr, upstream of n-ras (protein)
- 5′-utr, 5′-untranslated region
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Affiliation(s)
- Sandrine A. Tinton
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB (Flanders Interuniversity Institute for Biotechnology)–Ghent University, Technologiepark 927, B-9052 Gent-Zwijnaarde, Belgium
| | - Bert Schepens
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB (Flanders Interuniversity Institute for Biotechnology)–Ghent University, Technologiepark 927, B-9052 Gent-Zwijnaarde, Belgium
| | - Yanik Bruynooghe
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB (Flanders Interuniversity Institute for Biotechnology)–Ghent University, Technologiepark 927, B-9052 Gent-Zwijnaarde, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB (Flanders Interuniversity Institute for Biotechnology)–Ghent University, Technologiepark 927, B-9052 Gent-Zwijnaarde, Belgium
| | - Sigrid Cornelis
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB (Flanders Interuniversity Institute for Biotechnology)–Ghent University, Technologiepark 927, B-9052 Gent-Zwijnaarde, Belgium
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120
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Intine RV, Dundr M, Vassilev A, Schwartz E, Zhao Y, Zhao Y, Depamphilis ML, Maraia RJ. Nonphosphorylated human La antigen interacts with nucleolin at nucleolar sites involved in rRNA biogenesis. Mol Cell Biol 2004; 24:10894-904. [PMID: 15572691 PMCID: PMC533991 DOI: 10.1128/mcb.24.24.10894-10904.2004] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Revised: 08/20/2004] [Accepted: 09/17/2004] [Indexed: 02/07/2023] Open
Abstract
La is a RNA-binding protein implicated in multiple pathways related to the production of tRNAs, ribosomal proteins, and other components of the translational machinery (D. J. Kenan and J. D. Keene, Nat. Struct. Mol. Biol. 11:303-305, 2004). While most La is phosphorylated and resides in the nucleoplasm, a fraction is in the nucleolus, the site of ribosome production, although the determinants of this localization are incompletely known. In addition to its conserved N-terminal domain, human La harbors a C-terminal domain that contains an atypical RNA recognition motif and a short basic motif (SBM) adjacent to phosphoserine-366. We report that nonphosphorylated La (npLa) is concentrated in nucleolar sites that correspond to the dense fibrillar component that harbors nascent pol I transcripts as well as fibrillarin and nucleolin, which function in early phases of rRNA maturation. Affinity purification and native immunoprecipitation of La and fluorescence resonance energy transfer in the nucleolus reveal close association with nucleolin. Moreover, La lacking the SBM does not localize to nucleoli. Lastly, La exhibits SBM-dependent, phosphorylation-sensitive interaction with nucleolin in a yeast two-hybrid assay. The data suggest that interaction with nucleolin is, at least in part, responsible for nucleolar accumulation of La and that npLa may be involved in ribosome biogenesis.
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Affiliation(s)
- Robert V Intine
- Laboratory of Molecular Growth Regulation, National Institute of Child Health & Human Development, 6 Center Dr., Rm. 416, Bethesda, MD 20892-2753, USA
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121
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Bonnal S, Pileur F, Orsini C, Parker F, Pujol F, Prats AC, Vagner S. Heterogeneous nuclear ribonucleoprotein A1 is a novel internal ribosome entry site trans-acting factor that modulates alternative initiation of translation of the fibroblast growth factor 2 mRNA. J Biol Chem 2004; 280:4144-53. [PMID: 15525641 DOI: 10.1074/jbc.m411492200] [Citation(s) in RCA: 114] [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
Alternative initiation of translation of the human fibroblast growth factor 2 (FGF-2) mRNA at five in-frame CUG or AUG translation initiation codons requires various RNA cis-acting elements, including an internal ribosome entry site (IRES). Here we describe the purification of a trans-acting factor controlling FGF-2 mRNA translation achieved by several biochemical purification approaches. We have identified the heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) as a factor that binds to the FGF-2 5'-leader RNA and that also complements defective FGF-2 translation in vitro in rabbit reticulocyte lysate. Recombinant hnRNP A1 stimulates in vitro translation at the four IRES-dependent initiation codons but has no effect on the cap-dependent initiation codon. Consistent with a role of hnRNP A1 in the control of alternative initiation of translation, short interfering RNA-mediated knock down of hnRNP A1 specifically inhibits translation at the four IRES-dependent initiation codons. Furthermore, hnRNP A1 binds to the FGF-2 IRES, implicating this interaction in the control of alternative initiation of translation.
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Affiliation(s)
- Sophie Bonnal
- INSERM U589, Institut Louis Bugnard, Hopital Rangueil, TSA 50032, 31059 Toulouse Cedex 9, France
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122
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Schwartz EI, Intine RV, Maraia RJ. CK2 is responsible for phosphorylation of human La protein serine-366 and can modulate rpL37 5'-terminal oligopyrimidine mRNA metabolism. Mol Cell Biol 2004; 24:9580-91. [PMID: 15485924 PMCID: PMC522270 DOI: 10.1128/mcb.24.21.9580-9591.2004] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Revised: 08/04/2004] [Accepted: 08/12/2004] [Indexed: 11/20/2022] Open
Abstract
La protein binds precursors to 5S rRNA, tRNAs, and other transcripts that contain 3' UUU-OH and also promotes their maturation in the nucleus. Separate from this function, human La has been shown to positively modulate the translation of mRNAs that contain complex 5' regulatory motifs that direct internal initiation of translation. Nonphosphorylated La (npLa) inhibits pre-tRNA processing, while phosphorylation of human La serine-366 (S(366)) promotes pre-tRNA processing. npLa was found specifically associated with a class of mRNAs that have unusually short 5' untranslated regions comprised of terminal oligopyrimidine (5'TOP) tracts and that encode ribosomal proteins and translation elongation factors. Although La S(366) represents a CK2 phosphorylation site, there was no evidence that CK2 phosphorylates it in vivo. We used the CK2-specific inhibitor, 4,5,6,7-tetrabromo-2-azabenzimidazole (TBB), and antisense-mediated knockdown to demonstrate that CK2 is responsible for La S(366) phosphorylation in vivo. Hypophosphorylation was not associated with significant change in total La levels or proteolytic cleavage. Quantitative reverse transcription-PCR revealed increased association of the 5'TOP-mRNA encoding ribosomal protein L37 (rpL37) with La after TBB treatment. Transfection revealed more rpL37 mRNA associated with nonphosphorylatable La A(366) than with La S(366), concomitant with La A(366)-specific shift of a fraction of L37 mRNA off polysomes. The data indicate that CK2 phosphorylates La S(366) in vivo, that this limits 5'TOP mRNA binding, and that increasing npLa leads to greater association with potentially negative effects on TOP mRNA translation. Consistent with data that indicate that phosphorylation reverses negative effects of npLa on tRNA production, the present data suggest that CK2 phosphorylation of La can affect production of the translational machinery.
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Affiliation(s)
- Elena I Schwartz
- Laboratory of Molecular Growth Regulation, NICHD, NIH, Bethesda, MD 20892-2753, USA
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123
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Lu CC, Wu CW, Chang SC, Chen TY, Hu CR, Yeh MY, Chen JY, Chen MR. Epstein-Barr virus nuclear antigen 1 is a DNA-binding protein with strong RNA-binding activity. J Gen Virol 2004; 85:2755-2765. [PMID: 15448336 DOI: 10.1099/vir.0.80239-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA-1) plays key roles in both the regulation of gene expression and the replication of the EBV genome in latently infected cells. To characterize the RNA-binding activity of EBNA-1, it was demonstrated that EBNA-1 binds efficiently to RNA homopolymers that are composed of poly(G) and weakly to those composed of poly(U). All three RGG boxes of EBNA-1 contributed additively to poly(G)-binding activity and could mediate RNA binding when attached to a heterologous protein in an RNA gel mobility-shift assay. In vitro-transcribed EBV and non-EBV RNA probes revealed that EBNA-1 bound to most RNAs examined and the affinity increased as the content of G and U increased, as demonstrated in competition assays. Among these probes, the 5' non-coding region (NCR) (nt 131-278) of hepatitis C virus RNA appeared to be the strongest competitor for EBNA-1 binding to the EBV-encoded small nuclear RNA 1 (EBER1) probe, whereas a mutant 5' NCR RNA with partially disrupted secondary structure was a weak competitor. Furthermore, the interaction of endogenous EBNA-1 and EBER1 in EBV-infected cells was demonstrated by a ribonucleoprotein immunoprecipitation assay. These results revealed that EBNA-1 is a DNA-binding protein with strong binding activity to a relatively broad spectrum of RNA and suggested an additional biological impact of EBNA-1 through its ability to bind to RNA.
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Affiliation(s)
- Chih-Chung Lu
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Chia-Wei Wu
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Shin C Chang
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Tzu-Yi Chen
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Chwan-Ren Hu
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Ming-Yi Yeh
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Jen-Yang Chen
- National Health Research Institutes, Taipei, Taiwan
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
| | - Mei-Ru Chen
- Graduate Institute of Microbiology, College of Medicine, No. 1, Jen-Ai Road, 1st Section, National Taiwan University, Taipei, Taiwan
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124
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Nishimura K, Ueda K, Guwanan E, Sakakibara S, Do E, Osaki E, Yada K, Okuno T, Yamanishi K. A posttranscriptional regulator of Kaposi's sarcoma-associated herpesvirus interacts with RNA-binding protein PCBP1 and controls gene expression through the IRES. Virology 2004; 325:364-78. [PMID: 15246275 DOI: 10.1016/j.virol.2004.04.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Revised: 03/11/2004] [Accepted: 04/23/2004] [Indexed: 11/23/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV; also known as human herpesvirus 8, HHV-8) belongs to the gamma-herpesvirus subfamily. The KSHV ORF57 gene is thought to be a homolog of posttranscriptional regulators that are conserved in the herpesvirus family and are essential for replication. We generated specific monoclonal antibodies (mAbs) against the ORF57 protein that detected the 51-kDa protein expressed in the nucleus of KSHV-infected cells. We also found that the ORF57 protein interacted with poly(rC)-binding protein 1 (PCBP1), a cellular RNA-binding, posttranscriptional regulator. ORF57's interaction with PCBP1 enhanced the activity of not only poliovirus internal ribosome-entry site (IRES)-dependent translation but also X-linked inhibitor of apoptosis (XIAP) and KSHV vFLIP IRES. Actually, when ORF57 expression was induced by the expression of replication and transcription activator (RTA) in KSHV-infected cells, the expression of XIAP was enhanced. These results suggest that ORF57 binds to PCBP1 as a functional partner for posttranscriptional regulation and is involved in the regulation of the expression of both cellular and viral genes through IRESs.
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Affiliation(s)
- Ken Nishimura
- Department of Microbiology, Osaka University Medical School, Suita, Osaka 565-0871, Japan
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125
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Costa-Mattioli M, Svitkin Y, Sonenberg N. La autoantigen is necessary for optimal function of the poliovirus and hepatitis C virus internal ribosome entry site in vivo and in vitro. Mol Cell Biol 2004; 24:6861-70. [PMID: 15254251 PMCID: PMC444852 DOI: 10.1128/mcb.24.15.6861-6870.2004] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 04/02/2004] [Accepted: 04/30/2004] [Indexed: 12/12/2022] Open
Abstract
Translation of poliovirus and hepatitis C virus (HCV) RNAs is initiated by recruitment of 40S ribosomes to an internal ribosome entry site (IRES) in the mRNA 5' untranslated region. Translation initiation of these RNAs is stimulated by noncanonical initiation factors called IRES trans-activating factors (ITAFs). The La autoantigen is such an ITAF, but functional evidence for the role of La in poliovirus and HCV translation in vivo is lacking. Here, by two methods using small interfering RNA and a dominant-negative mutant of La, we demonstrate that depletion of La causes a dramatic reduction in poliovirus IRES function in vivo. We also show that 40S ribosomal subunit binding to HCV and poliovirus IRESs in vitro is inhibited by a dominant-negative form of La. These results provide strong evidence for a function of the La autoantigen in IRES-dependent translation and define the step of translation which is stimulated by La.
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Affiliation(s)
- Mauro Costa-Mattioli
- Department of Biochemistry and McGill Cancer Center, McGill University, McIntyre Medical Building, Montreal, Quebec, Canada H3G 1Y6
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126
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Horke S, Reumann K, Schweizer M, Will H, Heise T. Nuclear trafficking of La protein depends on a newly identified nucleolar localization signal and the ability to bind RNA. J Biol Chem 2004; 279:26563-70. [PMID: 15060081 DOI: 10.1074/jbc.m401017200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Here we provide evidence for an interaction-dependent subnuclear trafficking of the human La (hLa) protein, known as transient interaction partner of a variety of RNAs. Among these, precursor transcripts of certain RNAs are located in the nucleoplasm or nucleolus. Here we examined which functional domains of hLa are involved in its nuclear trafficking. By using green fluorescent-hLa fusion proteins, we discovered a nucleolar localization signal and demonstrated its functionality in a heterologous context. In addition, we revealed that the RRM2 motif of hLa is essential both for its RNA binding competence in vitro and in vivo and its exit from the nucleolus. Our data imply that hLa traffics between different subnuclear compartments, which depend decisively on a functional nucleolar localization signal as well as on RNA binding. Directed trafficking of hLa is fully consistent with its function in the maturation of precursor RNAs located in different subnuclear compartments.
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Affiliation(s)
- Sven Horke
- Heinrich-Pette-Institut fur Experimentelle Virologie und Immunologie an der Universitaat Hamburg, Martinistrasse 52, D-20251 Hamburg, Germany
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127
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Abstract
The X-linked inhibitor of apoptosis protein (XIAP) is the most potent and best studied intrinsic regulator of programmed cell death. The critical role XIAP plays in the control of apoptosis is also reflected in the complex ways the activity of XIAP is regulated. In addition to regulating the function of the protein, the synthesis of XIAP is also selectively regulated. XIAP is translated by a cap-independent mechanism of translation initiation that is mediated by a unique internal ribosome entry site (IRES) sequence element located in its 5' untranslated region. This allows XIAP mRNA to be actively translated during conditions of cellular stress when the majority of cellular protein synthesis is inhibited. The IRES regulation of XIAP translation points to an important mechanism in the control and regulation of apoptosis.
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Affiliation(s)
- Martin Holcik
- Solange Gauthier Karsh Molecular Genetics Laboratory, Department of Pediatrics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1 Canada.
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128
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Pickering BM, Mitchell SA, Spriggs KA, Stoneley M, Willis AE. Bag-1 internal ribosome entry segment activity is promoted by structural changes mediated by poly(rC) binding protein 1 and recruitment of polypyrimidine tract binding protein 1. Mol Cell Biol 2004; 24:5595-605. [PMID: 15169918 PMCID: PMC419896 DOI: 10.1128/mcb.24.12.5595-5605.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Revised: 01/07/2004] [Accepted: 03/26/2004] [Indexed: 11/20/2022] Open
Abstract
We have shown previously that an internal ribosome entry segment (IRES) directs the synthesis of the p36 isoform of Bag-1 and that polypyrimidine tract binding protein 1 (PTB-1) and poly(rC) binding protein 1 (PCBP1) stimulate IRES-mediated translation initiation in vitro and in vivo. Here, a secondary structural model of the Bag-1 IRES has been derived by using chemical and enzymatic probing data as constraints on the RNA folding algorithm Mfold. The ribosome entry window has been identified within this structural model and is located in a region in which many residues are involved in base-pairing interactions. The interactions of PTB-1 and PCBP1 with their cognate binding sites on the IRES disrupt many of the RNA-RNA interactions, and this creates a largely unstructured region of approximately 40 nucleotides that could permit ribosome binding. Mutational analysis of the PTB-1 and PCBP1 binding sites suggests that PCBP1 acts as an RNA chaperone to open the RNA in the vicinity of the ribosome entry window while PTB-1 is probably an essential part of the preinitiation complex.
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Affiliation(s)
- Becky M Pickering
- Department of Biochemistry, University of Leicester, LE1 7RH, United Kingdom
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129
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Stoneley M, Willis AE. Cellular internal ribosome entry segments: structures, trans-acting factors and regulation of gene expression. Oncogene 2004; 23:3200-7. [PMID: 15094769 DOI: 10.1038/sj.onc.1207551] [Citation(s) in RCA: 279] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Initiation of translation in eukaryotic cells can occur by two distinct mechanisms, cap-dependent scanning and internal ribosome entry. The latter mechanism requires the formation of a complex RNA structural element termed an internal ribosome entry segment (IRES). IRESs are located in the 5' untranslated region of the message, and in the presence of trans-acting factors allow the ribosome to be recruited to a site that is a considerable distance from the cap structure. Many cellular mRNAs have now been shown to contain IRESs and it is likely that up to 10% of all mRNAs have the capability to initiate translation by this mechanism. The majority of IRESs that have been identified thus far are found in mRNAs whose protein products are associated with the control of cell growth and cell death, including many growth factors, proto-oncogenes and proteins required for apoptosis. In this review, we discuss the cellular situations when IRESs are required, the trans-acting factors that are necessary for IRES function and deregulation of IRES-mediated translation in tumorigenesis.
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Affiliation(s)
- Mark Stoneley
- Department of Biochemistry, University of Leicester, University Rd, Leicester LE1 7RH, UK.
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130
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Abstract
The ability of oncogenic proteins to regulate the rate of translation of specific mRNA subsets may be a rapid and efficient mechanism to modulate the levels and, in many cases, the activity of the corresponding proteins. In the past few years, we have identified several RNA binding proteins with translation regulatory activity whose expression is markedly activated in the blast crisis of chronic myelogenous leukemia, which represents the most malignant disease stage. Perturbation of the activity of some RNA binding proteins suppresses the leukemogenic potential of BCR/ABL-expressing cells. Most importantly, we have identified some of the targets of these RNA binding proteins. Two of these targets, c/ebp alpha and mdm2 mRNAs, are directly relevant for the altered differentiation and survival of leukemic cells. The identification of mRNA targets translationally regulated by RNA binding proteins overexpressed in tumor cells may lead to the development of therapeutic strategies aimed at modulating the translation rate of specific mRNAs.
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Affiliation(s)
- Danilo Perrotti
- Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus OH 43210, USA.
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131
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Bieleski L, Hindley C, Talbot SJ. A polypyrimidine tract facilitates the expression of Kaposi's sarcoma-associated herpesvirus vFLIP through an internal ribosome entry site. J Gen Virol 2004; 85:615-620. [PMID: 14993645 DOI: 10.1099/vir.0.19733-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have identified a novel internal ribosome entry site (IRES) within a latently expressed Kaposi's sarcoma-associated herpesvirus (KSHV) gene (vCyclin) that controls the expression of a downstream open reading frame encoding an inhibitor of apoptosis (vFLIP). This IRES is the first such element to be identified in a DNA virus and may represent a novel mechanism through which this virus controls gene expression. We have used a dual luciferase reporter assay to identify important sequence elements essential for the activity of the IRES. A sequence of 32 nucleotides incorporating a polypyrimidine tract (PPT) was found to be required for the proper functioning of the IRES. We also show, using an electrophoretic mobility shift assay (EMSA), that proteins specific to a KSHV-infected cell line (BCP-1) but not a KSHV-negative cell line (HEK293) were able to form complexes with the IRES. By using an in vitro RNA binding assay, the cellular polypyrimidine tract binding protein (PTB, hnRNP-I) was found to bind to the IRES RNA. These results suggest that the interaction of PTB with the PPT may contribute to the correct functioning of the KSHV IRES in infected cells.
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Affiliation(s)
- Lara Bieleski
- University of Edinburgh, Centre for Infectious Diseases, Summerhall, Edinburgh EH9 1QH, UK
| | - Clemence Hindley
- University of Edinburgh, Centre for Infectious Diseases, Summerhall, Edinburgh EH9 1QH, UK
| | - Simon J Talbot
- University of Edinburgh, Centre for Infectious Diseases, Summerhall, Edinburgh EH9 1QH, UK
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132
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Izumi RE, Das S, Barat B, Raychaudhuri S, Dasgupta A. A peptide from autoantigen La blocks poliovirus and hepatitis C virus cap-independent translation and reveals a single tyrosine critical for La RNA binding and translation stimulation. J Virol 2004; 78:3763-76. [PMID: 15016896 PMCID: PMC371053 DOI: 10.1128/jvi.78.7.3763-3776.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Accepted: 11/25/2003] [Indexed: 02/05/2023] Open
Abstract
La, a 52-kDa autoantigen in patients with systemic lupus erythematosus, was one of the first cellular proteins identified to interact with viral internal ribosome entry site (IRES) elements and stimulate poliovirus (PV) and hepatitis C virus (HCV) IRES-mediated translation. Previous results from our laboratory have shown that a small, yeast RNA (IRNA) could selectively inhibit PV and HCV IRES-mediated translation by sequestering the La protein. Here we have identified an 18-amino-acid-long sequence from the N-terminal "La motif" which is required for efficient interaction of La with IRNA and viral 5' untranslated region (5'-UTR) elements. A synthetic peptide (called LAP, for La peptide) corresponding to this sequence (amino acids 11 to 28) of La was found to efficiently inhibit viral IRES-mediated translation in vitro. The LAP efficiently enters Huh-7 cells and preferentially inhibits HCV IRES-mediated translation programmed by a bicistronic RNA in vivo. The LAP does not bind RNA directly but appears to block La binding to IRNA and PV 5'-UTR. Competition UV cross-link and translation rescue experiments suggested that LAP inhibits IRES-mediated translation by interacting with proteins rather than RNA. Mutagenesis of LAP demonstrates that single amino acid changes in a highly conserved sequence within LAP are sufficient to eliminate the translation-inhibitory activity of LAP. When one of these mutations (Y23Q) is introduced into full-length La, the mutant protein is severely defective in interacting with the PV IRES element and consequently unable to stimulate IRES-mediated translation. However, the La protein with a mutation of the next tyrosine moiety (Y24Q) could still interact with PV 5'-UTR and stimulate viral IRES-mediated translation significantly. These results underscore the importance of the La N-terminal amino acids in RNA binding and viral RNA translation. The possible role of the LAP sequence in La-RNA binding and stimulation of viral IRES-mediated translation is discussed.
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Affiliation(s)
- Raquel E Izumi
- Department of Microbiology, Immunology and Molecular Genetics, UCLA School of Medicine, University of California-Los Angeles, Los Angeles, California 90095, USA
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133
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Alfano C, Sanfelice D, Babon J, Kelly G, Jacks A, Curry S, Conte MR. Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. Nat Struct Mol Biol 2004; 11:323-9. [PMID: 15004549 DOI: 10.1038/nsmb747] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Accepted: 02/19/2004] [Indexed: 11/08/2022]
Abstract
The La protein is a conserved component of eukaryotic ribonucleoprotein complexes that binds the 3' poly(U)-rich elements of nascent RNA polymerase III (pol III) transcripts to assist folding and maturation. This specific recognition is mediated by the N-terminal domain (NTD) of La, which comprises a La motif and an RNA recognition motif (RRM). We have determined the solution structures of both domains and show that the La motif adopts an alpha/beta fold that comprises a winged-helix motif elaborated by the insertion of three helices. Chemical shift mapping experiments show that these insertions are involved in RNA interactions. They further delineate a distinct surface patch on each domain-containing both basic and aromatic residues-that interacts with RNA and accounts for the cooperative binding of short oligonucleotides exhibited by the La NTD.
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Affiliation(s)
- Caterina Alfano
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, St. Michael's Building, Portsmouth PO1 2DT, UK
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134
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Van Eden ME, Byrd MP, Sherrill KW, Lloyd RE. Demonstrating internal ribosome entry sites in eukaryotic mRNAs using stringent RNA test procedures. RNA (NEW YORK, N.Y.) 2004; 10:720-30. [PMID: 15037781 PMCID: PMC1370562 DOI: 10.1261/rna.5225204] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Accepted: 01/13/2004] [Indexed: 05/18/2023]
Abstract
The dicistronic assay for internal ribosome entry site (IRES) activity is the most widely used method for testing putative sequences that may drive cap-independent translation initiation. This assay typically involves the transfection of cells with dicistronic DNA test constructs. Many of the reports describing eukaryotic IRES elements have been criticized for the use of inadequate methods for the detection of aberrant RNAs that may form in transfected cells using this assay. Here we propose the combined use of a new RNAi-based method together with RT-PCR to effectively identify aberrant RNAs. We illustrate the use of these methods for analysis of RNAs generated in cells transfected with dicistronic test DNAs containing either the hepatitis C virus (HCV) IRES or the X-linked inhibitor of apoptosis (XIAP) cellular IRES. Both analyses indicated aberrantly spliced transcripts occurred in cells transfected with the XIAP dicistronic DNA construct. This contributed to the unusually high levels of apparent IRES activity exhibited by the XIAP 5' UTR in vivo. Cells transfected directly with dicistronic RNA exhibited much lower levels of XIAP IRES activity, resembling the lower levels observed after translation of dicistronic RNA in rabbit reticulocyte lysates. No aberrantly spliced transcripts could be detected following direct RNA transfection of cells. Interestingly, transfection of dicistronic DNA or RNA containing the HCV IRES did not form aberrantly spliced transcripts. These observations stress the importance of using alternative test procedures (e.g., direct RNA transfection) in conjunction with a combination of sensitive RNA analyses for discerning IRES-containing sequences in eukaryotic mRNAs.
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Affiliation(s)
- Marc E Van Eden
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030-3498, USA
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135
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Van Eden ME, Byrd MP, Sherrill KW, Lloyd RE. Translation of cellular inhibitor of apoptosis protein 1 (c-IAP1) mRNA is IRES mediated and regulated during cell stress. RNA (NEW YORK, N.Y.) 2004; 10:469-81. [PMID: 14970392 PMCID: PMC1370942 DOI: 10.1261/rna.5156804] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cellular inhibitor of apoptosis protein 1 (c-IAP1) can regulate apoptosis through its interaction with downstream TNF receptor effectors (TRAF1 and TRAF2), by binding to and inhibiting certain caspases, and by controlling the levels of specific proapoptotic stimuli (e.g., Smac/DIABLO) within the cell. Studies involving the expression of c-IAP1 mRNA and protein in cells and tissues have provided evidence suggesting c-IAP1 expression may be posttranscriptionally controlled. Because the 5'-UTR of c-IAP1 mRNA is unusually long, contains multiple upstream AUG codons, and has the potential to form thermodynamically stable secondary structures, we investigated the possibility it contained an internal ribosome entry site (IRES) that may regulate its expression. In the present study, the c-IAP1 5'-UTR exhibited IRES activity when dicistronic RNA constructs were translated in rabbit reticulocyte lysate (RRL) and in transiently transfected cells. IRES-mediated translation was similar to that exhibited by the hepatitis C virus IRES but varied significantly in RRL and in HeLa, HepG2, and 293T cells, indicating the c-IAP1 IRES was system and cell type specific. IRES-mediated translation was maintained in mono- and dicistronic constructs in which the UTR was inserted downstream from a stable hairpin that prevented cap-dependent ribosome scanning. In cells, the presence or absence of a methylated cap did not significantly affect the translation of polyadenylated, monocistronic RNAs containing the c-IAP1 5'-UTR. IRES-mediated translation was stimulated in transfected cells treated with low doses of pro-apoptotic stimuli (i.e., etoposide and sodium arsenite) that inhibited endogenous cellular translation.
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Affiliation(s)
- Marc E Van Eden
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030-3498, USA
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136
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Choi K, Kim JH, Li X, Paek KY, Ha SH, Ryu SH, Wimmer E, Jang SK. Identification of cellular proteins enhancing activities of internal ribosomal entry sites by competition with oligodeoxynucleotides. Nucleic Acids Res 2004; 32:1308-17. [PMID: 14981151 PMCID: PMC390288 DOI: 10.1093/nar/gkh300] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2003] [Revised: 01/30/2004] [Accepted: 02/03/2004] [Indexed: 02/05/2023] Open
Abstract
The translation of numerous eukaryotic mRNAs is mediated by internal ribosomal entry sites (IRESs). IRES-dependent translation requires both canonical translation initiation factors and IRES-specific trans-acting factors (ITAFs). Here we report a strategy to identify and characterize ITAFs required for IRES-dependent translation. This process involves steps for identifying oligodeoxynucleotides affecting IRES-dependent translation, purifying proteins interacting with the inhibitory DNA, identifying the specific proteins with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry, and confirming the roles of these proteins in IRES-dependent translation by depletion and repletion of proteins from an in vitro translation system. Using this strategy, we show that poly(rC)-binding proteins 1 and 2 enhance translation through polioviral and rhinoviral IRES elements.
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Affiliation(s)
- Kobong Choi
- Department of Life Science, Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang, Kyungbuk 790-784, Korea
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137
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Cencig S, Nanbru C, Le SY, Gueydan C, Huez G, Kruys V. Mapping and characterization of the minimal internal ribosome entry segment in the human c-myc mRNA 5' untranslated region. Oncogene 2004; 23:267-77. [PMID: 14712232 DOI: 10.1038/sj.onc.1207017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human c-myc proto-oncogene is transcribed from four alternative promoters generating transcripts with 5' untranslated regions of various lengths. These transcripts encode two proteins, c-Myc1 and c-Myc2, from two initiation codons, CUG and AUG, respectively. We and others have previously demonstrated that the region of c-myc transcripts between nucleotides (nt) -363 and -94 upstream from the CUG start codon contained an internal ribosome entry site leading to the cap-independent translation of c-myc open reading frames (ORFs). Here, we mapped a 50-nt sequence (-143 -94), which is sufficient to promote internal translation initiation of c-myc ORFs. Interestingly, this 50-nt element can be further dissected into two segments of 14 nt, each capable of activating internal translation initiation. We also demonstrate that this 50-nt element acts as the ribosome landing site from which the preinitiation ribosomal complex scans the mRNA until the CUG or AUG start codons.
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Affiliation(s)
- Sabrina Cencig
- Laboratoire de Chimie Biologique, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, rue des Profs Jeener et Brachet 12, 6041 Gosselies, Belgium
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138
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Kozak M. Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene 2004; 318:1-23. [PMID: 14585494 DOI: 10.1016/s0378-1119(03)00774-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Translation of some mRNAs is postulated to occur via an internal initiation mechanism which is said to be augmented by a variety of RNA-binding proteins. A pervasive problem is that the RNA sequences to which the proteins bind were not rigorously proven to function as internal ribosome entry sites (IRESs). Critical examination of the evidence reveals flaws that leave room for alternative interpretations, such as the possibility that IRES elements might function as cryptic promoters, splice sites, or sequences that modulate cleavage by RNases. The growing emphasis on IRES-binding proteins diverts attention from these fundamental unresolved issues. Many of the putative IRES-binding proteins are heterogeneous nuclear ribonucleoproteins that have recognized roles in RNA processing or stability and no recognized role in translation. Thus the mechanism whereby they promote internal initiation, if indeed they do, is not obvious. Some recent experiments were said to support the idea that IRES-binding proteins cause functionally important changes in folding of the RNA, but the evidence is not convincing when examined closely. The proteins that bind to some (not all) viral IRES elements include a subset of authentic initiation factors. This has not been demonstrated with any candidate IRES of cellular origin, however; and even with viral RNAs, the required chase experiment has not been done to prove that a pre-bound initiation factor actually mediates subsequent entry of ribosomes. In short, the focus on IRES-binding proteins has gotten us no closer to understanding the mechanism of internal initiation. Given the aforementioned uncertainty about whether other mechanisms (splicing, cryptic promoters) might underlie what-appears-to-be internal initiation, a temporary solution might be to redefine IRES to mean "internal regulatory expression sequence." This compromise would allow the sequences to be used for gene expression studies, for which they sometimes work, without asserting more than has been proven about the mechanism.
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Affiliation(s)
- Marilyn Kozak
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.
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139
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Inada M, Guthrie C. Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc Natl Acad Sci U S A 2004; 101:434-9. [PMID: 14704279 PMCID: PMC327165 DOI: 10.1073/pnas.0307425100] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
La is a conserved eukaryotic RNA-binding protein best known for its role in the biogenesis of noncoding RNAs transcribed by RNA polymerase III. To broaden our understanding of the function of the La homologous protein (Lhp1) in Saccharomyces cerevisiae, we have taken a genomics approach. Lhp1 ribonucleoprotein complexes were immunoprecipitated and bound RNAs were examined by hybridization to whole-genome microarrays that include >6,000 ORFs, documented noncoding RNAs, and the intervening intergenic regions. Demonstrating the validity of this approach, associations with previously known Lhp1p-associated RNAs were detected and associations with additional noncoding RNAs, including multiple tRNAs and small nucleolar RNAs, were revealed. Indicating that this approach provides a robust method for discovering RNAs, the data also identify associations between Lhp1p and several intergenic regions, three of which encode the recently annotated putative snoRNAs: RUF1, RUF2, and RUF3. Unexpectedly, we find that Lhp1p is also associated with a subset of coding mRNAs. These mRNAs include many ribosomal protein transcripts as well as the mRNA encoding Hac1p, a transcription factor required during the unfolded protein stress response. In cells lacking LHP1, Hac1p levels are decreased 2- to 3-fold, whereas no changes are detected in the levels of spliced or unspliced HAC1 mRNA or in the stability of Hac1p. Finally, although LHP1 is dispensable for growth under standard conditions, we find that it is required when the unfolded protein response is induced at elevated temperatures. These results suggest that Lhp1p may play a novel role in the translation of one or more cellular mRNAs.
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Affiliation(s)
- Maki Inada
- Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, CA 94143-2200, USA
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140
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Martin MM, Garcia JA, McFarland JD, Duffy AA, Gregson JP, Elton TS. Translation of the human angiotensin II type 1 receptor mRNA is mediated by a highly efficient internal ribosome entry site. Mol Cell Endocrinol 2003; 212:51-61. [PMID: 14654250 DOI: 10.1016/j.mce.2003.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activation of the angiotensin II type 1 receptor (AT1R) is closely involved in the pathogenesis of cardiovascular disease. The human AT1R (hAT1R) mRNA splice variants have long 5'-untranslated regions (5'-UTRs) ranging from 272 to 414 bp that have the potential to form stable secondary structures. In this study, we show that the 5'-UTR of hAT(1)R mRNAs contains an internal ribosome entry site (IRES) located within the first 40 bp of the proximal end of exon 1. Experiments utilizing the hAT1R 5'-UTR as a molecular decoy demonstrate a reduction in IRES activity of approximately 50%. This inhibition is most efficient for the hAT1R IRES suggesting that a defined set of trans-factors are required to initiate translation through this cis-element. Translation initiation from the hAT1R IRES appears to be physiologically relevant since IRES activity was maintained during serum starvation, a cellular stress known to inhibit cap-dependent translation. These results suggest that cap-independent translation initiation by internal ribosome entry may represent an important mechanism for the regulation of hAT1R expression.
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Affiliation(s)
- Mickey M Martin
- Department of Chemistry and Biochemistry, Brigham Young University, C211 BNSN, P.O. Box 25700, Provo, UT 84602-5700, USA
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141
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Intine RV, Tenenbaum SA, Sakulich AL, Keene JD, Maraia RJ. Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs. Mol Cell 2003; 12:1301-7. [PMID: 14636586 DOI: 10.1016/s1097-2765(03)00429-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The La protein facilitates the production of tRNAs in the nucleus and the translation of specific mRNAs in the cytoplasm. We report that human La that is phosphorylated on serine 366 (pLa) is nucleoplasmic and associated with precursor tRNAs and other nascent RNA polymerase III transcripts while nonphosphorylated (np)La is cytoplasmic and associated with a subset of mRNAs that contain 5'-terminal oligopyrimidine (5'TOP) motifs known to control protein synthesis. Thus, La ribonucleoproteins (RNP) exist in distinct states that differ in subcellular localization, serine 366 phosphorylation, and associated RNAs. These results are consistent with a model in which the relative concentrations of the La S366 isoforms in different subcellular compartments in conjunction with the relative concentrations of specific RNA ligands in these compartments determine the differential association of npLa and pLa with their respective classes of associated RNAs.
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Affiliation(s)
- Robert V Intine
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Development, Bethesda, MD 20892, USA
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142
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Kobayashi N, Saeki K, Yuo A. Granulocyte-macrophage colony-stimulating factor and interleukin-3 induce cell cycle progression through the synthesis of c-Myc protein by internal ribosome entry site-mediated translation via phosphatidylinositol 3-kinase pathway in human factor-dependent leukemic cells. Blood 2003; 102:3186-95. [PMID: 12855588 DOI: 10.1182/blood-2003-02-0567] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To investigate the roles of c-myc during hematopoietic proliferation induced by growth factors, we used factor-dependent human leukemic cell lines (MO7e and F36P) in which proliferation, cell cycle progression, and c-Myc expression were strictly regulated by granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-3 (IL-3). In these cell lines, both c-myc mRNA and c-Myc protein stability were not affected by GM-CSF and IL-3, suggesting a regulation of c-Myc protein at the translational level. However, rapamycin, an inhibitor of cap-dependent translation, did not block c-myc induction by GM-CSF and IL-3. Thus, we studied the cap-independent translation, the internal ribosome entry site (IRES), during c-Myc protein synthesis using dicistronic reporter gene plasmids and found that GM-CSF and IL-3 activated c-myc IRES to initiate translation. c-myc IRES activation, c-Myc protein expression, and cell cycle progression were all blocked by a phosphatidylinositol 3-kinase (PI3K) inhibitor, LY294002. In another factor-dependent cell line, UT7, we observed the cell cycle progression and up-regulation of c-Myc protein, c-myc mRNA, and c-myc IRES simultaneously, which were all inhibited by LY294002. Results indicate that hematopoietic growth factors induce cell cycle progression via IRES-mediated translation of c-myc though the PI3K pathway in human factor-dependent leukemic cells.
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Affiliation(s)
- Norihiko Kobayashi
- Department of Hematology, Research Institute, International Medical Center of Japan, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
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143
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Fraser M, Leung B, Jahani-Asl A, Yan X, Thompson WE, Tsang BK. Chemoresistance in human ovarian cancer: the role of apoptotic regulators. Reprod Biol Endocrinol 2003; 1:66. [PMID: 14609433 PMCID: PMC270001 DOI: 10.1186/1477-7827-1-66] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Accepted: 10/07/2003] [Indexed: 01/31/2023] Open
Abstract
Ovarian cancer is among the most lethal of all malignancies in women. While chemotherapy is the preferred treatment modality, chemoresistance severely limits treatment success. Recent evidence suggests that deregulation of key pro- and anti-apoptotic pathways is a key factor in the onset and maintenance of chemoresistance. Furthermore, the discovery of novel interactions between these pathways suggests that chemoresistance may be multi-factorial. Ultimately, the decision of the cancer cell to live or die in response to a chemotherapeutic agent is a consequence of the overall apoptotic capacity of that cell. In this review, we discuss the biochemical pathways believed to promote cell survival and how they modulate chemosensitivity. We then conclude with some new research directions by which the fundamental mechanisms of chemoresistance can be elucidated.
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Affiliation(s)
- Michael Fraser
- Department of Obstetrics & Gynecology and Cellular & Molecular Medicine, University of Ottawa, Ottawa Health Research Institute, Ottawa, Canada K1Y 4E9, Canada
| | - Brendan Leung
- Department of Obstetrics & Gynecology and Cellular & Molecular Medicine, University of Ottawa, Ottawa Health Research Institute, Ottawa, Canada K1Y 4E9, Canada
| | - Arezu Jahani-Asl
- Department of Obstetrics & Gynecology and Cellular & Molecular Medicine, University of Ottawa, Ottawa Health Research Institute, Ottawa, Canada K1Y 4E9, Canada
| | - Xiaojuan Yan
- Department of Obstetrics & Gynecology and Cellular & Molecular Medicine, University of Ottawa, Ottawa Health Research Institute, Ottawa, Canada K1Y 4E9, Canada
| | - Winston E Thompson
- Department of Obstetrics & Gynecology and Cooperative Reproductive Science Research Center, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Benjamin K Tsang
- Department of Obstetrics & Gynecology and Cellular & Molecular Medicine, University of Ottawa, Ottawa Health Research Institute, Ottawa, Canada K1Y 4E9, Canada
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144
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Cardinali B, Carissimi C, Gravina P, Pierandrei-Amaldi P. La protein is associated with terminal oligopyrimidine mRNAs in actively translating polysomes. J Biol Chem 2003; 278:35145-51. [PMID: 12840030 DOI: 10.1074/jbc.m300722200] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
La is an abundant, mostly nuclear, RNA-binding protein that interacts with regions rich in pyrimidines. In the nucleus it has a role in the metabolism of several small RNAs. A number of studies, however, indicate that La protein is also implicated in cytoplasmic functions such as translation. The association of La in vivo with endogenous mRNAs engaged with polysomes would support this role, but this point has never been addressed yet. Terminal oligopyrimidine (TOP) mRNAs, which code for ribosomal proteins and other components of the translational apparatus, bear a TOP stretch at the 5' end, which is necessary for the regulation of their translation. La protein can bind the TOP sequence in vitro and activates TOP mRNA translation in vivo. Here we have quantified La protein in the cytoplasm of Xenopus oocytes and embryo cells and have shown in embryo cells that it is associated with actively translating polysomes. Disruption of polysomes by EDTA treatment displaces La in messenger ribonucleoprotein complexes sedimenting at 40-60 S. The results of polysome treatment with either low concentrations of micrococcal nuclease or with high concentrations of salt indicate, respectively, that La association with polysomes is mediated by mRNA and that it is not an integral component of ribosomes. Moreover, the analysis of messenger ribonucleoprotein complexes dissociated from translating polysomes shows that La protein associates with TOP mRNAs in vivo when they are translated, in line with a positive role of La in the translation of this class of mRNAs previously observed in cultured cells.
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Affiliation(s)
- Beatrice Cardinali
- Istituto di Biologia Cellulare CNR, Via Ramarini 32, 00016 Monterotondo Scalo, Italy.
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145
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Evans JR, Mitchell SA, Spriggs KA, Ostrowski J, Bomsztyk K, Ostarek D, Willis AE. Members of the poly (rC) binding protein family stimulate the activity of the c-myc internal ribosome entry segment in vitro and in vivo. Oncogene 2003; 22:8012-20. [PMID: 12970749 DOI: 10.1038/sj.onc.1206645] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 5' untranslated region of the proto-oncogene c-myc contains an internal ribosome entry segment and c-Myc translation can be initiated by cap-independent as well as cap-dependent mechanisms. In contrast to the process of cap-dependent initiation, the trans-acting factor requirements for cellular internal ribosome entry are poorly understood. Here, we show that members of the poly (rC) binding protein family, poly (rC) binding protein 1 (PCBP1), poly (rC) binding protein 2 (PCBP2) and hnRNPK were able to activate the IRES in vitro up to threefold when added in combination with upstream of N-ras and unr-interacting protein. The interactions of PCBP1, PCBP2 and hnRNPK with c-myc-IRES-RNA were shown to be specific by ultraviolet crosslinking analysis and electrophoretic mobility shift assays, while immunoprecipitation of the three proteins using specific antibodies followed by reverse transcriptase-polymerase chain reaction showed that they were able to bind c-myc mRNA. c-myc-IRES-mediated translation from the reporter vector was stimulated by cotransfection of plasmids encoding PCBP1, PCBP2 and hnRNPK. Interestingly, the mutated version of the c-myc IRES that is prevalent in patients with multiple myeloma bound hnRNPK more efficiently in vitro and was stimulated by hnRNPK to a greater extent in vivo.
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Affiliation(s)
- Joanne R Evans
- Department of Biochemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
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146
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Reddy RK, Mao C, Baumeister P, Austin RC, Kaufman RJ, Lee AS. Endoplasmic reticulum chaperone protein GRP78 protects cells from apoptosis induced by topoisomerase inhibitors: role of ATP binding site in suppression of caspase-7 activation. J Biol Chem 2003; 278:20915-24. [PMID: 12665508 DOI: 10.1074/jbc.m212328200] [Citation(s) in RCA: 565] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A large number of correlative studies have established that the activation of the unfolded protein response (UPR) alters the cell's sensitivity to chemotherapeutic agents. Although the induction of the glucose-regulated proteins (GRPs) is commonly used as an indicator for the UPR, the direct role of the GRPs in conferring resistance to DNA damaging agents has not been proven. We report here that without the use of endoplasmic reticulum (ER) stress inducers, specific overexpression of GRP78 results in reduced apoptosis and higher colony survival when challenged with topoisomerase II inhibitors, etoposide and doxorubicin, and topoisomerase I inhibitor, camptothecin. While investigating the mechanism for the GRP78 protective effect against etoposide-induced cell death, we discovered that in contrast to the UPR, GRP78 overexpression does not result in G1 arrest or depletion of topoisomerase II. Caspase-7, an executor caspase that is associated with the ER, is activated by etoposide. We show here that specific expression of GRP78 blocks caspase-7 activation by etoposide both in vivo and in vitro, and this effect can be reversed by addition of dATP in a cell-free system. Recently, it was reported that ectopically expressed GRP78 and caspases-7 and -12 form a complex, thus coupling ER stress to the cell death program. However, the mechanism of how GRP78, a presumably ER lumen protein, can regulate cytosolic effectors of apoptosis is not known. Here we provide evidence that a subpopulation of GRP78 can exist as an ER transmembrane protein, as well as co-localize with caspase-7, as confirmed by fluorescence microscopy. Co-immunoprecipitation studies further reveal endogenous GRP78 constitutively associates with procaspase-7 but not with procaspase-3. Lastly, a GRP78 mutant deleted of its ATP binding domain fails to bind procaspase-7 and loses its protective effect against etoposide-induced apoptosis.
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Affiliation(s)
- Ramachandra K Reddy
- Department of Biochemistry and Molecular Biology and the USC/Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90089-9176, USA
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147
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Pudi R, Abhiman S, Srinivasan N, Das S. Hepatitis C virus internal ribosome entry site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen. J Biol Chem 2003; 278:12231-40. [PMID: 12540850 DOI: 10.1074/jbc.m210287200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The human La autoantigen has been shown to interact with the internal ribosome entry site (IRES) of hepatitis C virus (HCV) in vitro. Using a yeast three-hybrid system, we demonstrated that, in addition to full-length La protein, both N- and C-terminal halves were able to interact with HCV IRES in vivo. The exogenous addition of purified full-length and truncated La proteins in rabbit reticulocyte lysate showed dose-dependent stimulation of HCV IRES-mediated translation. However, an additive effect was achieved adding the terminal halves together in the reaction, suggesting that both might play critical roles in achieving full stimulatory activity of the full-length La protein. Using computational analysis, three-dimensional structures of the RNA recognition motifs (RRM) of the La protein were independently modeled. Of the three putative RRMs, RRM2 was predicted to have a good binding pocket for the interaction with the HCV IRES around the GCAC motif near the initiator AUG and RRM3 binds perhaps in a different location. This observation was further investigated by the filter-binding and toe-printing assays. The results presented here strongly suggest that both the N- and C-terminal halves can interact independently with the HCV IRES and are involved in stimulating internal initiation of translation.
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Affiliation(s)
- Renuka Pudi
- Department of Microbiology and Cell Biology and the Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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148
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Abstract
The crucial role of cell death in many diseases is obvious and has spurred intense research to understand the regulation of apoptotic pathways. Caspase activation is central to many of the apoptotic pathways. In recent years, the study of the regulation of caspase activation and activity in various cell lines and in diseases has revealed highly complex mechanisms regulating cell survival or cell death. In this review, the major natural cellular anticaspase factors are described with particular attention to the inhibitors that prevent active caspases from committing the cell to irreversible destruction. The major group of caspase inhibitors known is the inhibitor of apoptosis proteins (IAP) and this review describes the characteristics of IAP, regulation of IAP expression, and mechanisms of action of IAP. However, other proteins including Bcl-2 family members, heat shock proteins, caspase-like decoy, calpains and proteases, and lipid moieties in the form of phosphoinositides also can function as caspase inhibitors. The current knowledge of the inhibition of these non-IAP factors is described herein.
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Affiliation(s)
- Andréa C LeBlanc
- Department of Neurology, The Bloomfield Center for Research in Aging, H3T 1E2, Montreal, Quebec, Canada.
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149
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Mitchell SA, Spriggs KA, Coldwell MJ, Jackson RJ, Willis AE. The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions with PTB and unr. Mol Cell 2003; 11:757-71. [PMID: 12667457 DOI: 10.1016/s1097-2765(03)00093-5] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have shown previously that polypyrimidine tract binding protein 1 (PTB) binds and activates the Apaf-1 internal ribosome entry segment (IRES) when the protein upstream of N-ras (unr) is prebound. Here we show that the Apaf-1 IRES is highly active in neuronal-derived cell lines due to the presence of the neuronal-enhanced version of PTB, nPTB. The unr and PTB/nPTB binding sites have been located on the Apaf-1 IRES RNA, and a structural model for the IRES bound to these proteins has been derived. The ribosome landing site has been located to a single-stranded region, and this is generated by the binding of the nPTB and unr to the RNA. These data suggest that unr and nPTB act as RNA chaperones by changing the structure of the IRES into one that permits translation initiation.
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Affiliation(s)
- Sally A Mitchell
- Department of Biochemistry, University of Leicester, University Road, LE1 7RH, Leicester, United Kingdom
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150
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Trotta R, Vignudelli T, Candini O, Intine RV, Pecorari L, Guerzoni C, Santilli G, Byrom MW, Goldoni S, Ford LP, Caligiuri MA, Maraia RJ, Perrotti D, Calabretta B. BCR/ABL activates mdm2 mRNA translation via the La antigen. Cancer Cell 2003; 3:145-60. [PMID: 12620409 DOI: 10.1016/s1535-6108(03)00020-5] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In a BCR/ABL-expressing myeloid precursor cell line, p53 levels were markedly downmodulated. Expression of MDM2, the negative regulator of p53, was upregulated in a tyrosine kinase-dependent manner in growth factor-independent BCR/ABL-expressing cells, and in accelerated phase and blast crisis CML samples. Increased MDM2 expression was associated with enhanced mdm2 mRNA translation, which required the interaction of the La antigen with mdm2 5' UTR. Expression of MDM2 correlated with that of La and was suppressed by La siRNAs and by a dominant negative La mutant, which also enhanced the susceptibility to drug-induced apoptosis of BCR/ABL-transformed cells. By contrast, La overexpression led to increased MDM2 levels and enhanced resistance to apoptosis. Thus, La-dependent activation of mdm2 translation might represent an important molecular mechanism involved in BCR/ABL leukemogenesis.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Autoantigens
- Blotting, Northern
- Blotting, Western
- Drug Resistance, Neoplasm
- Fusion Proteins, bcr-abl/physiology
- GRB2 Adaptor Protein
- Growth Substances/metabolism
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Mice
- Nuclear Proteins
- Protein Biosynthesis
- Protein-Tyrosine Kinases/metabolism
- Proteins/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins c-mdm2
- RNA, Messenger/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacology
- RNA-Binding Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Tumor Suppressor Protein p53/metabolism
- Up-Regulation
- SS-B Antigen
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Affiliation(s)
- Rossana Trotta
- Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson Medical College, Philadelphia, PA 19107, USA
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