1
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Abstract
Eukaryotic mRNAs possess 5' caps that are determinants for their function. A structural characteristic of 5' caps is methylation, with this feature already present in early eukaryotes such as Trypanosoma. While the common cap-0 (m7 GpppN) shows a rather simple methylation pattern, the Trypanosoma cap-4 displays seven distinguished additional methylations within the first four nucleotides. The study of essential biological functions mediated by these unique structural features of the cap-4 and thereby of the metabolism of an important class of human pathogenic parasites is hindered by the lack of reliable preparation methods. Herein we describe the synthesis of custom-made nucleoside phosphoramidite building blocks for m62 Am and m3 Um, their incorporation into short RNAs, the efficient construction of the 5'-to-5' triphosphate bridge to guanosine by using a solid-phase approach, the selective enzymatic methylation at position N7 of the inverted guanosine, and enzymatic ligation to generate trypanosomatid mRNAs of up to 40 nucleotides in length. This study introduces a reliable synthetic strategy to the much-needed cap-4 RNA probes for integrated structural biology studies, using a combination of chemical and enzymatic steps.
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Affiliation(s)
- Josef Leiter
- University of InnsbruckInstitute of Organic Chemistry and Center for Molecular BiosciencesInnrain 80-826020InnsbruckAustria
| | - Dennis Reichert
- University of MünsterDepartment of ChemistryInstitute of BiochemistryWilhelm-Klemm-Strasse 248149MünsterGermany
| | - Andrea Rentmeister
- University of MünsterDepartment of ChemistryInstitute of BiochemistryWilhelm-Klemm-Strasse 248149MünsterGermany
| | - Ronald Micura
- University of InnsbruckInstitute of Organic Chemistry and Center for Molecular BiosciencesInnrain 80-826020InnsbruckAustria
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2
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Chen S, Gao G. MicroRNAs recruit eIF4E2 to repress translation of target mRNAs. Protein Cell 2017; 8:750-761. [PMID: 28755203 PMCID: PMC5636748 DOI: 10.1007/s13238-017-0444-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) recruit the RNA-induced silencing complex (RISC) to repress the translation of target mRNAs. While the 5′ 7-methylguanosine cap of target mRNAs has been well known to be important for miRNA repression, the underlying mechanism is not clear. Here we show that TNRC6A interacts with eIF4E2, a homologue of eIF4E that can bind to the cap but cannot interact with eIF4G to initiate translation, to inhibit the translation of target mRNAs. Downregulation of eIF4E2 relieved miRNA repression of reporter expression. Moreover, eIF4E2 downregulation increased the protein levels of endogenous IMP1, PTEN and PDCD4, whose expression are repressed by endogenous miRNAs. We further provide evidence showing that miRNA enhances eIF4E2 association with the target mRNA. We propose that miRNAs recruit eIF4E2 to compete with eIF4E to repress mRNA translation.
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Affiliation(s)
- Shaohong Chen
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangxia Gao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100101, China.
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3
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Takizawa N, Fujiwara T, Yamasaki M, Saito A, Fukao A, Nomoto A, Mizumoto K. The essential role for the RNA triphosphatase Cet1p in nuclear import of the mRNA capping enzyme Cet1p-Ceg1p complex of Saccharomyces cerevisiae. PLoS One 2013; 8:e78000. [PMID: 24205062 PMCID: PMC3813497 DOI: 10.1371/journal.pone.0078000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/08/2013] [Indexed: 11/18/2022] Open
Abstract
mRNA capping is the first cotranscriptional modification of mRNA in the nucleus. In Saccharomyces cerevisiae, the first two steps of mRNA capping are catalyzed by the RNA triphosphatase Cet1p and the RNA guanylyltransferase Ceg1p. Cet1p and Ceg1p interact to form a mRNA capping enzyme complex and the guanylyltransferase activity of Ceg1p is stimulated by binding with Cet1p. The Cet1p-Ceg1p complex needs to be transported into the nucleus, where mRNA capping occurs. However, the molecular mechanism of nuclear transport of the Cet1p-Ceg1p complex is not known. Here, we show that Cet1p is responsible and that the Cet1p-Ceg1p interaction is essential for the nuclear localization of the Cet1p-Ceg1p complex. The results indicate that the Cet1p-Ceg1p interaction is important not only for the activation of Ceg1p, but also for nuclear import of the complex.
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Affiliation(s)
- Naoki Takizawa
- Laboratory of Basic Biology, Institute of Microbial Chemistry, Tokyo, Japan
- * E-mail:
| | - Toshinobu Fujiwara
- Laboratory of Basic Biology, Institute of Microbial Chemistry, Tokyo, Japan
| | - Manabu Yamasaki
- Laboratory of Basic Biology, Institute of Microbial Chemistry, Tokyo, Japan
| | - Ayako Saito
- Department of Molecular Health Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Akira Fukao
- Laboratory of Basic Biology, Institute of Microbial Chemistry, Tokyo, Japan
| | - Akio Nomoto
- Laboratory of Basic Biology, Institute of Microbial Chemistry, Tokyo, Japan
| | - Kiyohisa Mizumoto
- Department of Biochemistry, School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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4
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Kassem HS, Girolami F, Sanoudou D. Molecular genetics made simple. Glob Cardiol Sci Pract 2012; 2012:6. [PMID: 25610837 PMCID: PMC4239820 DOI: 10.5339/gcsp.2012.6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 06/01/2012] [Indexed: 01/24/2023] Open
Abstract
Genetics have undoubtedly become an integral part of biomedical science and clinical practice, with important implications in deciphering disease pathogenesis and progression, identifying diagnostic and prognostic markers, as well as designing better targeted treatments. The exponential growth of our understanding of different genetic concepts is paralleled by a growing list of genetic terminology that can easily intimidate the unfamiliar reader. Rendering genetics incomprehensible to the clinician however, defeats the very essence of genetic research: its utilization for combating disease and improving quality of life. Herein we attempt to correct this notion by presenting the basic genetic concepts along with their usefulness in the cardiology clinic. Bringing genetics closer to the clinician will enable its harmonious incorporation into clinical care, thus not only restoring our perception of its simple and elegant nature, but importantly ensuring the maximal benefit for our patients.
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Affiliation(s)
- Heba Sh Kassem
- Pathology Department and Clinical Genomics Center, Alexandria Faculty of Medicine, Egypt ; Magdi Yacoub Foundation Serving Egypt, Egypt
| | | | - Despina Sanoudou
- Department of Pharmacology, Medical School, University of Athens, Greece
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5
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Kiraga-Motoszko K, Niedzwiecka A, Modrak-Wojcik A, Stepinski J, Darzynkiewicz E, Stolarski R. Thermodynamics of molecular recognition of mRNA 5' cap by yeast eukaryotic initiation factor 4E. J Phys Chem B 2011; 115:8746-54. [PMID: 21650456 DOI: 10.1021/jp2012039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanisms underlying the recognition of the mRNA 5' terminal structure called "cap" by the eukaryotic initiation factor 4E (eIF4E) are crucial for cap-dependent translation. To gain a deeper insight into how the yeast eIF4E interacts with the cap structure, isothermal titration calorimetry and the van't Hoff analysis based on intrinsic protein fluorescence quenching upon titration with a series of chemical cap analogs were performed, providing a consistent thermodynamic description of the binding process in solution. Equilibrium association constants together with thermodynamic parameters revealed similarities and differences between yeast and mammalian eIF4Es. The yeast eIF4E complex formation was enthalpy-driven and entropy-opposed for each cap analog at 293 K. A nontrivial isothermal enthalpy–entropy compensation was found, described by a compensation temperature, T(c) = 411 ± 18 K. For a low affinity analog, 7-methylguanosine monophosphate, a heat capacity change was detected, ΔC(p)° = +5.2 ± 1.3 kJ·mol(-1)·K(-1). The charge-related interactions involving the 5′-5′ triphosphate bridge of the cap and basic amino acid side chains at the yeast eIF4E cap-binding site were significantly weaker (by ΔΔH°(vH) of about +10 kJ·mol(-1)) than those for the mammalian homologues, suggesting their optimization during the evolution.
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Affiliation(s)
- Katarzyna Kiraga-Motoszko
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
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6
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A metazoan/plant-like capping enzyme and cap modified nucleotides in the unicellular eukaryote Trichomonas vaginalis. PLoS Pathog 2010; 6:e1000999. [PMID: 20664792 PMCID: PMC2904801 DOI: 10.1371/journal.ppat.1000999] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 06/11/2010] [Indexed: 01/12/2023] Open
Abstract
The cap structure of eukaryotic messenger RNAs is initially elaborated through three enzymatic reactions: hydrolysis of the 5′-triphosphate, transfer of guanosine through a 5′-5′ triphosphate linkage and N7-methylation of the guanine cap. Three distinctive enzymes catalyze each reaction in various microbial eukaryotes, whereas the first two enzymes are fused into a single polypeptide in metazoans and plants. In addition to the guanosine cap, adjacent nucleotides are 2′-O-ribose methylated in metazoa and plants, but not in yeast. Analyses of various cap structures have suggested a linear phylogenetic trend of complexity. These findings have led to a model in which plants and metazoa evolved a two-component capping apparatus and modification of adjacent nucleotides while many microbial eukaryotes maintained the three-component system and did not develop modification of adjacent nucleotides. Here, we have characterized a bifunctional capping enzyme in the divergent microbial eukaryote Trichomonas vaginalis using biochemical and phylogenetic analyses. This unicellular parasite was found to harbor a metazoan/plant-like capping apparatus that is represented by a two-domain polypeptide containing a C-terminus guanylyltransferase and a cysteinyl phosphatase triphosphatase, distinct from its counterpart in other microbial eukaryotes. In addition, T. vaginalis mRNAs contain a cap 1 structure represented by m7GpppAmpUp or m7GpppCmpUp; a feature typical of metazoan and plant mRNAs but absent in yeast mRNAs. Phylogenetic and biochemical analyses of the origin of the T. vaginalis capping enzyme suggests a complex evolutionary model where differential gene loss and/or acquisition occurred in the development of the RNA capping apparatus and cap modified nucleotides during eukaryote diversification. The protozoan parasite Trichomonas vaginalis is the cause of the most common non-viral sexually transmitted disease worldwide. Evolutionary analyses place Trichomonas in a super group called the Excavata, which includes the kinetoplastids and is highly divergent from fungi, metazoa and plants. Despite the vast evolutionary distances that separate these different eukaryotic lineages, a simplified view of eukaryotic evolution based on the complexity of nucleotide modifications at the 5′ end of mRNAs and the distribution of different types of enzymatic apparatus that confer these modifications has been proposed. Our analyses of the T. vaginalis capping enzyme challenges this view and provides the first example of a two-component capping apparatus typically found in metazoa and plants in a protozoan. The 5′-end nucleotide structure of T. vaginalis mRNAs is also shown to contain additional modified nucleotides, similar to that observed for metazoan and plant mRNAs and unlike that found in most eukaryotic microbes and fungi. Evolutionary analyses of the T. vaginalis capping enzyme indicates that this multicellular type capping apparatus may have come into existence earlier than previously thought.
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7
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Ghosh A, Lima CD. Enzymology of RNA cap synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:152-72. [PMID: 21956912 DOI: 10.1002/wrna.19] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The 5' guanine-N7 methyl cap is unique to cellular and viral messenger RNA (mRNA) and is the first co-transcriptional modification of mRNA. The mRNA cap plays a pivotal role in mRNA biogenesis and stability, and is essential for efficient splicing, mRNA export, and translation. Capping occurs by a series of three enzymatic reactions that results in formation of N7-methyl guanosine linked through a 5'-5' inverted triphosphate bridge to the first nucleotide of a nascent transcript. Capping of cellular mRNA occurs co-transcriptionally and in vivo requires that the capping apparatus be physically associated with the RNA polymerase II elongation complex. Certain capped mRNAs undergo further methylation to generate distinct cap structures. Although mRNA capping is conserved among viruses and eukaryotes, some viruses have adopted strategies for capping mRNA that are distinct from the cellular mRNA capping pathway.
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Affiliation(s)
- Agnidipta Ghosh
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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8
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Bush MS, Hutchins AP, Jones AME, Naldrett MJ, Jarmolowski A, Lloyd CW, Doonan JH. Selective recruitment of proteins to 5' cap complexes during the growth cycle in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:400-12. [PMID: 19453450 DOI: 10.1111/j.1365-313x.2009.03882.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Translation of most mRNAs is performed in a cap-dependent manner, requiring a protein complex, the cap complex, to regulate the accessibility of the message to the 40S ribosome. The cap complex initiates protein translation by binding to the 5' cap of an mRNA and recruiting ribosomes to begin translation. Compared to animals and yeast, there are significant plant-specific differences in the regulation of cap-dependent mRNA translation, but these are poorly understood. Here, we purified proteins that bind to the 5' cap during the Arabidopsis growth cycle. The protein profile of the cap-binding complexes varies during the various stages of the growth cycle in suspension culture cells. Using Western blotting, the cap complexes of quiescent cells were found to be composed of only three major proteins: eIF4isoE, which is primarily a cytoplasmic protein, and eIF4E and CBP80, which accumulate in the nucleus. However, when cells proliferate, at least 10 major proteins bind directly or indirectly to the 5' cap. Proteomic, Western blotting and immunoprecipitation data establish that the spectrum of RNA helicases in the cap complexes also changes during the growth cycle. Cap complexes from proliferating cultures mainly contain eIF4A, which associates with at least four cap complexes, but eIF4A is replaced by additional helicases in quiescent cells. These findings suggest that the dynamic and selective recruitment of various proteins to mRNA 5' cap complexes could play an important role in the regulation of gene expression.
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Affiliation(s)
- Maxwell S Bush
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
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9
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Quality control of mRNP in the nucleus. Chromosoma 2008; 117:419-29. [PMID: 18563427 DOI: 10.1007/s00412-008-0166-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/03/2008] [Accepted: 05/05/2008] [Indexed: 12/30/2022]
Abstract
Formation of functional mRNA-protein particles requires a plethora of nuclear cotranscriptional and posttranscriptional RNA processing and packaging steps. Faithful execution of these events is closely monitored by surveillance systems that prevent nuclear export of, and/or rapidly degrade, faulty transcripts. Parts of this quality control also serve to eliminate a large number of noncoding RNAs produced by RNA polymerase II. Here, we discuss which aberrant features trigger messenger ribonucleoprotein quality control, how the process is executed, and how it is connected to the transcription machinery and the nuclear pore complex.
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10
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Isaksson A, Berggren M, Ekeland-Sjöberg K, Samuelsson T, Ricksten A. Cell specific internal translation efficiency of Epstein-Barr virus present in solid organ transplant patients. J Med Virol 2007; 79:573-81. [PMID: 17385682 DOI: 10.1002/jmv.20854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The U leader exon in the 5' untranslated region of the Epstein-Barr virus nuclear antigen 1 (EBNA1) gene contains an internal ribosome entry site, the EBNA internal ribosome entry segment (IRES), which promotes cap-independent translation and increases the expression level of the EBNA1 protein. It was previously reported that immunosuppressed organ transplanted patients showed an alternatively spliced EBNA1 transcript, excluding the EBNA IRES element. To further investigate the function of the EBNA IRES, sequence analysis of the EBNA IRES mRNA was performed in samples from seven organ transplant patients. Two nucleotide changes, G --> A at position 67531 and C --> U at position 67585 were found in the EBNA IRES mRNA, relative to the corresponding genomic Epstein-Barr virus (EBV) sequence in all patients. Moreover, the patient derived EBNA IRES mRNA was shown to differ from the IRES mRNA derived from the cell line B95.8 at position 67531 and from the cell lines Rael and P3HR1 at positions 67531 and 67585. cDNA from the various EBNA IRES sequences were cloned into bicistronic vectors, respectively, and used in transient transfection experiments in six human cell lines. The patient specific sequence significantly decreased the IRES activity in T-cells, while the base changes had no significant impact on the activity in B- or in epithelial cells. The genetic mechanisms behind EBV-associated diseases are complex, involving gene regulation by alternative promoters, alternative splicing, and translational control. The nucleotide changes in the patient specific EBNA IRES transcript and its influence on the translational activity, might illustrate new strategies utilised by the EBV to adapt to the immune control in patients with EBV associated diseases.
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Affiliation(s)
- Asa Isaksson
- Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Göteborg University, Gothenburg, Sweden
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11
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Abstract
Processing of eukaryotic pre-mRNAs is an important step for the translation of proteins. These processing events include the addition of a cap structure at the 5' terminus of the pre-mRNA, the splicing out of introns and the acquisition of a polyadenosine tail at the 3' terminus of the pre-mRNA. It has now become apparent that the RNA processing events can significantly influence each other. RNA polymerase II appears as a key player in these processes, cooperating with numerous processing factors that are involved in capping, splicing, and polyadenylation. More specifically, the carboxyterminal domain of the large subunit of the enzyme plays a critical role in coordination of the processing events. The number of interactions between the various RNA processing events identified so far reflects the complexity of these reactions. As more studies focus on these interactions, additional links and cellular partners will undoubtedly be discovered.
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Affiliation(s)
- Amélie Parent
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4 Canada
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12
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Tan YM, Loke KY. Isolated haploinsufficiency of exon 1 of the SHOX gene in a patient with idiopathic short stature. J Clin Pathol 2006; 59:773-4. [PMID: 16803952 PMCID: PMC1860432 DOI: 10.1136/jcp.2005.028894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
This paper reports the case of a 16-year-old woman with idiopathic short stature (ISS) who was detected to be haploinsufficient in only exon 1 of the short stature homeobox-containing (SHOX) gene by RQ-PCR and had two copies of the other six exons intact. The translation of the SHOX protein and of the SHOX promoter may be potentially affected if the deletion of exon 1 is extended further upstream. Further studies may help in determining the significance of partial exonic deletions of the SHOX gene in relation to ISS.
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Affiliation(s)
- Y-M Tan
- Department of Paediatrics, Faculty of Medicine, National University of Singapore.
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13
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Schmidt A, Lindner A, Nieger M, Ruiz-Delgado MDC, Ramirez FJ. Syntheses, pi-stacking interactions and base-pairings of uracil pyridinium salts and uracilyl betaines with nucleobases. Org Biomol Chem 2006; 4:3056-66. [PMID: 16886072 DOI: 10.1039/b606249k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reaction of 6-chlorouracil with 4-(dimethylamino)pyridine, 4-methylpyridine, and pyridin-4-yl-morpholine yielded pyridinium-substituted uracils as chlorides which were converted into pyridinium uracilates by deprotonation. These heterocyclic mesomeric betaines are cross-conjugated and thus possess separate cationic (pyridinium) and anionic (uracilate) moieties. Calculations and X-ray single crystal analyses were performed in order to characterize these systems and to compare the salts with the betaines. (1)H NMR experiments in D(2)O proved pi-interactions between the uracilyl betaines and adenine, adenosine, as well as adeninium. No pi-stacking interactions were detected between the betaines and guanosine. The acidic N8-H group of the uracil pyridinium salts caused acid-base reactions which were observed in parallel to pi-stacking interactions. Self-complementarity of the modified uracils was detected by (1)H NMR experiments in DMSO-d(6) and electrospray ionisation mass spectrometry (ESIMS). Ab initio calculations predicted base-pairings of the modified uracils with adeninium, cytosine, and guanine. Several geometries of hydrogen-bonded associates were calculated. Hoogsteen pairings between the uracil-4-(dimethylamino)pyridinium salt and adeninium, as well as associates between the corresponding betaine plus cytosine, and the betaine plus guanine were calculated, and the most stable conformations were determined. In the ESI mass spectra, prominent peaks of associates between the modified uracils and adeninium, cytosine, cytidine, guanosine and d(CpGp) were detected.
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Affiliation(s)
- Andreas Schmidt
- Clausthal University of Technology, Institute of Organic Chemistry, Leibnizstrasse 6, D-38678, Clausthal-Zellerfeld, Germany.
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14
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Oulhen N, Cormier P. [eIF4E and developmental decisions: when translation drives the development]. Med Sci (Paris) 2006; 22:507-13. [PMID: 16687119 DOI: 10.1051/medsci/2006225507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Regulation of mRNA translation is an important regulatory step in gene expression. During embryonic development, mRNA translation is tightly regulated to produce the protein at the right place, at the right time. The eukaryotic initiation factor 4E (eIF4E) is a major target for the regulation of cap-dependent translation, that plays a key role during embryogenesis including gametogenesis, fertilization and establishment of embryonic axes. In this review, we describe recent advances illustrating the importance of the translational regulator eIF4E and its partners in developmental decisions. double dagger.
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Affiliation(s)
- Nathalie Oulhen
- Station Biologique de Roscoff, Cycle Cellulaire et Développement, Unité Mer et Santé (UMR 7150), Université Pierre-et-Marie Curie (EI 37), Centre National de la Recherche Scientifique, Institut National des Sciences de l'Univers, Roscoff, France
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15
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Lewdorowicz M, Yoffe Y, Zuberek J, Jemielity J, Stepinski J, Kierzek R, Stolarski R, Shapira M, Darzynkiewicz E. Chemical synthesis and binding activity of the trypanosomatid cap-4 structure. RNA (NEW YORK, N.Y.) 2004; 10:1469-78. [PMID: 15273325 PMCID: PMC1370633 DOI: 10.1261/rna.7510504] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Leishmania and other trypanosomatids are early eukaryotes that possess unusual molecular features, including polycistronic transcription and trans-splicing of pre-mRNAs. The spliced leader RNA (SL RNA) is joined to the 5' end of all mRNAs, thus donating a 5' cap that is characterized by complex modifications. In addition to the conserved m7GTP, linked via a 5'-5'-triphosphate bound to the first nucleoside of the mRNA, the trypanosomatid 5' cap includes 2'-O methylations on the first four ribose moieties and unique base methylations on the first adenine and the fourth uracil, resulting in the cap-4 structure, m7Gpppm3(6,6,2')Apm2'Apm2' Cpm2(3,2')U, as reported elsewhere previously. A library of analogs that mimic the cap structure to different degrees has been synthesized. Their differential affinities to the cap binding proteins make them attractive compounds for studying the molecular basis of cap recognition, and in turn, they may have potential therapeutic significance. The interactions between cap analogs and eIF4E, a cap-binding protein that plays a key role in initiation of translation, can be monitored by measuring intrinsic fluorescence quenching of the tryptophan residues. In the present communication we describe the multistep synthesis of the trypanosomatid cap-4 structure. The 5' terminal mRNA tetranucleotide fragment (pm3(6,6,2')Apm2'Apm2'Cpm2(3,2')U) was synthesized by the phosphoramidite solid phase method. After deprotection and purification, the 5'-phosphorylated tetranucleotide was chemically coupled with m7GDP to yield the cap-4 structure. Biological activity of this newly synthesized compound was confirmed in binding studies with eIF4E from Leishmania that we recently cloned (LeishIF4E-1), using the fluorescence time-synchronized titration method.
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Affiliation(s)
- Magdalena Lewdorowicz
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, 93 Zwirki and Wigury St., 02-089, Poland
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16
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Abstract
A variety of posttranscriptional mechanisms affects the processing, subcellular localization, and translation of messenger RNAs (mRNAs). Translational control appears to occur primarily at the initiation rather than the elongation stage. It has been suggested that translation is mediated largely by means of a cap-binding/scanning mechanism. On the basis of recent findings, we propose here that differential binding of particular mRNAs to eukaryotic 40S ribosomal subunits before translation may also selectively affect rates of polypeptide chain production. In this view, ribosomal subunits themselves are considered to be regulatory elements or filters that mediate interactions between particular mRNAs and components of the translation machinery. Differences in these interactions affect how efficiently individual mRNAs compete for ribosomal subunits. These competitive interactions would depend in part on the complementarity between sequences in mRNA and rRNA, as well as on structural differences among ribosomes in different cell types. By these means, translation may either be enhanced through increased recruitment of ribosomes or inhibited through strong interactions that sequester mRNAs. We propose that ribosomal filters may be important in cell differentiation and describe experimental tests for the filter hypothesis.
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Affiliation(s)
- Vincent P Mauro
- Department of Neurobiology, The Scripps Research Institute and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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17
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Miyoshi H, Dwyer DS, Keiper BD, Jankowska-Anyszka M, Darzynkiewicz E, Rhoads RE. Discrimination between mono- and trimethylated cap structures by two isoforms of Caenorhabditis elegans eIF4E. EMBO J 2002; 21:4680-90. [PMID: 12198170 PMCID: PMC126203 DOI: 10.1093/emboj/cdf473] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Primitive eukaryotes like Caenorhabditis elegans produce mRNAs capped with either m(7)GTP or m(3)(2,2,7)GTP. Caenorhabditis elegans also expresses five isoforms of the cap-binding protein eIF4E. Some isoforms (e.g. IFE-3) bind to m(7)GTP-Sepharose exclusively, whereas others (e.g. IFE-5) bind to both m(7)GTP- and m(3)(2,2,7)GTP-Sepharose. To examine specificity differences, we devised molecular models of the tertiary structures of IFE-3 and IFE-5, based on the known structure of mouse eIF4E-1. We then substituted amino acid sequences of IFE-5 with homologous sequences from IFE-3. As few as two changes (N64Y/V65L) converted the cap specificity of IFE-5 to essentially that of IFE-3. Molecular dynamics simulations suggested that the width and depth of the cap-binding cavity were larger in IFE-5 than in IFE-3 or the N64Y/V65L variant, supporting a model in which IFE-3 discriminates against m(3)(2,2,7)GTP by steric hindrance. Furthermore, the affinity of IFE-5 (but not IFE-3) for m(3)(2,2,7)GTP was reversibly increased when thiol reagents were removed. This was correlated with the formation of a disulfide bond between Cys-122 and Cys-126. Thus, translation of m(3)(2,2,7)GTP-capped mRNAs may be regulated by intracellular redox state.
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Affiliation(s)
- Hiroshi Miyoshi
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130-3932, USA
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Bujnicki JM, Rychlewski L. In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses. Protein Eng Des Sel 2002; 15:101-8. [PMID: 11917146 DOI: 10.1093/protein/15.2.101] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Escherichia coli RrmJ gene product has recently been shown to be the 23S rRNA:U2552 specific 2'-O-ribose methyltransferase (MTase) (RrmJ). Its structure has been solved and refined to 1.5 A resolution, demonstrating conservation of the three-dimensional fold and key catalytic side chains with the vaccinia virus VP39 protein, which functions as an mRNA 5'm(7)G-cap-N-specific 2'-O-ribose MTase. Using the amino acid sequence of RrmJ as an initial probe in an iterative search of sequence databases, we identified a homologous domain in the sequence of the L protein of non-segmented, negative-sense, single-stranded RNA viruses. The plausibility of the prediction was confirmed by homology modeling and checking whether important residues at substrate/ligand-binding sites were conserved. The predicted structural compatibility and the conservation of the active site between the novel putative MTase domain and genuine 2'-O-ribose MTases, together with the available results of biochemical studies, strongly suggest that this domain is a 5'm(7)G-cap-N-specific 2'-O-ribose MTase (i.e. the cap 1 MTase). Evolutionary relationships between these proteins are also discussed.
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Affiliation(s)
- Janusz M Bujnicki
- Bioinformatics Laboratory, International Institute of Cell and Molecular Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland.
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Thoma C, Hasselblatt P, Köck J, Chang SF, Hockenjos B, Will H, Hentze MW, Blum HE, von Weizsäcker F, Offensperger WB. Generation of stable mRNA fragments and translation of N-truncated proteins induced by antisense oligodeoxynucleotides. Mol Cell 2001; 8:865-72. [PMID: 11684021 DOI: 10.1016/s1097-2765(01)00364-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Binding of phosphorothioate-modified antisense oligodeoxynucleotides (AS ODNs) to target mRNAs is commonly thought to mediate RNA degradation or block of translation. Here we demonstrate cleavage of target mRNAs within the AS ODN binding region with subsequent degradation of the 5' but not the 3' cleavage product. Some, if not all, 3' mRNA fragments lacked a 5' cap structure, whereas their poly(A) tail length remained unchanged. Furthermore, they were efficiently translated into N-terminally truncated proteins as demonstrated in three settings: production of shortened hepadnaviral surface proteins, alteration of the subcellular localization of a fluorescent protein, and shift of the transcription factor C/EBPalpha isoform expression levels. Thus, AS treatment may result in the synthesis of N-truncated proteins with biologically relevant effects.
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Affiliation(s)
- C Thoma
- Department of Medicine II, University of Freiburg, Hugstetter Strasse 55, D-79106 Freiburg, Germany
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Abstract
RNA editing can be broadly defined as any site-specific alteration in an RNA sequence that could have been copied from the template, excluding changes due to processes such as RNA splicing and polyadenylation. Changes in gene expression attributed to editing have been described in organisms from unicellular protozoa to man, and can affect the mRNAs, tRNAs, and rRNAs present in all cellular compartments. These sequence revisions, which include both the insertion and deletion of nucleotides, and the conversion of one base to another, involve a wide range of largely unrelated mechanisms. Recent advances in the development of in vitro editing and transgenic systems for these varied modifications have provided a better understanding of similarities and differences between the biochemical strategies, regulatory sequences, and cellular factors responsible for such RNA processing events.
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Affiliation(s)
- J M Gott
- Center for RNA Molecular Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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21
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Bujnicki JM, Rychlewski L. Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein. Genome Biol 2001; 2:RESEARCH0038. [PMID: 11574057 PMCID: PMC56899 DOI: 10.1186/gb-2001-2-9-research0038] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2001] [Revised: 06/11/2001] [Accepted: 06/29/2001] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The reovirus lambda2 protein catalyzes mRNA capping, that is, addition of a guanosine to the 5' end of each transcript in a 5'-to-5' orientation, as well as transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the N7 atom of the added guanosyl moiety and subsequently to the ribose 2'-O atom of the first template-encoded nucleotide. The structure of the human reovirus core has been solved at 3.6 A resolution, revealing a series of domains that include a putative guanylyltransferase domain and two putative methyltransferase (MTase) domains. It has been suggested that the order of domains in the lambda2 protein corresponds to the order of reactions in the pathway and that the m7G (cap 0) and the 2'-O-ribose (cap 1) MTase activities may be exerted by the MTase 1 and the MTase 2 domains, respectively. RESULTS We show that the reovirus MTase 1 domain shares a putative active site with the structurally characterized 2'-O-ribose MTases, including vaccinia virus cap 1 MTase, whereas the MTase 2 domain is structurally similar to glycine N-MTase. CONCLUSIONS On the basis of our analysis of the structural details we propose that the previously suggested functional assignments of the MTase 1 and MTase 2 domains should be swapped.
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Affiliation(s)
- J M Bujnicki
- Bioinformatics Laboratory, International Institute of Cell and Molecular Biology, ul ks Trojdena 4, 02-109 Warsaw, Poland.
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Mair G, Ullu E, Tschudi C. Cotranscriptional cap 4 formation on the Trypanosoma brucei spliced leader RNA. J Biol Chem 2000; 275:28994-9. [PMID: 10880518 DOI: 10.1074/jbc.m004193200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
mRNA cap formation in trypanosomatid protozoa is mediated through trans-splicing of the capped spliced leader (SL) sequence of the SL RNA onto the 5' end of all mRNAs. The SL RNA cap structure in Trypanosoma brucei is unique among eukaryotes and consists of 7-methylguanosine (m(7)G) followed by four methylated nucleotides (cap 4): m(7)Gpppm(2)(6)AmpAmpCmpm(3)Um. Using transcriptional arrest in permeable T. brucei cells, we have analyzed the temporal progression of cap 4 formation on the 140-nucleotide-long SL RNA. m(7)G capping of the SL RNA could be detected on prematurely terminated SL RNA transcripts of 56 nucleotides in length and longer. Subsequent modifications characteristic of the SL RNA cap 4 were added successively in a 5' to 3' direction and appeared to be independent of core ribonucleoprotein formation. Transcripts between 56 and 67 nucleotides in length were partially modified and carried methyl groups on the first two adenosine residues, whereas a fully modified cap 4 structure was present on transcripts arrested at position 117 and beyond. Taken together, our results are consistent with a cotranscriptional mechanism for generating the cap 4 structure on the SL RNA.
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Affiliation(s)
- G Mair
- Departments of Internal Medicine and Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520-8022, USA
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Gingras AC, Raught B, Sonenberg N. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu Rev Biochem 2000; 68:913-63. [PMID: 10872469 DOI: 10.1146/annurev.biochem.68.1.913] [Citation(s) in RCA: 1630] [Impact Index Per Article: 67.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic translation initiation factor 4F (eIF4F) is a protein complex that mediates recruitment of ribosomes to mRNA. This event is the rate-limiting step for translation under most circumstances and a primary target for translational control. Functions of the constituent proteins of eIF4F include recognition of the mRNA 5' cap structure (eIF4E), delivery of an RNA helicase to the 5' region (eIF4A), bridging of the mRNA and the ribosome (eIF4G), and circularization of the mRNA via interaction with poly(A)-binding protein (eIF4G). eIF4 activity is regulated by transcription, phosphorylation, inhibitory proteins, and proteolytic cleavage. Extracellular stimuli evoke changes in phosphorylation that influence eIF4F activity, especially through the phosphoinositide 3-kinase (PI3K) and Ras signaling pathways. Viral infection and cellular stresses also affect eIF4F function. The recent determination of the structure of eIF4E at atomic resolution has provided insight about how translation is initiated and regulated. Evidence suggests that eIF4F is also implicated in malignancy and apoptosis.
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Affiliation(s)
- A C Gingras
- Department of Biochemistry McGill University, Montréal, Québec, Canada.
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