1
|
Hernández-Alvarez L, Oliveira AB, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP. Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m 7GTP cap recognition. Comput Struct Biotechnol J 2021; 19:2027-2044. [PMID: 33995900 PMCID: PMC8085901 DOI: 10.1016/j.csbj.2021.03.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Atomistic details on perturbations induced by Lm4E-IP1 binding are described. The modulation of LmIF4E-1 affinity for the cap is confirmed by energetic analyses. Signaling paths between the allosteric and othosteric sites of LmIF4E-1 are predicted. Lm4E-IP1 binding increases the side-chain entropy of W83 and R172 of LmIF4E-1. A mechanism of dynamic allostery is proposed for the regulation mediated by Lm4E-IP1.
During their life cycle, Leishmania parasites display a fine-tuned regulation of the mRNA translation through the differential expression of isoforms of eukaryotic translation initiation factor 4E (LeishIF4Es). The interaction between allosteric modulators such as 4E-interacting proteins (4E-IPs) and LeishIF4E affects the affinity of this initiation factor for the mRNA cap. Here, several computational approaches were employed to elucidate the molecular bases of the previously-reported allosteric modulation in L. major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Molecular dynamics (MD) simulations and accurate binding free energy calculations (ΔGbind) were combined with network-based modeling of residue-residue correlations. We also describe the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems. Through community network calculations, the differences in the allosteric pathways of allosterically-inhibited and active forms of LmIF4E-1 were revealed. The ΔGbind values show significant differences between the active and inhibited systems, which are in agreement with the available experimental data. Our study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E-IP1. These findings are not only essential for the understanding of a critical process of trypanosomatids’ gene expression but also for gaining insight into the allostery of eukaryotic IF4Es, which could be useful for structure-based design of drugs against this protein family.
Collapse
Affiliation(s)
- Lilian Hernández-Alvarez
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Antonio B Oliveira
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Center for Theoretical Biological Physics, Rice University, Huston, TX, United States
| | - Jorge Enrique Hernández-González
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge Chahine
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Suman de Araujo
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| |
Collapse
|
2
|
Cheng MY, Tao WB, Yuan BF, Feng YQ. Methods for isolation of messenger RNA from biological samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:289-298. [PMID: 33300893 DOI: 10.1039/d0ay01912g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNA molecules contain many chemical modifications that can regulate a variety of biological processes. Messenger RNA (mRNA) molecules are critical components in the central dogma of molecular biology. The discovery of reversible chemical modifications in eukaryotic mRNA brings forward a new research field in RNA modification-mediated regulation of gene expression. The modifications in mRNA generally exist in low abundance. The use of highly pure mRNA is critical for the confident identification of new modifications as well as for the accurate quantification of existing modifications in mRNA. In addition, isolation of highly pure mRNA is the first step in many biological research studies. Therefore, the methods for isolating highly pure mRNA are important for mRNA-based downstream studies. A variety of methods for isolating mRNA have been developed in the past few decades and new methods continuously emerge. This review focuses on the methodologies and protocols for isolating mRNA populations. In addition, we discuss the advantages and limitations of these methods. We hope this paper will provide a general view of mRNA isolation strategies and facilitate studies that involve mRNA modifications and functions.
Collapse
Affiliation(s)
- Ming-Yu Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.
| | | | | | | |
Collapse
|
3
|
Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F. Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum. RNA Biol 2018; 15:937-954. [PMID: 29966484 PMCID: PMC6161686 DOI: 10.1080/15476286.2018.1481697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.
Collapse
Affiliation(s)
- Zhen Liao
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Jonas Kjellin
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Marc P Hoeppner
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden.,c Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology , Kiel , Germany
| | - Manfred Grabherr
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden
| | - Fredrik Söderbom
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| |
Collapse
|
4
|
Papic N, Maxwell CI, Delker DA, Liu S, Heale BSE, Hagedorn CH. RNA-sequencing analysis of 5' capped RNAs identifies many new differentially expressed genes in acute hepatitis C virus infection. Viruses 2012; 4:581-612. [PMID: 22590687 PMCID: PMC3347324 DOI: 10.3390/v4040581] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/31/2012] [Accepted: 04/03/2012] [Indexed: 12/28/2022] Open
Abstract
We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. We identified 100, 684, and 1,844 significantly differentially expressed annotated genes in acutely infected proliferative Huh 7.5 cells at 6, 48, and 72 hours, respectively (fold change ≥ 1.5 and Bonferroni adjusted p-values < 0.05). Most of the differentially expressed genes (>80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. These genes are critical components of host immune, inflammatory and oncogenic pathways and provide new information regarding changes that may benefit the virus or mediate HCV induced pathology. RNAi knockdown studies of newly identified highly upregulated FUT1 and KLHDC7B genes provide evidence that their gene products regulate and facilitate HCV replication in hepatocytes. Our approach also identified novel Pol II unannotated transcripts that were upregulated. Results further identify new pathways that regulate HCV replication in hepatocytes and suggest that our approach will have general applications in studying viral-host interactions in model systems and clinical biospecimens.
Collapse
Affiliation(s)
- Neven Papic
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Christopher I. Maxwell
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
- Huntsman Cancer Institute, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
| | - Don A. Delker
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Shuanghu Liu
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Bret S. E. Heale
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Curt H. Hagedorn
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
- Department of Experimental Pathology, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-801-587-4619; Fax: +1-801-585-0187
| |
Collapse
|
5
|
Folkers ME, Delker DA, Maxwell CI, Nelson CA, Schwartz JJ, Nix DA, Hagedorn CH. ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver. PLoS One 2011; 6:e14697. [PMID: 21359205 PMCID: PMC3040182 DOI: 10.1371/journal.pone.0014697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 01/24/2011] [Indexed: 01/02/2023] Open
Abstract
Microarray studies of chronic hepatitis C infection have provided valuable
information regarding the host response to viral infection. However, recent
studies of the human transcriptome indicate pervasive transcription in
previously unannotated regions of the genome and that many RNA transcripts have
short or lack 3′ poly(A) ends. We hypothesized that using ENCODE tiling
arrays (1% of the genome) in combination with affinity purifying Pol II
RNAs by their unique 5′ m7GpppN cap would identify previously
undescribed annotated and unannotated genes that are differentially expressed in
liver during hepatitis C virus (HCV) infection. Both 5′-capped and
poly(A)+ populations of RNA were analyzed using ENCODE tiling arrays.
Sixty-four annotated genes were significantly increased in HCV cirrhotic as
compared to control liver; twenty-seven (42%) of these genes were
identified only by analyzing 5′ capped RNA. Thirty-one annotated genes
were significantly decreased; sixteen (50%) of these were identified only
by analyzing 5′ capped RNA. Bioinformatic analysis showed that capped RNA
produced more consistent results, provided a more extensive expression profile
of intronic regions and identified upregulated Pol II transcriptionally active
regions in unannotated areas of the genome in HCV cirrhotic liver. Two of these
regions were verified by PCR and RACE analysis. qPCR analysis of liver biopsy
specimens demonstrated that these unannotated transcripts, as well as IRF1,
TRIM22 and MET, were also upregulated in hepatitis C with mild inflammation and
no fibrosis. The analysis of 5′ capped RNA in combination with ENCODE
tiling arrays provides additional gene expression information and identifies
novel upregulated Pol II transcripts not previously described in HCV infected
liver. This approach, particularly when combined with new RNA sequencing
technologies, should also be useful in further defining Pol II transcripts
differentially regulated in specific disease states and in studying RNAs
regulated by changes in pre-mRNA splicing or 3′ polyadenylation
status.
Collapse
Affiliation(s)
- Milan E. Folkers
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
| | - Don A. Delker
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
| | - Christopher I. Maxwell
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
| | - Cassie A. Nelson
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
| | - Jason J. Schwartz
- Department of Surgery, University of Utah,
Salt Lake City, Utah, United States of America
| | - David A. Nix
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
| | - Curt H. Hagedorn
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
- Department of Experimental Pathology,
University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| |
Collapse
|
6
|
Feketová Z, Masek T, Vopálenský V, Pospísek M. Ambiguous decoding of the CUG codon alters the functionality of the Candida albicans translation initiation factor 4E. FEMS Yeast Res 2010; 10:558-69. [PMID: 20491942 DOI: 10.1111/j.1567-1364.2010.00629.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic translation initiation factor 4E is an essential and highly conserved protein. As a part of the translational machinery, it plays a key role in the recruitment of mRNA via binding to its m(7)GpppN 5' terminal cap structure. The opportunistic human pathogen Candida albicans is the only known eukaryotic organism with the ability to survive defects in mRNA capping, which suggests unique features of its eIF4E protein. Here, we provide the first experimental evidence of the function of the C. albicans putative gene orf19.7626 as an eIF4E protein. We also show that Ca4E(Leu116) and Ca4E(Ser116) protein variants, both of which occur naturally in C. albicans due to the ambiguous decoding of the CUG(116) codon, display different sensitivities to elevated temperature. Our results clearly point to the importance of the S4-H4 loop for the function of the Ca4E translation initiation factor, and suggest the possible regulatory role of the codon-reading ambiguity within this loop in C. albicans. We proved Saccharomyces cerevisiae as a useful tool organism for studies of C. albicans translation initiation apparatus.
Collapse
Affiliation(s)
- Zuzana Feketová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | | | | |
Collapse
|
7
|
Liu W, Zhao R, McFarland C, Kieft J, Niedzwiecka A, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Jones DNM, Davis RE. Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps. J Biol Chem 2009; 284:31336-49. [PMID: 19710013 PMCID: PMC2781531 DOI: 10.1074/jbc.m109.049858] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 08/19/2009] [Indexed: 01/02/2023] Open
Abstract
The eukaryotic translation initiation factor eIF4E recognizes the mRNA cap, a key step in translation initiation. Here we have characterized eIF4E from the human parasite Schistosoma mansoni. Schistosome mRNAs have either the typical monomethylguanosine (m(7)G) or a trimethylguanosine (m(2,2,7)G) cap derived from spliced leader trans-splicing. Quantitative fluorescence titration analyses demonstrated that schistosome eIF4E has similar binding specificity for both caps. We present the first crystal structure of an eIF4E with similar binding specificity for m(7)G and m(2,2,7)G caps. The eIF4E.m(7)GpppG structure demonstrates that the schistosome protein binds monomethyl cap in a manner similar to that of single specificity eIF4Es and exhibits a structure similar to other known eIF4Es. The structure suggests an alternate orientation of a conserved, key Glu-90 in the cap-binding pocket that may contribute to dual binding specificity and a position for mRNA bound to eIF4E consistent with biochemical data. Comparison of NMR chemical shift perturbations in schistosome eIF4E on binding m(7)GpppG and m(2,2,7)GpppG identified key differences between the two complexes. Isothermal titration calorimetry demonstrated significant thermodynamics differences for the binding process with the two caps (m(7)G versus m(2,2,7)G). Overall the NMR and isothermal titration calorimetry data suggest the importance of intrinsic conformational flexibility in the schistosome eIF4E that enables binding to m(2,2,7)G cap.
Collapse
Affiliation(s)
- Weizhi Liu
- From the Departments of Biochemistry and Molecular Genetics and
| | - Rui Zhao
- From the Departments of Biochemistry and Molecular Genetics and
| | - Craig McFarland
- From the Departments of Biochemistry and Molecular Genetics and
| | - Jeffrey Kieft
- From the Departments of Biochemistry and Molecular Genetics and
| | - Anna Niedzwiecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Biological Physics Group, Institute of Physics, Polish Academy of Sciences, 32/46 Lotnikow Avenue, 02-668 Warsaw, Poland
| | | | - Janusz Stepinski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - David N. M. Jones
- **Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | | |
Collapse
|
8
|
Bajak EZ, Hagedorn CH. Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA. Methods Mol Biol 2008; 419:147-60. [PMID: 18369981 DOI: 10.1007/978-1-59745-033-1_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microarray-based screening technologies have revealed a larger than expected diversity of gene expression profiles for many cells, tissues, and organisms. The complexity of RNA species, defined by their molecular structure, represents a major new development in biology. RNA not only carries genetic information in the form of templates and components of the translational machinery for protein synthesis but also directly regulates gene expression as exemplified by micro-RNAs (miRNAs). Recent evidence has demonstrated that 5' capped and 3' polyadenylated ends are not restricted to mRNAs, but that they are also present in precursors of both miRNAs and some antisense RNA transcripts. In addition, as many as 40% of transcribed RNAs may lack 3' poly(A) ends. In concert with the presence of a 5' cap (m7 GpppN), the length of the 3' poly(A) end plays a critical role in determining the translational efficiency, stability, and the cellular distribution of a specific mRNA. RNAs with short or lacking 3' poly(A) ends, that escape isolation and amplification with oligo(dT)-based methods, provide a challenge in RNA biology and gene expression studies. To circumvent the limitations of 3' poly(A)-dependent RNA isolation methods, we developed an efficient RNA purification system that binds the 5' cap of RNA with a high-affinity variant of the cap-binding protein eIF4E. This system can be used in differential selection approaches to isolate subsets of RNAs, including those with short 3' poly(A) ends that are likely targets of post-transcriptional regulation of gene expression. The length of the 3' poly(A) ends can be defined using a rapid polymerase chain reaction (PCR)- based approach.
Collapse
Affiliation(s)
- Edyta Z Bajak
- Department of Medicine and Pharmacology, University of Kansas Medical Center, Kansas City, KS, USA
| | | |
Collapse
|
9
|
Volpon L, Osborne MJ, Topisirovic I, Siddiqui N, Borden KLB. Cap-free structure of eIF4E suggests a basis for conformational regulation by its ligands. EMBO J 2006; 25:5138-49. [PMID: 17036047 PMCID: PMC1630411 DOI: 10.1038/sj.emboj.7601380] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 09/13/2006] [Indexed: 12/31/2022] Open
Abstract
The activity of the eukaryotic translation initiation factor eIF4E is modulated through conformational response to its ligands. For example, eIF4G and eIF4E-binding proteins (4E-BPs) modulate cap affinity, and thus physiological activity of eIF4E, by binding a site distal to the 7-methylguanosine cap-binding site. Further, cap binding substantially modulates eIF4E's affinity for eIF4G and the 4E-BPs. To date, only cap-bound eIF4E structures were reported. In the absence of structural information on the apo form, the molecular underpinnings of this conformational response mechanism cannot be established. We report here the first cap-free eIF4E structure. Apo-eIF4E exhibits structural differences in the cap-binding site and dorsal surface relative to cap-eIF4E. Analysis of structure and dynamics of apo-eIF4E, and changes observed upon ligand binding, reveal a molecular basis for eIF4E's conformational response to these ligands. In particular, alterations in the S4-H4 loop, distal to either the cap or eIF4G binding sites, appear key to modulating these effects. Mutation in this loop mimics these effects. Overall, our studies have important implications for the regulation of eIF4E.
Collapse
Affiliation(s)
- Laurent Volpon
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC, Canada
| | - Michael J Osborne
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC, Canada
| | - Ivan Topisirovic
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC, Canada
| | - Nadeem Siddiqui
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC, Canada
| | - Katherine LB Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC, Canada
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, 2950, Chemin Polytechnique, Montréal, Québec, Canada H3T 1J4. Tel.: +1 514 343 6291; Fax: +1 514 343 5839; E-mail:
| |
Collapse
|
10
|
Friedland DE, Wooten WNB, LaVoy JE, Hagedorn CH, Goss DJ. A mutant of eukaryotic protein synthesis initiation factor eIF4E(K119A) has an increased binding affinity for both m7G cap analogues and eIF4G peptides. Biochemistry 2005; 44:4546-50. [PMID: 15766285 DOI: 10.1021/bi047645m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eukaryotic multisubunit initiation factor eIF4F is an essential component of the translational machinery. Recognition of the cap structure of mRNA, m(7)GpppN, where N is any nucleotide, by eIF4E is required for initiation of translation. Here we compare the equilibrium and thermodynamic binding characteristics of wild-type eIF4E and a high-affinity mutant, eIF4E(K119A), with those of cap analogues and eIF4G peptides. The temperature-dependent K(d) values for cap analogues were markedly lower, indicating tighter binding, with the eIF4E(K119A) mutant compared with wild-type eIF4E. Although interactions with cap analogues were found to be enthalpically driven, entropic contributions were also significant. Moreover, the binding affinities of eIF4G peptides were 2-4-fold tighter for eIF4E(K119A) than for eIF4E(wt). These results demonstrate that the binding affinity for both the mRNA cap and eIF4G peptides can be simultaneously altered by point mutations distant from either binding site. Entropic contributions to binding suggesting hydrophobic interactions are larger in the mutant protein and are most likely due to a conformational change.
Collapse
Affiliation(s)
- D E Friedland
- Department of Chemistry, Hunter College, and Graduate Center of the City University of New York, New York, New York 10021, USA
| | | | | | | | | |
Collapse
|
11
|
von der Haar T, Gross JD, Wagner G, McCarthy JEG. The mRNA cap-binding protein eIF4E in post-transcriptional gene expression. Nat Struct Mol Biol 2004; 11:503-11. [PMID: 15164008 DOI: 10.1038/nsmb779] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Accepted: 04/22/2004] [Indexed: 11/09/2022]
Abstract
Eukaryotic initiation factor 4E (eIF4E) has central roles in the control of several aspects of post-transcriptional gene expression and thereby affects developmental processes. It is also implicated in human diseases. This review explores the relationship between structural, biochemical and biophysical aspects of eIF4E and its function in vivo, including both long-established roles in translation and newly emerging ones in nuclear export and mRNA decay pathways.
Collapse
Affiliation(s)
- Tobias von der Haar
- Post-transcriptional Control Group, Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, PO Box 88, Manchester M60 1QD, UK.
| | | | | | | |
Collapse
|
12
|
Lou H, Choi YH, LaVoy JE, Major ME, Hagedorn CH. Analysis of mutant NS5B proteins encoded by isolates from chimpanzees chronically infected following clonal HCV RNA inoculation. Virology 2004; 317:65-72. [PMID: 14675625 DOI: 10.1016/j.virol.2003.08.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We hypothesized that mutations in the HCV NS5B polymerase, which occur during infection, may affect RNA-dependent RNA polymerase (RdRp) activity. NS5B proteins corresponding to a genotype 1a infectious clone and mutants identified in chimpanzees following inoculation with the clone were expressed and purified and their in vitro RdRp activity was compared to a NS5B genotype 1b control. A Gln-65-to-His mutation increased RdRp activity by 1.8-fold as compared to the infectious clone. Moreover, this NS5B1a protein had RdRp activity similar to the NS5B1b control. Three NS5B proteins representing mutations found in another animal had no in vitro RdRp activity. All mutations were maintained in the majority circulating virus for at least 216 weeks. The results demonstrate that some in vivo mutations of NS5B directly enhance in vitro RdRp activity. In addition, they suggest that the in vitro RdRp activity of NS5B may not always reflect in vivo activity within replication complexes.
Collapse
Affiliation(s)
- Hong Lou
- Department of Medicine and Genetics Program-Winship Cancer Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | | | |
Collapse
|
13
|
Choi YH, Hagedorn CH. Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3' poly(A) end phenotype. Proc Natl Acad Sci U S A 2003; 100:7033-8. [PMID: 12777618 PMCID: PMC165825 DOI: 10.1073/pnas.1232347100] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2003] [Indexed: 11/18/2022] Open
Abstract
The use of DNA microarrays has revolutionized the manner in which mRNA populations are analyzed. One limitation of the current technology is that mRNAs are often purified on the basis of their 3' poly(A) ends, which can be extremely short or absent in some mRNAs. To circumvent this limitation, we have developed a procedure for the purification of eukaryotic mRNAs using a mutant version of the mRNA 5' cap-binding protein (eIF4E) with increased affinity for the m7GTP moiety of the cap. By using this procedure, we have compared the populations of mammalian mRNAs purified by oligo(dT) and 5' cap selection with oligonucleotide microarrays. This analysis has identified a subpopulation of mRNAs that are present with short 3' poly(A) ends at steady state and are missed or underrepresented after purification by oligo(dT). These mRNAs may respond to specific posttranscriptional control mechanisms such as cytoplasmic polyadenylation.
Collapse
Affiliation(s)
- Youkyung Hwang Choi
- Department of Medicine, Genetics Program, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | |
Collapse
|
14
|
Tomoo K, Shen X, Okabe K, Nozoe Y, Fukuhara S, Morino S, Sasaki M, Taniguchi T, Miyagawa H, Kitamura K, Miura KI, Ishida T. Structural features of human initiation factor 4E, studied by X-ray crystal analyses and molecular dynamics simulations. J Mol Biol 2003; 328:365-83. [PMID: 12691746 DOI: 10.1016/s0022-2836(03)00314-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structural features of human eIF4E were investigated by X-ray crystal analyses of its cap analog (m(7)GTP and m(7)GpppA) complexes and molecular dynamics (MD) simulations of cap-free and cap-bound eIF4Es, as well as the cap-bound Ser209-phosphorylated eIF4E. Crystal structure analyses at 2.0 A resolution revealed that the molecule forms a temple-bell-shaped surface of eight antiparallel beta-structures, three alpha-helices and ten loop structures, where the N-terminal region corresponds to the handle of the bell. This concave backbone provides a scaffold for the mRNA cap-recognition pocket consisting of three receiving parts for the 5'-terminal m(7)G base, the triphosphate, and the second nucleotide. The m(7)G base is sandwiched between the two aromatic side-chains of Trp102 and Trp56. The two (m(7)G)NH-O (Glu103 carboxy group) hydrogen bonds stabilize the stacking interaction. The basic residues of Arg157 and Lys162 and water molecules construct a binding pocket for the triphosphate moiety, where a universal hydrogen-bonding network is formed. The flexible C-terminal loop region unobserved in the m(7)GTP complex was clearly observed in the m(7)GpppA complex, as a result of the fixation of this loop by the interaction with the adenosine moiety, indicating the function of this loop as a receiving pocket for the second nucleotide. On the other hand, MD simulation in an aqueous solution system revealed that the cap-binding pocket, especially its C-terminal loop structure, is flexible in the cap-free eIF4E, and the entrance of the cap-binding pocket becomes narrow, although the depth is relatively unchanged. SDS-PAGE analyses showed that this structural instability is highly related to the fast degradation of cap-free eIF4E, compared with cap-bound or 4E-BP/cap-bound eIF4E, indicating the conferment of structural stability of eIF4E by the binary or ternary complex formation. MD simulation of m(7)GpppA-bound Ser209-phosphorylated eIF4E showed that the size of the cap-binding entrance is dependent on the ionization state in the Ser209 phosphorylation, which is associated with the regulatory function through the switching on/off of eIF4E phosphorylation.
Collapse
Affiliation(s)
- Koji Tomoo
- Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|