DOCSLIB.ORG

CHARACTERIZING the INTERACTION BETWEEN PDCD4 and Eif3 with RESPECT to TRANSLATION REGULATION

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
CHARACTERIZING the INTERACTION BETWEEN PDCD4 and Eif3 with RESPECT to TRANSLATION REGULATION CHARACTERIZING THE INTERACTION BETWEEN PDCD4 AND eIF3 WITH RESPECT TO TRANSLATION REGULATION DIVYA SHARMA KHANDIGA Master of Science, Bangalore University, India 2009 A Thesis/Project Submitted to the School of Graduate Studies of the University of Lethbridge in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE Department of Chemistry and Biochemistry University of Lethbridge LETHBRIDGE, ALBERTA, CANADA © Divya Sharma Khandiga, 2017 CHARACTERIZING THE INTERACTION BETWEEN PDCD4 AND eIF3 WITH RESPECT TO TRANSLATION REGULATION DIVYA SHARMA KHANDIGA Date of Defense: December 12, 2017 Dr. N. Thakor Assistant Professor Ph.D. Thesis Supervisor Dr. M. Roussel Professor Ph.D. Thesis Co-supervisor Dr. U. Kothe Associate Professor Ph.D. Thesis Examination Committee Member Dr. R. Golsteyn Associate Professor Ph.D. Thesis Examination Committee Member Dr. R. Fahlman Professor Ph.D. External Examiner University of Alberta Edmonton, Alberta Dr. M. Gerken Professor Ph.D. Chair, Thesis Examination Committee Dedication To my beloved family and friends, My inspiration, my parents Subraya Sharma and Kamala Sharma My dearly loved husband Samarth, sister Dr. Lakshmi and brother-in-law Dr. Pradeep My cute little niece Mithali and nephew Aathreya My adorable brother Dr. Ganesh, sister Dr. Sharadha, Silly Vidya and little angels My loving cousins and in-laws I am grateful to have them in my life, it is their well wishes, teachings, support and love that have enabled me to achieve success and happiness in life. iii Abstract Programmed cell death protein 4 (PDCD4) inhibits IRES-mediated translation of anti- apoptotic proteins such as XIAP. PDCD4 was shown to directly interact with the XIAP IRES element and inhibit translation initiation. Additionally, our lab reported that a eukaryotic initiation factor, eIF3 interacts with the XIAP IRES to facilitate ribosome recruitment. Interestingly, the activity of PDCD4 and eIF3 are regulated by common regulatory kinases called S6K1 and 2. Therefore, to investigate the possibility of interaction between PDCD4 and eIF3 as well as their co-regulation by S6K1 and 2, I have performed co-immunoprecipitation assays in glioblastoma and S6K double knockout MEFs. The results of in cellulo assays demonstrate RNA-independent PDCD4-eIF3 interactions. In addition, eIF3F, one of the 13 eIF3 subunits has been demonstrated to interact directly with PDCD4. This study suggests that the interaction of PDCD4 with eIF3F may have a role in regulating global and/or transcript-specific translation. iv Acknowledgments I would like to thank my supervisor Dr. Nehal Thakor for providing me an opportunity to pursue my master’s in his laboratory. He has been a constant support and helped me to work my way through the master’s program. I would also like to thank my committee members, Drs. Roy Golsteyn, Marc Roussel and Ute Wieden-Kothe for their valuable feedback and guidance. Lastly, I would like to thank my lab mates for helping me with my experiments and for all the encouraging words when my experiments were a total disaster. v Table of Contents Table of Contents....................................................................................................... vi List of Tables............................................................................................................. viii List of Figures........................................................................................................... ix List of Abbreviations................................................................................................. x 1. Introduction 1 1.1. Description of eukaryotic translation initiation............................................ 1 1.1.1. Cap-dependent translation initiation.................................................. 2 1.1.2. Cap-independent translation initiation............................................... 5 1.1.2.1 Significance of cap-independent translation.......................... 6 1.1.2.2 Discovery and classification of IRESes................................. 9 1.1.2.3 Mechanism of IRES-mediated translation............................ 10 1.2. Apoptosis..................................................................................................... 13 1.2.1 Extrinsic apoptosis pathway.......................................................... 14 1.2.2 Intrinsic apoptosis pathway ........................................................... 15 1.2.3 Anti and pro-apoptotic proteins..................................................... 16 1.3 mTOR pathway............................................................................................ 19 1.3.1 S6K................................................................................................. 20 1.3.2 Regulation of protein translation by S6K...................................... 22 1.4 PDCD4......................................................................................................... 25 1.5 Role of eIF3 in translation and apoptosis.................................................... 26 1.6 Objectives.................................................................................................... 28 2. Materials and methods...................................................................................... 30 2.1. Cell lines and constructs.............................................................................. 30 2.2. Transfection and transformation.................................................................. 31 2.3. Plasmid purification..................................................................................... 32 2.4. Optimization of protein purification ........................................................... 33 2.5. Recombinant protein purification................................................................ 34 2.6. Western blot assay....................................................................................... 35 2.7. FLAG-immunoprecipitation........................................................................ 36 2.8. FLAG-IP to detect RNA-independent protein-protein interaction.............. 36 2.9. eIF3F immunoprecipitation......................................................................... 37 2.10. In vitro pull-down assay.............................................................................. 37 2.11. Luciferase assay........................................................................................... 38 3. Results................................................................................................................. 39 3.1. FLAG-IP to detect interaction between eIF3 and PDCD4.......................... 39 3.2. eIF3F IP to detect the interaction between PDCD4 and eIF3F................... 41 3.3. Co-IP in the presence and absence of RNaseA to detect if the eIF3 and PDCD4 interaction is RNA-dependent....................................................... 43 3.4. Optimization of recombinant protein purification....................................... 45 3.5. Western blotting to confirm His-PDCD4 and GST-eIF3F expression........ 47 vi 3.6. In vitro pull-down of GST-tagged protein to detect direct interaction between PDCD4 and eIF3F........................................................................ 49 3.7. Co-IP in S6K wild-type and knockout MEFs.............................................. 50 3.8. FLAG-IP during serum starvation.............................................................. 52 3.9. Luciferase reporter assay to investigate the role of eIF3F in cap- dependent translation.................................................................................. 54 4. Discussion........................................................................................................... 57 4.1. Discussion................................................................................................... 57 4.2. Future directions......................................................................................... 62 4.2.1. Short-term vision........................................................................... 62 4.2.2. Future oriented outlook................................................................. 65 References................................................................................................................. 67 vii List of Tables 2.1 List of constructs, application of the constructs and their source........................ 30 viii List of Figures 1.1 Schematic representation of cap-dependent translation initiation................. 4 1.2 Schematic representation of the extrinsic and intrinsic pathway of apoptosis......................................................................................................... 16 1.3 Schematic representation of S6K mediated translation regulation................ 29 3.1 PDCD4 interacts with eIF3............................................................................ 40 3.2 eIF3F interacts with PDCD4.......................................................................... 42 3.3 PDCD4 protein levels are higher in SF767 and A172 in comparison to the other cell lines.......................................................................................... 43 3.4 Schematic diagram representing the types of interactions detected by IP..... 44 3.5 The PDCD4-eIF3 interaction is RNA-independent....................................... 45 3.6 Coomassie staining to detect protein induction............................................. 47 3.7 Western blot assay to confirm protein
Load more

Recommended publications
  • Composition of Herpesvirus Ribonucleoprotein Complexes †
    Abstract Composition of Herpesvirus Ribonucleoprotein Complexes † Eric S. Pringle 1,2,* and Craig McCormick 1,2 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; [email protected] 2 Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada * Correspondence: [email protected] † Presented at Viruses 2020—Novel Concepts in Virology, Barcelona, Spain, 5–7 February 2020. Published: 4 July 2020 Abstract: Herpesvirus genomes are decoded by host RNA polymerase enzymes, generating messenger ribonucleotides (mRNA) that are post-transcriptionally modified and exported to the cytoplasm through the combined work of host and viral factors. These viral mRNA bear 5′-m7GTP caps and poly(A) tails that should permit the assembly of canonical host eIF4F cap-binding complexes to initiate protein synthesis. However, the precise mechanisms of translation initiation remain to be investigated for Kaposi’s sarcoma-associated herpesvirus (KSHV) and other herpesviruses. During KSHV lytic replication in lymphoid cells, the activation of caspases leads to the cleavage of eIF4G and depletion of eIF4F. Translating mRNPs depleted of eIF4F retain viral mRNA, suggesting that non-eIF4F translation initiation is sufficient to support viral protein synthesis. To identify proteins required to support viral protein synthesis, we isolated and characterized actively translating messenger ribonucleoprotein (mRNP) complexes by ultracentrifugation and sucrose-gradient fractionation followed by quantitative mass spectrometry. The abundance of host translation initiation factors available to initiate viral protein synthesis were comparable between cells undergoing KSHV lytic or latent replication. The translation initiation factors eIF4E2, NCBP1, eIF4G2, and eIF3d were detected in association with actively translating mRNP complexes during KSHV lytic replication, but their depletion by RNA silencing did not affect virion production.
    [Show full text]
  • Structural Characterization of the Human Eukaryotic Initiation Factor 3 Protein Complex by Mass Spectrometry*□S
    Supplemental Material can be found at: http://www.mcponline.org/cgi/content/full/M600399-MCP200 /DC1 Research Structural Characterization of the Human Eukaryotic Initiation Factor 3 Protein Complex by Mass Spectrometry*□S Eugen Damoc‡, Christopher S. Fraser§, Min Zhou¶, Hortense Videler¶, Greg L. Mayeurʈ, John W. B. Hersheyʈ, Jennifer A. Doudna§, Carol V. Robinson¶**, and Julie A. Leary‡ ‡‡ Protein synthesis in mammalian cells requires initiation The initiation phase of eukaryotic protein synthesis involves factor eIF3, an ϳ800-kDa protein complex that plays a formation of an 80 S ribosomal complex containing the initi- Downloaded from central role in binding of initiator methionyl-tRNA and ator methionyl-tRNAi bound to the initiation codon in the mRNA to the 40 S ribosomal subunit to form the 48 S mRNA. This is a multistep process promoted by proteins initiation complex. The eIF3 complex also prevents pre- called eukaryotic initiation factors (eIFs).1 Currently at least 12 mature association of the 40 and 60 S ribosomal subunits eIFs, composed of at least 29 distinct subunits, have been and interacts with other initiation factors involved in start identified (1). Mammalian eIF3, the largest initiation factor, is a codon selection. The molecular mechanisms by which multisubunit complex with an apparent molecular mass of www.mcponline.org eIF3 exerts these functions are poorly understood. Since ϳ800 kDa. This protein complex plays an essential role in its initial characterization in the 1970s, the exact size, translation by binding directly to the 40 S ribosomal subunit composition, and post-translational modifications of and promoting formation of the 43 S preinitiation complex ⅐ ⅐ mammalian eIF3 have not been rigorously determined.
    [Show full text]
  • A Versatile Eif3d in Translational Control of Stress Adaptation
    ll Spotlight A Versatile eIF3d in Translational Control of Stress Adaptation Longfei Jia1 and Shu-Bing Qian1,* 1Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA *Correspondence: [email protected] https://doi.org/10.1016/j.molcel.2020.12.016 Lamper et al. (2020) reported that eIF3d-mediated cap-dependent translation is subject to regulation by phosphorylation during chronic glucose deprivation, providing a mechanism underlying selective translation of stress genes essential for cell survival. A remarkable feature of all living organ- tion, however, overall translation is because eIF3d contains a natural HIV-1 isms is the ability to sense fluctuations reduced only by 60% (An et al., protease cleavage site. Remarkably, of environmental cues and respond to 2020). This does not necessarily mean glucose starvation led to an increased adverse conditions by adjusting cellular that the remaining 40% of translation cap-binding activity of eIF3d by 10- activities. Protein synthesis consumes solely relies on cap-independent mech- fold. Since phosphorylation is a common a lion’s share of cellular energy. Not sur- anisms. Notably, most mRNAs are still mechanism in stress signaling pathways, prisingly, many stress conditions sup- capped when the canonical eIF4F is in- the authors confirmed nutrient-depen- press global protein synthesis as part hibited. Although cap-dependent trans- dent phosphorylation of eIF3d. Using of the stress response. However, trans- lation is widely believed to be driven biochemical and genetic approaches, lation of certain mRNAs needs to be through eIF4F, alternative mechanisms they not only mapped the phosphoryla- maintained or even upregulated to sus- likely exist to mediate cap-dependent tion sites but also identified CK2 as tain vital functions.
    [Show full text]
  • Structural Studies of the Eif4e–Vpg Complex Reveal a Direct Competition for Capped RNA: Implications for Translation
    Structural studies of the eIF4E–VPg complex reveal a direct competition for capped RNA: Implications for translation Luciana Coutinho de Oliveiraa,1,2, Laurent Volpona,1, Amanda K. Rahardjoa, Michael J. Osbornea, Biljana Culjkovic-Kraljacica, Christian Trahanb, Marlene Oeffingerb,c,d, Benjamin H. Kwoka, and Katherine L. B. Bordena,3 aInstitute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada; bDepartment for Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; cDépartement de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada; and dDivision of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada Edited by Lynne E. Maquat, University of Rochester School of Medicine and Dentistry, Rochester, NY, and approved October 16, 2019 (received for review March 19, 2019) Viruses have transformed our understanding of mammalian RNA of eIF4E can be targeted in patients to provide clinical benefit, processing, including facilitating the discovery of the methyl-7- highlighting its critical importance. guanosine (m7G)caponthe5′ end of RNAs. The m7Gcapisrequired Viruses have paved the way for our understanding of many for RNAs to bind the eukaryotic translation initiation factor eIF4E aspects of host-cell RNA processing, including m7G capping. and associate with the translation machinery across plant and ani- Indeed, studies into cytoplasmic polyhedrosis virus (CPV) infec- mal kingdoms. The potyvirus-derived viral genome-linked protein tion in silkworm and vaccinia virus (VV) in mammalian cells were (VPg) is covalently bound to the 5′ end of viral genomic RNA (gRNA) critical for the elucidation of the m7G cap structure over 40 y ago and associates with host eIF4E for successful infection.
    [Show full text]
  • Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
    Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes.
    [Show full text]
  • The Eif3 Complex of Typanosoma Brucei: Composition Conservation Does Not Imply the Conservation of Structural Assembly and Subunits Function
    Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 1 The eIF3 complex of Typanosoma brucei: composition conservation does not imply the 2 conservation of structural assembly and subunits function 3 4 Kunrao Li,1,2 Shuru Zhou,1,2 Qixuan Guo,3 Xin Chen,1,2 Dehua Lai,2,4 Zhaorong Lun,2,4,5 and 5 Xuemin Guo1,2,5 6 7 1Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, 8 Guangzhou, China 9 2Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, 10 Guangzhou, China 11 3Chengde Nursing Vocational College, Chende, China 12 4Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, 13 Sun Yat-Sen University, Guangzhou, China 14 15 5Corresponding author. Email, [email protected]; or [email protected] 16 K.L. and S.Z. contributed equally to this work 17 18 Running head: Characterization of the eIF3 of Trypanosoma brucei 19 Keywords: Translation, Eukaryotic initiation factor 3, Trypanosome 20 1 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 21 ABSTRACT 22 The multisubunit eukaryotic initiation factor 3 (eIF3) plays multiple roles in translation, but 23 poorly understood in trypanosomes. The putative subunits eIF3a and eIF3f of Trypanosoma 24 brucei (TbIF3a and TbIF3f) were overexpressed and purified, and 11 subunits were identified, 25 TbIF3a through l minus j, which form a tight complex. Both TbIF3a and TbIF3f are essential for 26 viability of T. brucei. RNAi knockdown of either of them severely reduced total translation and 27 the ratio of polysome/80S peak area.
    [Show full text]
  • WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US).
    [Show full text]
  • Structure of Ah
    Eliseev, B., Yeramala, L., Leitner, A., Karuppasamy, M., Raimondeau, E., Huard, K., ... Schaffitzel, C. (2018). Structure of a human cap-dependent 48S translation pre-initiation complex. Nucleic Acids Research, 46(5), 2678- 2689. [gky054]. https://doi.org/10.1093/nar/gky054 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1093/nar/gky054 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Oxford University Press at https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky054/4833217 . Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/pure/about/ebr-terms 2678–2689 Nucleic Acids Research, 2018, Vol. 46, No. 5 Published online 1 February 2018 doi: 10.1093/nar/gky054 Structure of a human cap-dependent 48S translation pre-initiation complex Boris Eliseev1, Lahari Yeramala1, Alexander Leitner2, Manikandan Karuppasamy1, Etienne Raimondeau1, Karine Huard1, Elena Alkalaeva3, Ruedi Aebersold2,4 and Christiane Schaffitzel1,5,* 1European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France, 2ETH Zurich,¨ Institute of Molecular Systems Biology,
    [Show full text]
  • Type of the Paper (Article
    Supplementary figures and tables E g r 1 F g f2 F g f7 1 0 * 5 1 0 * * e e e * g g g * n n n * a a a 8 4 * 8 h h h * c c c d d d * l l l o o o * f f f * n n n o o o 6 3 6 i i i s s s s s s e e e r r r p p p x x x e e e 4 2 4 e e e n n n e e e g g g e e e v v v i i i t t t 2 1 2 a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d J a k 2 N o tc h 2 H if1 * 3 4 6 * * * e e e g g g n n n a a * * a * h h * h c c c 3 * d d * d l l l * o o o f f 2 f 4 n n n o o o i i i s s s s s s e e e r r 2 r p p p x x x e e e e e e n n n e e 1 e 2 g g g e e 1 e v v v i i i t t t a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Z e b 2 C d h 1 S n a i1 * * 7 1 .5 4 * * e e e g g g 6 n n n * a a a * h h h c c c 3 * d d d l l l 5 o o o f f f 1 .0 * n n n * o o o i i i 4 * s s s s s s e e e r r r 2 p p p x x x 3 e e e e e e n n n e e e 0 .5 g g g 2 e e e 1 v v v i i i t t t a a a * l l l e e e 1 * R R R 0 0 .0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d M m p 9 L o x V im 2 0 0 2 0 8 * * * e e e * g g g 1 5 0 * n n n * a a a * h h h * c c c 1 5 * 6 d d d l l l 1 0 0 o o o f f f n n n o o o i i i 5 0 s s s s s s * e e e r r r 1 0 4 3 0 p p p * x x x e e e * e e e n n n e e e 2 0 g g g e e e 5 2 v v v i i i t t t a a a l l l 1 0 e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Supplementary Figure 1.
    [Show full text]
  • Systematically Profiling the Expression of Eif3 Subunits in Glioma Reveals
    Chai et al. Cancer Cell Int (2019) 19:155 https://doi.org/10.1186/s12935-019-0867-1 Cancer Cell International PRIMARY RESEARCH Open Access Systematically profling the expression of eIF3 subunits in glioma reveals the expression of eIF3i has prognostic value in IDH-mutant lower grade glioma Rui‑Chao Chai1,4,6†, Ning Wang2†, Yu‑Zhou Chang3, Ke‑Nan Zhang1,6, Jing‑Jun Li1,6, Jun‑Jie Niu5, Fan Wu1,6*, Yu‑Qing Liu1,6* and Yong‑Zhi Wang1,3,4,6* Abstract Background: Abnormal expression of the eukaryotic initiation factor 3 (eIF3) subunits plays critical roles in tumo‑ rigenesis and progression, and also has potential prognostic value in cancers. However, the expression and clinical implications of eIF3 subunits in glioma remain unknown. Methods: Expression data of eIF3 for patients with gliomas were obtained from the Chinese Glioma Genome Atlas (CGGA) (n 272) and The Cancer Genome Atlas (TCGA) (n 595). Cox regression, the receiver operating characteristic (ROC) curves= and Kaplan–Meier analysis were used to study= the prognostic value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were utilized for functional prediction. Results: In both the CGGA and TCGA datasets, the expression levels of eIF3d, eIF3e, eIF3f, eIF3h and eIF3l highly were associated with the IDH mutant status of gliomas. The expression of eIF3b, eIF3i, eIF3k and eIF3m was increased with the tumor grade, and was associated with poorer overall survival [All Hazard ratio (HR) > 1 and P < 0.05]. By contrast, the expression of eIF3a and eIF3l was decreased in higher grade gliomas and was associated with better overall sur‑ vival (Both HR < 1 and P < 0.05).
    [Show full text]
  • PCI Proteins Eif3e and Eif3m Define Distinct Translation Initiation Factor 3 Complexes
    PCI Proteins eIF3e and eIF3m Define Distinct Translation Initiation Factor 3 Complexes The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Zhou, Chunshui, Fatih Arslan, Susan Wee, Srinivasan Krishnan, Alexander R. Ivanov, Anna Oliva, Janet Leatherwood, and Dieter A. Wolf. 2005. PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes. BMC Biology 3:14. Published Version doi:10.1186/1741-7007-3-14 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:4595136 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA BMC Biology BioMed Central Research article Open Access PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes Chunshui Zhou1,5, Fatih Arslan1, Susan Wee1, Srinivasan Krishnan2, Alexander R Ivanov3, Anna Oliva4, Janet Leatherwood4 and Dieter A Wolf*1,3 Address: 1Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts, 02115, USA, 2Applied Biosystems Inc., Framingham, Massachusetts, USA, 3Harvard NIEHS Center Proteomics Facility, Harvard School of Public Health, Boston, Massachusetts, USA, 4Department of Molecular Genetics and Microbiology, State University of New York, Stony Brook, New York, USA and 5Department of
    [Show full text]
  • Translation Initiation Factor Eif3h Targets Specific Transcripts To
    Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis Avik Choudhuria,b, Umadas Maitraa,1, and Todd Evansb,1 aDepartment of Developmental and Molecular Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461; and bDepartment of Surgery, Weill Cornell Medical College, New York, NY 10065 Edited by Igor B. Dawid, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, and approved April 30, 2013 (received for review February 14, 2013) Eukaryotic translation initiation factor 3 (eIF3) plays a central role eukaryotes. These—eIF3d, eIF3e, eIF3f, eIF3h, eIF3j, eIF3k, in translation initiation and consists of five core (conserved) sub- eIF3l, and eIF3m—were designated “non-core” subunits (4). units present in both budding yeast and higher eukaryotes. Higher In contrast to the budding yeast, the genome of the fission eukaryotic eIF3 contains additional (noncore or nonconserved) yeast Schizosaccharomyces pombe contains structural homologs subunits of poorly defined function, including sub-unit h (eIF3h), of at least five noncore (nonconserved) eIF3 subunits—eIF3d, which in zebrafish is encoded by two distinct genes (eif3ha and eIF3e, eIF3f, eIF3h, and eIF3m. The gene encoding eIF3f is eif3hb). Previously we showed that eif3ha encodes the predominant essential for growth, whereas eIF3d, eIF3e, and eIF3h are dis- isoform during zebrafish embryogenesis and that depletion of this pensable for growth and viability (5–11). However, deleted factor causes defects in the development of the brain and eyes. To strains show specific phenotypes including defects in meiosis/ investigate the molecular mechanism governing this regulation, we sporulation (6, 9, 11).
    [Show full text]