The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation
In eukaryotic cells protein synthesis initiation factor eIF4E controls mRNA selection by interacting with the mRNA 5’ cap. A family of binding proteins, termed the 4E-BPs, interact with eIF4E to hinder ribosome recruitment and repress translation of their target mRNAs. The yeast Saccharomyces cerevisiae has two 4E-BPs Caf20p and Eap1p that regulate distinct but overlapping sets of mRNAs. Here, we describe genome wide experiments to identify protein and RNA partners of each 4E-BP, with a greater focus on Caf20p. We present evidence that the 4E-BPs unexpectedly bind to ribosomes, an interaction that is not dependent on eIF4E binding. We also define a core set of over 500 Caf20p target mRNAs that fall into two classes with distinct features. One mRNA class, representing 25% of the targets, binds Caf20p independently of its eIF4E interaction and instead via a novel 3’ UTR interaction. Our data indicate that these proteins can repress mRNA-specific protein synthesis independently of their known role as eIF4E-binding proteins.
Vyšlo v časopise:
The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation. PLoS Genet 11(5): e32767. doi:10.1371/journal.pgen.1005233
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005233
Souhrn
In eukaryotic cells protein synthesis initiation factor eIF4E controls mRNA selection by interacting with the mRNA 5’ cap. A family of binding proteins, termed the 4E-BPs, interact with eIF4E to hinder ribosome recruitment and repress translation of their target mRNAs. The yeast Saccharomyces cerevisiae has two 4E-BPs Caf20p and Eap1p that regulate distinct but overlapping sets of mRNAs. Here, we describe genome wide experiments to identify protein and RNA partners of each 4E-BP, with a greater focus on Caf20p. We present evidence that the 4E-BPs unexpectedly bind to ribosomes, an interaction that is not dependent on eIF4E binding. We also define a core set of over 500 Caf20p target mRNAs that fall into two classes with distinct features. One mRNA class, representing 25% of the targets, binds Caf20p independently of its eIF4E interaction and instead via a novel 3’ UTR interaction. Our data indicate that these proteins can repress mRNA-specific protein synthesis independently of their known role as eIF4E-binding proteins.
Zdroje
1. Jackson RJ, Hellen CU, Pestova TV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11: 113–127. doi: 10.1038/nrm2838 20094052
2. Hinnebusch AG (2014) The scanning mechanism of eukaryotic translation initiation. Annu Rev Biochem 83: 779–812. doi: 10.1146/annurev-biochem-060713-035802 24499181
3. Sonenberg N, Hinnebusch AG (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136: 731–745. doi: 10.1016/j.cell.2009.01.042 19239892
4. Wek RC, Jiang HY, Anthony TG (2006) Coping with stress: eIF2 kinases and translational control. Biochem Soc Trans 34: 7–11. 16246168
5. Kapp LD, Lorsch JR (2004) The molecular mechanics of eukaryotic translation. Annu Rev Biochem 73: 657–704. 15189156
6. Valasek LS (2012) 'Ribozoomin'—translation initiation from the perspective of the ribosome-bound eukaryotic initiation factors (eIFs). Curr Protein Pept Sci 13: 305–330. 22708493
7. Jennings MD, Zhou Y, Mohammad-Qureshi SS, Bennett D, Pavitt GD (2013) eIF2B promotes eIF5 dissociation from eIF2*GDP to facilitate guanine nucleotide exchange for translation initiation. Genes Dev 27: 2696–2707. doi: 10.1101/gad.231514.113 24352424
8. Richter JD, Sonenberg N (2005) Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433: 477–480. 15690031
9. Gingras AC, Raught B, Sonenberg N (2001) Regulation of translation initiation by FRAP/mTOR. Genes Dev 15: 807–826. 11297505
10. Nakamura A, Sato K, Hanyu-Nakamura K (2004) Drosophila cup is an eIF4E binding protein that associates with Bruno and regulates oskar mRNA translation in oogenesis. Dev Cell 6: 69–78. 14723848
11. Nelson MR, Leidal AM, Smibert CA (2004) Drosophila Cup is an eIF4E-binding protein that functions in Smaug-mediated translational repression. EMBO J 23: 150–159. 14685270
12. Altmann M, Schmitz N, Berset C, Trachsel H (1997) A novel inhibitor of cap-dependent translation initiation in yeast: p20 competes with eIF4G for binding to eIF4E. EMBO J 16: 1114–1121. 9118949
13. Cosentino GP, Schmelzle T, Haghighat A, Helliwell SB, Hall MN, et al. (2000) Eap1p, a novel eukaryotic translation initiation factor 4E-associated protein in Saccharomyces cerevisiae. Mol Cell Biol 20: 4604–4613. 10848587
14. Ibrahimo S, Holmes LE, Ashe MP (2006) Regulation of translation initiation by the yeast eIF4E binding proteins is required for the pseudohyphal response. Yeast 23: 1075–1088. 17083129
15. Mascarenhas C, Edwards-Ingram LC, Zeef L, Shenton D, Ashe MP, et al. (2008) Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae. Mol Biol Cell 19: 2995–3007. doi: 10.1091/mbc.E07-11-1173 18417611
16. Buchan JR, Muhlrad D, Parker R (2008) P bodies promote stress granule assembly in Saccharomyces cerevisiae. J Cell Biol 183: 441–455. doi: 10.1083/jcb.200807043 18981231
17. Rendl LM, Bieman MA, Vari HK, Smibert CA (2012) The eIF4E-binding protein Eap1p functions in Vts1p-mediated transcript decay. PLoS One 7: e47121. doi: 10.1371/journal.pone.0047121 23071728
18. Blewett NH, Goldstrohm AC (2012) A eukaryotic translation initiation factor 4E-binding protein promotes mRNA decapping and is required for PUF repression. Mol Cell Biol 32: 4181–4194. 22890846
19. Cridge AG, Castelli LM, Smirnova JB, Selley JN, Rowe W, et al. (2010) Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins. Nucleic Acids Res 38: 8039–8050. doi: 10.1093/nar/gkq686 20705650
20. Costello JL, Castelli LM, Rowe W, Talavera D, Kershaw CJ, et al. (2014) Global mRNA selection mechanisms for translation initiation. Genome Biol accepted.
21. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737–741. 14562106
22. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631–636. 16429126
23. Rowe W, Kershaw CJ, Castelli LM, Costello JL, Ashe MP, et al. (2014) Puf3p induces translational repression of genes linked to oxidative stress. Nucleic Acids Res 42: 1026–1041. doi: 10.1093/nar/gkt948 24163252
24. LaCava J, Chandramouli N, Jiang H, Rout MP (2013) Improved native isolation of endogenous Protein A-tagged protein complexes. Biotechniques 54: 213–216. doi: 10.2144/000114012 23581468
25. Ka M, Park YU, Kim J (2008) The DEAD-box RNA helicase, Dhh1, functions in mating by regulating Ste12 translation in Saccharomyces cerevisiae. Biochem Biophys Res Commun 367: 680–686. doi: 10.1016/j.bbrc.2007.12.169 18182159
26. Park YU, Hur H, Ka M, Kim J (2006) Identification of translational regulation target genes during filamentous growth in Saccharomyces cerevisiae: regulatory role of Caf20 and Dhh1. Eukaryot Cell 5: 2120–2127. 17041186
27. Sobel SG, Wolin SL (1999) Two yeast La motif-containing proteins are RNA-binding proteins that associate with polyribosomes. Mol Biol Cell 10: 3849–3862. 10564276
28. Kershaw CJ, Castelli LM, Costello JL, Talavera D, Rowe W, et al. (2014) The yeast La Related Protein Slf1p is a Key Activator of Translation During the Oxidative Stress Response. PLOS Genetics in press.
29. Rajyaguru P, She M, Parker R (2012) Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol Cell 45: 244–254. doi: 10.1016/j.molcel.2011.11.026 22284680
30. Duncan CD, Mata J (2011) Widespread cotranslational formation of protein complexes. PLoS Genet 7: e1002398. doi: 10.1371/journal.pgen.1002398 22144913
31. Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, et al. (2012) PaxDb, a database of protein abundance averages across all three domains of life. Mol Cell Proteomics 11: 492–500. doi: 10.1074/mcp.O111.014704 22535208
32. Danaie P, Altmann M, Hall MN, Trachsel H, Helliwell SB (1999) CLN3 expression is sufficient to restore G1-to-S-phase progression in Saccharomyces cerevisiae mutants defective in translation initiation factor eIF4E. Biochem J 340 (Pt 1): 135–141. 10229668
33. Polymenis M, Schmidt EV (1997) Coupling of cell division to cell growth by translational control of the G1 cyclin CLN3 in yeast. Genes Dev 11: 2522–2531. 9334317
34. Flick K, Wittenberg C (2005) Multiple pathways for suppression of mutants affecting G1-specific transcription in Saccharomyces cerevisiae. Genetics 169: 37–49. 15677747
35. Chial HJ, Stemm-Wolf AJ, McBratney S, Winey M (2000) Yeast Eap1p, an eIF4E-associated protein, has a separate function involving genetic stability. Curr Biol 10: 1519–1522. 11114520
36. Sezen B, Seedorf M, Schiebel E (2009) The SESA network links duplication of the yeast centrosome with the protein translation machinery. Genes Dev 23: 1559–1570. doi: 10.1101/gad.524209 19571182
37. Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP (2014) Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508: 66–71. doi: 10.1038/nature13007 24476825
38. Munchel SE, Shultzaberger RK, Takizawa N, Weis K (2011) Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay. Mol Biol Cell 22: 2787–2795. doi: 10.1091/mbc.E11-01-0028 21680716
39. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889–3894. 12660367
40. Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, et al. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467: 103–107. doi: 10.1038/nature09322 20811459
41. O'Leary SE, Petrov A, Chen J, Puglisi JD (2013) Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure 21: 2197–2207. doi: 10.1016/j.str.2013.09.016 24183571
42. Cawley A, Warwicker J (2012) eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions. Nucleic Acids Res 40: 7666–7675. doi: 10.1093/nar/gks511 22718971
43. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208. doi: 10.1093/nar/gkp335 19458158
44. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol 6: e255. doi: 10.1371/journal.pbio.0060255 18959479
45. Castelli LM, Lui J, Campbell SG, Rowe W, Zeef LA, et al. (2011) Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated. Mol Biol Cell 22: 3379–3393. doi: 10.1091/mbc.E11-02-0153 21795399
46. Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, et al. (2004) A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21: 947–962. 15334558
47. Chu D, Kazana E, Bellanger N, Singh T, Tuite MF, et al. (2014) Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J 33: 21–34. doi: 10.1002/embj.201385651 24357599
48. Ptushkina M, von der Haar T, Vasilescu S, Frank R, Birkenhager R, et al. (1998) Cooperative modulation by eIF4G of eIF4E-binding to the mRNA 5' cap in yeast involves a site partially shared by p20. EMBO J 17: 4798–4808. 9707439
49. Amrani N, Ghosh S, Mangus DA, Jacobson A (2008) Translation factors promote the formation of two states of the closed-loop mRNP. Nature 453: 1276–1280. doi: 10.1038/nature06974 18496529
50. Amberg DC, Burke DJ, Strathern JN (2005) Methods in Yeast Genetics. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. 230 p.
51. Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, et al. (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32: 223–226. doi: 10.1038/nbt.2839 24727771
52. Taylor EJ, Campbell SG, Griffiths CD, Reid PJ, Slaven JW, et al. (2010) Fusel alcohols regulate translation initiation by inhibiting eIF2B to reduce ternary complex in a mechanism that may involve altering the integrity and dynamics of the eIF2B body. Mol Biol Cell 21: 2202–2216. doi: 10.1091/mbc.E09-11-0962 20444979
53. Trotter EW, Rand JD, Vickerstaff J, Grant CM (2008) The yeast Tsa1 peroxiredoxin is a ribosome-associated antioxidant. Biochem J 412: 73–80. doi: 10.1042/BJ20071634 18271751
54. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140. doi: 10.1093/bioinformatics/btp616 19910308
55. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44–57. doi: 10.1038/nprot.2008.211 19131956
56. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57: 289–300.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2015 Číslo 5
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Drosophila Spaghetti and Doubletime Link the Circadian Clock and Light to Caspases, Apoptosis and Tauopathy
- Autoselection of Cytoplasmic Yeast Virus Like Elements Encoding Toxin/Antitoxin Systems Involves a Nuclear Barrier for Immunity Gene Expression
- Parp3 Negatively Regulates Immunoglobulin Class Switch Recombination
- PERK Limits Lifespan by Promoting Intestinal Stem Cell Proliferation in Response to ER Stress