Human-like eukaryotic translation initiation factor 3 from Neurospora crassa

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Smith, M Duane ^a   Gu, Yu ^a   Querol Audí, Jordi ^a,c   Vogan, Jacob M ^a   Nitido, Adam ^a   Cate, Jamie H D ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; INITIATION FACTOR 3; MESSENGER RNA; PROTEIN BINDING; PROTEIN SUBUNIT; START CODON;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; GENETIC ANALYSIS; NEUROSPORA CRASSA; NONHUMAN; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN SUBUNIT; START CODON; GENETICS; HELA CELL LINE; HUMAN; PROTEIN SYNTHESIS; RIBOSOME;

CODON, INITIATOR; EUKARYOTIC INITIATION FACTOR-3; HELA CELLS; HUMANS; NEUROSPORA CRASSA; PROTEIN BINDING; PROTEIN BIOSYNTHESIS; PROTEIN SUBUNITS; RIBOSOMES; RNA, MESSENGER;

EID: 84892563850     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078715     Document Type: Article

References (47)

1. Damoc E, Fraser CS, Zhou M, Videler H, Mayeur GL, et al. (2007) Structural characterization of the human eukaryotic initiation factor 3 protein complex by mass spectrometry. Molecular & Cellular Proteomics 6: 1135-1146.
2. Hinnebusch AG (2006) eIF3: a versatile scaffold for translation initiation complexes. Trends Biochem Sci 31: 553-562.
3. Hashem Y, des Georges A, Dhote V, Langlois R, Liao Hstau Y, et al. (2013) Structure of the Mammalian Ribosomal 43S Preinitiation Complex Bound to the Scanning Factor DHX29. Cell 153: 1108-1119.
4. Fraser CS, Doudna JA (2007) Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol 5: 29-38.
5. Lopez-Lastra M, Rivas A, Barria MI (2005) Protein synthesis in eukaryotes: the growing biological relevance of cap-independent translation initiation. Biological Research 38: 121-146.
6. Gilbert WV (2010) Alternative ways to think about cellular internal ribosome entry. The Journal of Biological Chemistry 285: 29033-29038.
7. Hershey JW (2010) Regulation of protein synthesis and the role of eIF3 in cancer. Brazilian Journal of Medical and Biological Research = Revista brasileira de pesquisas medicas e biologicas 43: 920-930.
8. Choudhuri A, Maitra U, Evans T (2013) Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis. Proceedings of the National Academy of Sciences of the United States of America 110: 9818-9823.
9. Curran SP, Ruvkun G (2007) Lifespan regulation by evolutionarily conserved genes essential for viability. PLoS Genetics 3: e56.
10. Desai C, Horvitz HR (1989) Caenorhabditis elegans mutants defective in the functioning of the motor neurons responsible for egg laying. Genetics 121: 703-721.
11. Querol-Audí J, Sun C, Vogan JM, Smith MD, Gu Y, et al. (2013) Architecture of Human Translation Initiation Factor 3. Structure 21: 920-928.
12. Sun C, Todorovic A, Querol-Audí J, Bai Y, Villa N, et al. (2011) Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3). Proceedings of the National Academy of Sciences of the United States of America 108: 20473-20478.
13. Siridechadilok B, Fraser CS, Hall RJ, Doudna JA, Nogales E (2005) Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310: 1513-1515.
14. George N. Bistis DDP, and Nick D Read (2003) Different cell types in Neurospora crassa. Fungal Genet Newsl 50: 17-19.
15. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, et al. (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiology and Molecular Biology Reviews 68: 1-108.
16. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
17. Atwood KC, Mukai F (1953) Indispensable Gene Functions in Neurospora. Proceedings of the National Academy of Sciences of the United States of America 39: 1027-1035.
18. McCluskey K (2003) The fungal genetics stock center: From molds to molecules. Advances in Applied Microbiology 52: 245-262.
19. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, et al. (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proceedings of the National Academy of Sciences of the United States of America 103: 10352-10357.
20. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
21. Lee DW, Seong KY, Pratt RJ, Baker K, Aramayo R (2004) Properties of unpaired DNA required for efficient silencing in Neurospora crassa. Genetics 167: 131-150.
22. Selker EU (1990) Premeiotic instability of repeated sequences in Neurospora crassa. Annual Review of Genetics 24: 579-613.
23. Phan L, Zhang XL, Asano K, Anderson J, Vornlocher HP, et al. (1998) Identification of a translation initiation factor 3 (eIF3) core complex, conserved in yeast and mammals, that interacts with eIF5. Molecular and Cellular Biology 18: 4935-4946.
24. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
25. Sha Z, Brill LM, Cabrera R, Kleifeld O, Scheliga JS, et al. (2009) The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries. Molecular Cell 36: 141-152.
26. Kim TH, Kim BH, Yahalom A, Chamovitz DA, von Arnim AG (2004) Translational regulation via 59 mRNA leader sequences revealed by mutational analysis of the Arabidopsis translation initiation factor subunit eIF3h. The Plant Cell 16: 3341-3356.
27. Kim BH, Cai X, Vaughn JN, von Arnim AG (2007) On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biology 8: R60.
28. Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, et al. (2010) The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. RNA 16: 748-761.
29. Ray A, Bandyopadhyay A, Matsumoto T, Deng H, Maitra U (2008) Fission yeast translation initiation factor 3 subunit eIF3h is not essential for global translation initiation, but deletion of eif3h + affects spore formation. Yeast 25: 809-823.
30. Masutani M, Sonenberg N, Yokoyama S, Imataka H (2007) Reconstitution reveals the functional core of mammalian eIF3. The EMBO Journal 26: 3373-3383.
31. Masutani M, Machida K, Kobayashi T, Yokoyama S, Imataka H (2013) Reconstitution of eukaryotic translation initiation factor 3 by co-expression of the subunits in a human cell-derived in vitro protein synthesis system. Protein Expression and Purification 87: 5-10.
32. Zhou C, Arslan F, Wee S, Krishnan S, Ivanov AR, et al. (2005) PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes. BMC biology 3: 14.
33. Asano K, Phan L, Anderson J, Hinnebusch AG (1998) Complex formation by all five homologues of mammalian translation initiation factor 3 subunits from yeast Saccharomyces cerevisiae. The Journal of Biological Chemistry 273: 18573-18585.
34. Verlhac MH, Chen RH, Hanachi P, Hershey JW, Derynck R (1997) Identification of partners of TIF34, a component of the yeast eIF3 complex, required for cell proliferation and translation initiation. The EMBO Journal 16: 6812-6822.
35. Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, et al. (2013) Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Nucleic Acids Research 41: 7512-7521.
36. Zhang L, Pan X, Hershey JW (2007) Individual overexpression of five subunits of human translation initiation factor eIF3 promotes malignant transformation of immortal fibroblast cells. The Journal of Biological Chemistry 282: 5790-5800.
37. Honda S, Selker EU (2009) Tools for fungal proteomics: multifunctional Neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182: 11-23.
38. Tian C, Beeson WT, Iavarone AT, Sun J, Marletta MA, et al. (2009) Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proceedings of the National Academy of Sciences of the United States of America 106: 22157-22162.
39. Suloway C, Pulokas J, Fellmann D, Cheng A, Guerra F, et al. (2005) Automated molecular microscopy: the new Leginon system. Journal of Structural Biology 151: 41-60.
40. Lander GC, Stagg SM, Voss NR, Cheng A, Fellmann D, et al. (2009) Appion: an integrated, database-driven pipeline to facilitate EM image processing. Journal of Structural Biology 166: 95-102.
41. Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B (2009) DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. Journal of Structural Biology 166: 205-213.
42. Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. Journal of Structural Biology 142: 334-347.
43. Ludtke SJ, Baldwin PR, Chiu W (1999) EMAN: semiautomated software for high-resolution single-particle reconstructions. Journal of Structural Biology 128: 82-97.
44. Scheres SH, Nunez-Ramirez R, Sorzano CO, Carazo JM, Marabini R (2008) Image processing for electron microscopy single-particle analysis using XMIPP. Nature Protocols 3: 977-990.
45. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the IMAGIC image processing system. Journal of Structural Biology 116: 17-24.
46. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research 36: W465-469.
47. Zhou M, Sandercock AM, Fraser CS, Ridlova G, Stephens E, et al. (2008) Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proceedings of the National Academy of Sciences of the United States of America 105: 18139-18144.