Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 11, 2012, Pages

  Ren, Qian ^a   Wang, Qing S ^a   Firth, Andrew E ^b   Chan, Mandy M Y ^a   Gouw, Joost W ^a   Guarna, M Marta ^a   Foster, Leonard J ^a   Atkins, John F ^c,d   Jan, Eric ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY COLLEGE CORK   (Ireland)

^d UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Frameshifting; Genetic recoding; Israeli acute paralysis virus; Protein synthesis; Pseudoknot

Indexed keywords

METHIONINE; TRANSFER RNA; VIRUS PROTEIN;

ARTICLE; BASE PAIRING; DICISTROVIRIDAE; HONEYBEE; INTERNAL RIBOSOME ENTRY SITE; MASS SPECTROMETRY; MUTAGENESIS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; RIBOSOME; TRANSLATION INITIATION; VIRUS GENOME;

ANIMALS; BASE PAIRING; BASE SEQUENCE; BEES; DICISTROVIRIDAE; DNA, COMPLEMENTARY; DNA, INTERGENIC; EUKARYOTIC INITIATION FACTOR-2; EUKARYOTIC INITIATION FACTOR-4F; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PUPA; READING FRAMES; RIBOSOMES; RNA, TRANSFER; SELECTION, GENETIC;

ACUTE BEE PARALYSIS VIRUS; APIS MELLIFERA;

EID: 84863230270     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1111303109     Document Type: Article

References (35)

1. Bonning BC, Miller WA (2010) Dicistroviruses. Annu Rev Entomol 55:129-150.
2. Wilson JE, Powell MJ, Hoover SE, Sarnow P (2000) Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 20:4990-4999. (Pubitemid 30431553)
3. Cox-Foster DL, et al. (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:283-287. (Pubitemid 47574857)
4. Jan E, Kinzy TG, Sarnow P (2003) Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis. Proc Natl Acad Sci USA 100:15410-15415. (Pubitemid 38021003)
5. Jan E, Sarnow P (2002) Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J Mol Biol 324:889-902. (Pubitemid 41782981)
6. Pestova TV, Hellen CU (2003) Translation elongation after assembly of ribosomes on the cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev 17:181-186. (Pubitemid 36105891)
7. Sasaki J, Nakashima N (1999) Translation initiation at the CUU codon is mediated by the internal ribosome entry site of an insect picorna-like virus in vitro. J Virol 73:1219-1226. (Pubitemid 29036774)
8. Sasaki J, Nakashima N (2000) Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proc Natl Acad Sci USA 97:1512-1515. (Pubitemid 30118472)
9. Wilson JE, Pestova TV, Hellen CU, Sarnow P (2000) Initiation of protein synthesis from the A site of the ribosome. Cell 102:511-520.
10. Nishiyama T, et al. (2003) Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res 31:2434-2442. (Pubitemid 37442112)
11. Pfingsten JS, Costantino DA, Kieft JS (2006) Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science 314:1450-1454. (Pubitemid 44871950)
12. Pfingsten JS, Costantino DA, Kieft JS (2007) Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes. J Mol Biol 370:856-869. (Pubitemid 46899063)
13. Schuler M, et al. (2006) Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat Struct Mol Biol 13:1092-1096. (Pubitemid 44885919)
14. Zhu J, et al. (2011) Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Proc Natl Acad Sci USA 108:1839-1844.
15. Garrey JL, Lee YY, Au HH, Bushell M, Jan E (2010) Host and viral translational mechanisms during cricket paralysis virus infection. J Virol 84:1124-1138.
16. Jan E (2006) Divergent IRES elements in invertebrates. Virus Res 119:16-28.
17. Nakashima N, Uchiumi T (2009) Functional analysis of structural motifs in dicistroviruses. Virus Res 139:137-147.
18. Jang CJ, Lo MC, Jan E (2009) Conserved element of the dicistrovirus IGR IRES that mimics an E-site tRNA/ribosome interaction mediates multiple functions. J Mol Biol 387:42-58.
19. Hertz MI, Thompson SR (2011) In vivo functional analysis of the Dicistroviridae intergenic region internal ribosome entry sites. Nucleic Acids Res 39:7276-7288.
20. Jang CJ, Jan E (2010) Modular domains of the Dicistroviridae intergenic internal ribosome entry site. RNA 16:1182-1195.
21. Cevallos RC, Sarnow P (2005) Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J Virol 79:677-683. (Pubitemid 40053850)
22. Hatakeyama Y, Shibuya N, Nishiyama T, Nakashima N (2004) Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts. RNA 10:779-786. (Pubitemid 38529741)
23. Firth AE, Wang QS, Jan E, Atkins JF (2009) Bioinformatic evidence for a stem-loop structure 5′-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses. Virol J 6:193-200.
24. Sabath N, Price N, Graur D (2009) A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. Virol J 6:144-150.
25. Shibuya N, Nishiyama T, Kanamori Y, Saito H, Nakashima N (2003) Conditional rather than absolute requirements of the capsid coding sequence for initiation of methionine- independent translation in Plautia stali intestine virus. J Virol 77:12002-12010. (Pubitemid 37339854)
26. Vattem KM, Wek RC (2004) Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc Natl Acad Sci USA 101:11269-11274. (Pubitemid 39038336)
27. Maori E, et al. (2007) Isolation and characterization of Israeli acute paralysis virus, a dicistrovirus affecting honeybees in Israel: Evidence for diversity due to intraand inter-species recombination. J Gen Virol 88:3428-3438. (Pubitemid 350201854)
28. Agirre J, et al. (2011) Capsid protein identification and analysis of mature Triatoma virus (TrV) virions and naturally occurring empty particles. Virology 409:91-101.
29. Fernandez J, Yaman I, Sarnow P, Snider MD, Hatzoglou M (2002) Regulation of internal ribosomal entry site-mediated translation by phosphorylation of the translation initiation factor eIF2alpha. J Biol Chem 277:19198-19205. (Pubitemid 34952487)
30. Cencic R, et al. (2011) Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F. Proc Natl Acad Sci USA 108:1046-1051.
31. Robert F, et al. (2006) Initiation of protein synthesis by hepatitis C virus is refractory to reduced eIF2 GTP.Met-tRNA(i)(Met) ternary complex availability. Mol Biol Cell 17:4632-4644. (Pubitemid 44665734)
32. Costantino DA, Pfingsten JS, Rambo RP, Kieft JS (2008) tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol 15:57-64.
33. Atkins JF, Bjork GR (2009) A gripping tale of ribosomal frameshifting: Extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev 73:178-210.
34. Moore NF, Kearns A, Pullin JSK (1980) Characterization of cricket paralysis virus-induced polypeptides in Drosophila cells. J Virology 33:1-9. (Pubitemid 10157269)
35. Chan QW, Howes CG, Foster LJ (2006) Quantitative comparison of caste differences in honeybee hemolymph. Mol Cell Proteomics 5:2252-2262. (Pubitemid 46043025)