• 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, 113127.
  • 2
    Roberts LO, Jopling CL, Jackson RJ & Willis AE (2009) Viral strategies to subvert the mammalian translation machinery. Prog Mol Biol Transl Sci 90, 313367.
  • 3
    Balvay L, Soto Rifo R, Ricci EP, Decimo D & Ohlmann T (2009) Structural and functional diversity of viral IRESes. Biochim Biophys Acta 1789, 542557.
  • 4
    Ohlmann T, Rau M, Pain VM & Morley SJ (1996) The C-terminal domain of eukaryotic protein synthesis initiation factor (eIF) 4G is sufficient to support cap-independent translation in the absence of eIF4E. EMBO J 15, 13711382.
  • 5
    Kolupaeva VG, Lomakin IB, Pestova TV & Hellen CU (2003) Eukaryotic initiation factors 4G and 4A mediate conformational changes downstream of the initiation codon of the encephalomyocarditis virus internal ribosomal entry site. Mol Cell Biol 23, 687698.
  • 6
    de Breyne S, Yu Y, Unbehaun A, Pestova TV & Hellen CU (2009) Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites. Proc Natl Acad Sci USA 106, 91979202.
  • 7
    Pestova TV, Shatsky IN, Fletcher SP, Jackson RJ & Hellen CU (1998) A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev 12, 6783.
  • 8
    Wilson JE, Pestova TV, Hellen CU & Sarnow P (2000) Initiation of protein synthesis from the A site of the ribosome. Cell 102, 511520.
  • 9
    Balvay L, Lopez Lastra M, Sargueil B, Darlix JL & Ohlmann T (2007) Translational control of retroviruses. Nat Rev Microbiol 5, 128140.
  • 10
    Miele G, Mouland A, Harrison GP, Cohen E & Lever AM (1996) The human immunodeficiency virus type 1 5′ packaging signal structure affects translation but does not function as an internal ribosome entry site structure. J Virol 70, 944951.
  • 11
    Buck CB, Shen X, Egan MA, Pierson TC, Walker CM & Siliciano RF (2001) The human immunodeficiency virus type 1 gag gene encodes an internal ribosome entry site. J Virol 75, 181191.
  • 12
    Brasey A, Lopez-Lastra M, Ohlmann T, Beerens N, Berkhout B, Darlix JL & Sonenberg N (2003) The leader of human immunodeficiency virus type 1 genomic RNA harbors an internal ribosome entry segment that is active during the G2/M phase of the cell cycle. J Virol 77, 39393949.
  • 13
    Ricci EP, Soto Rifo R, Herbreteau CH, Decimo D & Ohlmann T (2008) Lentiviral RNAs can use different mechanisms for translation initiation. Biochem Soc Trans 36, 690693.
  • 14
    Soto-Rifo R, Limousin T, Rubilar PS, Ricci EP, Decimo D, Moncorge O, Trabaud MA, Andre P, Cimarelli A & Ohlmann T (2012) Different effects of the TAR structure on HIV-1 and HIV-2 genomic RNA translation. Nucleic Acids Res 40, 26532667.
  • 15
    Berkhout B, Arts K & Abbink TE (2011) Ribosomal scanning on the 5′-untranslated region of the human immunodeficiency virus RNA genome. Nucleic Acids Res 39, 52325244.
  • 16
    Chamond N, Locker N & Sargueil B (2010) The different pathways of HIV genomic RNA translation. Biochem Soc Trans 38, 15481552.
  • 17
    Svitkin YV, Pause A & Sonenberg N (1994) La autoantigen alleviates translational repression by the 5′ leader sequence of the human immunodeficiency virus type 1 mRNA. J Virol 68, 70017007.
  • 18
    Bolinger C, Sharma A, Singh D, Yu L & Boris-Lawrie K (2010) RNA helicase A modulates translation of HIV-1 and infectivity of progeny virions. Nucleic Acids Res 38, 16861696.
  • 19
    Gummuluru S & Emerman M (1999) Cell cycle- and Vpr-mediated regulation of human immunodeficiency virus type 1 expression in primary and transformed T-cell lines. J Virol 73, 54225430.
  • 20
    Pyronnet S, Dostie J & Sonenberg N (2001) Suppression of cap-dependent translation in mitosis. Genes Dev 15, 20832093.
  • 21
    Vallejos M, Deforges J, Plank TD, Letelier A, Ramdohr P, Abraham CG, Valiente-Echeverria F, Kieft JS, Sargueil B & Lopez-Lastra M (2011) Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res 39, 61866200.
  • 22
    Herbreteau CH, Weill L, Decimo D, Prevot D, Darlix JL, Sargueil B & Ohlmann T (2005) HIV-2 genomic RNA contains a novel type of IRES located downstream of its initiation codon. Nat Struct Mol Biol 12, 10011007.
  • 23
    Camerini V, Decimo D, Balvay L, Pistello M, Bendinelli M, Darlix JL & Ohlmann T (2008) A dormant internal ribosome entry site controls translation of feline immunodeficiency virus. J Virol 82, 35743583.
  • 24
    Nicholson MG, Rue SM, Clements JE & Barber SA (2006) An internal ribosome entry site promotes translation of a novel SIV Pr55(Gag) isoform. Virology 349, 325334.
  • 25
    Weill L, James L, Ulryck N, Chamond N, Herbreteau CH, Ohlmann T & Sargueil B (2010) A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA. Nucleic Acids Res 38, 13671381.
  • 26
    Locker N, Chamond N & Sargueil B (2011) A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3. Nucleic Acids Res 39, 23672377.
  • 27
    Pestova TV & Kolupaeva VG (2002) The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev 16, 29062922.
  • 28
    Elfakess R, Sinvani H, Haimov O, Svitkin Y, Sonenberg N & Dikstein R (2011) Unique translation initiation of mRNAs-containing TISU element. Nucleic Acids Res 39, 75987609.
  • 29
    Soto Rifo R, Ricci EP, Decimo D, Moncorge O & Ohlmann T (2007) Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation. Nucleic Acids Res 35, e121. doi:10.1093/nar/gkm682.
  • 30
    Lamphear BJ, Kirchweger R, Skern T & Rhoads RE (1995) Mapping of functional domains in eukaryotic protein synthesis initiation factor 4G (eIF4G) with picornaviral proteases. Implications for cap-dependent and cap-independent translational initiation. J Biol Chem 270, 2197521983.
  • 31
    Ohlmann T, Rau M, Morley SJ & Pain VM (1995) Proteolytic cleavage of initiation factor eIF-4 gamma in the reticulocyte lysate inhibits translation of capped mRNAs but enhances that of uncapped mRNAs. Nucleic Acids Res 23, 334340.
  • 32
    Borman AM, Kirchweger R, Ziegler E, Rhoads RE, Skern T & Kean KM (1997) eIF4G and its proteolytic cleavage products: effect on initiation of protein synthesis from capped, uncapped, and IRES-containing mRNAs. RNA 3, 186196.
  • 33
    Parsyan A, Svitkin Y, Shahbazian D, Gkogkas C, Lasko P, Merrick WC & Sonenberg N (2011) mRNA helicases: the tacticians of translational control. Nat Rev Mol Cell Biol 12, 235245.
  • 34
    Paillart JC, Dettenhofer M, Yu XF, Ehresmann C, Ehresmann B & Marquet R (2004) First snapshots of the HIV-1 RNA structure in infected cells and in virions. J Biol Chem 279, 4839748403.
  • 35
    Damgaard CK, Andersen ES, Knudsen B, Gorodkin J & Kjems J (2004) RNA interactions in the 5′ region of the HIV-1 genome. J Mol Biol 336, 369379.
  • 36
    Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC & Weeks KM (2008) High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 6, e96.
  • 37
    Pause A, Methot N, Svitkin Y, Merrick WC & Sonenberg N (1994) Dominant negative mutants of mammalian translation initiation factor eIF-4A define a critical role for eIF-4F in cap-dependent and cap-independent initiation of translation. EMBO J 13, 12051215.
  • 38
    Bordeleau ME, Mori A, Oberer M, Lindqvist L, Chard LS, Higa T, Belsham GJ, Wagner G, Tanaka J & Pelletier J (2006) Functional characterization of IRESes by an inhibitor of the RNA helicase eIF4A. Nat Chem Biol 2, 213220.
  • 39
    Salminen MO, Koch C, Sanders-Buell E, Ehrenberg PK, Michael NL, Carr JK, Burke DS & McCutchan FE (1995) Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology 213, 8086.
  • 40
    Pestova TV, Hellen CU & Shatsky IN (1996) Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry. Mol Cell Biol 16, 68596869.
  • 41
    Paillart JC, Skripkin E, Ehresmann B, Ehresmann C & Marquet R (1996) A loop–loop ‘kissing’ complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc Natl Acad Sci USA 93, 55725577.
  • 42
    Lu K, Heng X, Garyu L, Monti S, Garcia EL, Kharytonchyk S, Dorjsuren B, Kulandaivel G, Jones S, Hiremath A et al. (2011) NMR detection of structures in the HIV-1 5′-leader RNA that regulate genome packaging. Science 334, 242245.
  • 43
    Andersen ES, Contera SA, Knudsen B, Damgaard CK, Besenbacher F & Kjems J (2004) Role of the trans-activation response element in dimerization of HIV-1 RNA. J Biol Chem 279, 2224322249.
  • 44
    Dasso MC, Milburn SC, Hershey JW & Jackson RJ (1990) Selection of the 5′-proximal translation initiation site is influenced by mRNA and eIF-2 concentrations. Eur J Biochem 187, 361371.
  • 45
    Ben-Asouli Y, Banai Y, Hauser H & Kaempfer R (2000) Recognition of 5′-terminal TAR structure in human immunodeficiency virus-1 mRNA by eukaryotic translation initiation factor 2. Nucleic Acids Res 28, 10111018.
  • 46
    Bannwarth S & Gatignol A (2005) HIV-1 TAR RNA: the target of molecular interactions between the virus and its host. Curr HIV Res 3, 6171.
  • 47
    Pisareva VP, Pisarev AV, Komar AA, Hellen CU & Pestova TV (2008) Translation initiation on mammalian mRNAs with structured 5′UTRs requires DExH-box protein DHX29. Cell, 135, 12371250.
  • 48
    Yu Y, Sweeney TR, Kafasla P, Jackson RJ, Pestova TV & Hellen CU (2011) The mechanism of translation initiation on Aichivirus RNA mediated by a novel type of picornavirus IRES. EMBO J 30, 44234436.
  • 49
    Yedavalli VS, Neuveut C, Chi YH, Kleiman L & Jeang KT (2004) Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function. Cell 119, 381392.
  • 50
    Lee CS, Dias AP, Jedrychowski M, Patel AH, Hsu JL & Reed R (2008) Human DDX3 functions in translation and interacts with the translation initiation factor eIF3. Nucleic Acids Res 36, 47084718.
  • 51
    Shih JW, Wang WT, Tsai TY, Kuo CY, Li HK & Wu Lee YH (2012) Critical roles of RNA helicase DDX3 and its interactions with eIF4E/PABP1 in stress granule assembly and stress response. Biochem J 441, 119129.
  • 52
    Jones CN, Wilkinson KA, Hung KT, Weeks KM & Spremulli LL (2008) Lack of secondary structure characterizes the 5′ ends of mammalian mitochondrial mRNAs. RNA 14, 862871.
  • 53
    Kozak M (1991) A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes. Gene Expr 1, 111115.
  • 54
    Elfakess R & Dikstein R (2008) A translation initiation element specific to mRNAs with very short 5′UTR that also regulates transcription. PLoS One 3, e3094.
  • 55
    Andreev DE, Terenin IM, Dunaevsky YE, Dmitriev SE & Shatsky IN (2006) A leaderless mRNA can bind to mammalian 80S ribosomes and direct polypeptide synthesis in the absence of translation initiation factors. Mol Cell Biol 26, 31643169.
  • 56
    Ventoso I, Blanco R, Perales C & Carrasco L (2001) HIV-1 protease cleaves eukaryotic initiation factor 4G and inhibits cap-dependent translation. Proc Natl Acad Sci USA 98, 1296612971.
  • 57
    Alvarez E, Castello A, Menendez-Arias L & Carrasco L (2006) HIV protease cleaves poly(A)-binding protein. Biochem J 396, 219226.
  • 58
    Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K et al. (2012) Global landscape of HIV–human protein complexes. Nature 481, 365370.
  • 59
    Lu K, Heng X & Summers MF (2011) Structural determinants and mechanism of HIV-1 genome packaging. J Mol Biol 410, 609633.
  • 60
    Strong CL, Lanchy JM, Dieng-Sarr A, Kanki PJ & Lodmell JS (2009) A 5′UTR-spliced mRNA isoform is specialized for enhanced HIV-2 gag translation. J Mol Biol 391, 426437.
  • 61
    Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW Jr, Swanstrom R, Burch CL & Weeks KM (2009) Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460, 711716.