Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

“Even for those studies concluding that inhibition occurs at the level of translation initiation, the data are conflicting as in some studies translation inhibition was cap dependent and mediated by eIF4F, whereas in others it was cap independent and mediated via eIF6 (Filipowicz et al., 2008).”

“It is noteworthy that recent large-scale studies in cells demonstrated that the magnitude of translation inhibition of most mRNAs is moderate (~2-fold) (Baek et al., 2008; Selbach et al., 2008), and that similar results were obtained in cell-free translation extracts.”

“Surprisingly, it was reported recently that miRNAs can also stimulate rather than inhibit translation when cells enter quiescence (Vasudevan et al., 2007).”

“Once processed from its primary transcript precursor, an miRNA is then loaded into a protein complex, referred to as an RNA-induced silencing complex (RISC), which targets and inhibits protein expression from specific mRNAs (Hammond et al., 2001; Hutvagner and Zamore, 2002; Martinez et al., 2002).”

“The stunning progress on crystal structures of bacterial 70S ribosomes bound to mRNAs and tRNAs (Selmer et al., 2006; Yusupova et al., 2006) has provided atomic details of the path of mRNA and contacts made with tRNAs in the decoding sites.”

“These mechanisms might be similar to those by which Dhh1/Pat1 repress general translation in yeast during carbon starvation (Parker and Sheth, 2007).”

“It is noteworthy that some studies demonstrated the association of P-bodies and stress granules and suggested the possibility of exchange of material between P-bodies and stress granules (Anderson and Kedersha, 2008).”

“Studies in the nematode Caenorhabditis elegans demonstrated that inhibition of several components of the eIF4F complex including eIF4E and eIF4G or lowering their levels extends life span (Pan et al., 2007; Syntichaki et al., 2007; Curran and Ruvkun, 2007; Hansen et al., 2007; Henderson et al., 2006).”

“Phosphorylation of Pdcd4 leads to its ubiquitination and degradation by the proteasome (Dorrello et al., 2006).”

“ZBP1 blocks 60S joining to the 43S PIC (Huttelmaier et al., 2005).”

“The precedents for coordinate regulation of classes of mRNAs at the translational level have already been documented in yeast via Puf RNA-binding proteins (Gerber et al., 2004) and in mammalian systems where the coordinately expressed mRNAs were called “RNA operons” (reviewed in Keene, 2007).”

“Although several conflicting models have been proposed to explain the mechanism of translational repression by FMRP (reviewed in Klann and Richter, 2007), it was recently reported that FMRP binds to eIF4E via CYFIP1 (cytoplasmic FMRP interacting protein 1), thus displacing eIF4G and consequently inhibiting translation…”

“ATF4 suppresses memory because it inhibits the transcription factor CREB (cyclic AMP response element binding protein)-mediated gene expression, which is critical for long-term synaptic plasticity and memory (Barco et al., 2002).”

“In contrast to the disparate results obtained from studies in cells, in vitro experiments in cell-free translation extracts prepared from mammalian or Drosophila embryos all indicated that miRNAs suppress cap-dependent but not IRES-mediated translation (Mathonnet et al., 2007; Thermann and Hentze, 2007; Wakiyama et al…”

“Another study generated compounds that inhibit the eIF4E-eIF4G interaction and retard the growth of tumor cells (Moerke et al., 2007).”

“The 4E-BPs compete with eIF4G for a shared binding site on eIF4E (Marcotrigiano et al., 1999).”

“Studies in the nematode Caenorhabditis elegans demonstrated that inhibition of several components of the eIF4F complex including eIF4E and eIF4G or lowering their levels extends life span (Pan et al., 2007; Syntichaki et al., 2007; Curran and Ruvkun, 2007; Hansen et al., 2007; Henderson et al., 2006).”

“S6Ks also phosphorylate Pdcd4, which is a tumor suppressor that binds and suppresses eIF4A activity (Yang et al., 2003).”

“PABP also stimulates 60S subunit joining (Kahvejian et al., 2005), and findings from yeast suggest that the poly(A) tail is required to block the inhibitory effects of two RNA helicases on subunit joining factor eIF5B (Searfoss et al.”

“Studies in the nematode Caenorhabditis elegans demonstrated that inhibition of several components of the eIF4F complex including eIF4E and eIF4G or lowering their levels extends life span (Pan et al., 2007; Syntichaki et al., 2007; Curran and Ruvkun, 2007; Hansen et al., 2007; Henderson et al., 2006).”

“In the same vein, Barna et al. (2008) showed that activation of the Myc oncogene causes an increase in cap-dependent translation at the expense of IRES-dependent translation, and thus a reduction in Cdk11 levels, resulting in tumorigenesis.”

“This could be explained by augmented synaptic plasticity, as evidenced by a lower threshold of stimulation to achieve lasting LTP (Costa-Mattioli et al., 2005).”

“The foregoing mechanism is similar to that suggested originally from studies in Xenopus oocytes for the inhibition of translation by CPEB through Maskin, which binds to eIF4E (Stebbins-Boaz et al., 1999) (Figure 4A).”

“Likewise, antisense oligonucleotides to eIF4E inhibit tumor growth in mice while not causing any deleterious effects (Graff et al., 2007).”

“This model reveals strong similarities to 70S ribosomes, including the inter-subunit space containing the mRNA binding cleft and decoding sites (Spahn et al., 2004).”

“, 2007) and for eIF4E bound to a segment of eIF4G, which increases eIF4E’s affinity for the cap (Gross et al., 2003).”

“, 2004) and to oskar mRNA by Bruno (Chekulaeva et al., 2006; Nakamura et al., 2004).”

“Translational repression of oskar and nanos mRNA outside the posterior pole of the embryo is essential to buttress the targeting of the morphogens they encode, as the localization mechanisms for these mRNAs are inefficient (Bergsten and Gavis, 1999; Zimyanin et al., 2008).”

“In contrast to the disparate results obtained from studies in cells, in vitro experiments in cell-free translation extracts prepared from mammalian or Drosophila embryos all indicated that miRNAs suppress cap-dependent but not IRES-mediated translation (Mathonnet et al., 2007; Thermann and Hentze, 2007; Wakiyama et al…”

“It appears that eIF1 promotes scanning when nonAUG codons occupy the P-site by stabilizing an open conformation of the mRNA binding cleft of the 40S subunit, possibly by modulating the conformation of the “latch” to the mRNA entry channel (Passmore et al., 2007) (Figures 2A and 2B).”

“A switch from cap-dependent to cap-independent mRNA translation is mediated by hypoxia in large advanced breast cancers and is required for promoting angiogenesis and tumor survival and progression (Braunstein et al., 2007).”

“Studies in the nematode Caenorhabditis elegans demonstrated that inhibition of several components of the eIF4F complex including eIF4E and eIF4G or lowering their levels extends life span (Pan et al., 2007; Syntichaki et al., 2007; Curran and Ruvkun, 2007; Hansen et al., 2007; Henderson et al., 2006).”

“Recently, singlemolecule experiments were used to study the kinetics of ribosome movement on the mRNA during translation (Wen et al., 2008).”

“A cryo-EM model of the eIF3eIF4G-40S complex places eIF4G near the mRNA exit channel on the solvent side of the 40S subunit (Siridechadilok et al., 2005).”

“These results were interpreted to mean that the excessive translation could be deleterious to the synaptic plasticity required for learning and memory (Banko et al., 2005).”

“Bicoid represses the translation of caudal mRNA at the anterior of the embryo, where it is present, by binding simultaneously to the 3′UTR of caudal mRNA and to an eIF4E-related protein (d4E-HP) at the 5′ end of the mRNA (Figure 4A) (Cho et al., 2005).”

“Sampath et al. (2008) demonstrated a striking increase in ribosome recruitment to mRNA during the differentiation of ESCs into embryoid bodies.”

“, 2004), or recruiting the CCR4 deadenylase complex to specific target mRNAs (Chicoine et al., 2007; Kadyrova et al., 2007; Semotok et al., 2005; Zaessinger et al., 2006), also contribute importantly to embryonic patterning and development.”

“Cup, an eIF4E-binding protein, is recruited to nanos mRNA by Smaug (Nelson et al., 2004) and to oskar mRNA by Bruno (Chekulaeva et al.”

“A Ser209Ala mutant of eIF4E is unable to transform NIH 3T3 cultured cells (Topisirovic et al., 2004). Furthermore, Wendel et al. (2007) demonstrated that Ser209 is required for eIF4E’s oncogenic activity in a mouse model of B cell lymphoma.”

“The stunning progress on crystal structures of bacterial 70S ribosomes bound to mRNAs and tRNAs (Selmer et al., 2006; Yusupova et al., 2006) has provided atomic details of the path of mRNA and contacts made with tRNAs in the decoding sites.”

“These “gate-keeper” functions are neutralized at the AUG codon when eIF1 dissociates from its location near the P-site (Algire et al., 2005; Maag et al., 2005).”

“Binding to eIF4G helps to hold the two lobes of eIF4A together and align the DEAD-box motifs in the orientation required for ATP-dependent helicase activity (Schutz et al., 2008).”

“An intriguing new structural model envisions that eIF4G could interact with mRNA sequences both upstream and downstream of the nucleotides located in the decoding sites and could position eIF4A at the mRNA entry channel for its presumed role in unwinding secondary structure in advance of the scanning PIC (Marintchev e…”

“The factor eIF6 binds to 60S subunits and could thereby regulate ribosomal subunit joining, but evidence for a role in general translation initiation in vivo was obtained only recently (Gandin et al., 2008).”

“Interestingly, eIF3 was implicated in dissociation of 60S subunits from posttermination ribosomes following polypeptide termination, when ribosome recycling was reconstituted in vitro (Pisarev et al., 2007).”

“, 2004), or recruiting the CCR4 deadenylase complex to specific target mRNAs (Chicoine et al., 2007; Kadyrova et al., 2007; Semotok et al., 2005; Zaessinger et al., 2006), also contribute importantly to embryonic patterning and development.”

“Stimulation of eIF4F assembly is caused in part by the activation of the PI3K/Akt/mTOR pathway, which results in phosphorylation of 4E-BPs through different mechanisms (Buchkovich et al., 2008).”

“Interestingly, it is seen that domain IV of IF2 interacts with the accepter end of Met-tRNAi, explaining how IF2 stabilizes fMet-tRNAi binding until the 50S subunit joins (Simonetti et al., 2008).”

“The transforming activity of eIF4E can be explained by its ability to promote translation of a subset of mRNAs encoding proteins involved in regulating growth, proliferation, and apoptosis, most likely in a combinatorial fashion (Larsson et al., 2007; Mamane et al., 2007).”

“Indeed, UV crosslinking of substituted mRNAs in reconstituted mammalian 48S PICs revealed many similarities with the mRNA path in bacterial 70S complexes (Pisarev et al., 2008).”

“The tumor suppressor 14-3-3σ inhibits cap-dependent translation during mitosis through its binding to several initiation factors, which is expected to result in elevated IRES-dependent translation (Wilker et al., 2007).”

“This IRES uses different pseudoknot domains to contact 40S and 60S components and occupy the decoding center, placing the GCU triplet in the A-site (Schuler et al., 2006) where translation begins after a “pseudotranslocation” event moves the alanyltRNA decoding the GCU triplet into the P-site (Doudna and Sarnow, 2007;…”

“These “gate-keeper” functions are neutralized at the AUG codon when eIF1 dissociates from its location near the P-site (Algire et al., 2005; Maag et al., 2005).”

“, 2004), or recruiting the CCR4 deadenylase complex to specific target mRNAs (Chicoine et al., 2007; Kadyrova et al., 2007; Semotok et al., 2005; Zaessinger et al., 2006), also contribute importantly to embryonic patterning and development.”

“Surprisingly, this last interaction also stimulates initiation complex (IC) formation in vitro independently of a prior termination event (Amrani et al., 2008).”

“The IRESs of hepatitis C virus (HCV) dispense with eIF4F entirely, binding directly to the 40S, and require only eIF3 and either eIF2/eIF5 or eIF5B to pair tRNAi with the IRES start codon and produce a 48S PIC competent for subunit joining (Pestova et al., 2008; Terenin et al., 2008).”

“In early oogenesis when Maskin is absent, a different mechanism operates to silence the translation of maternal mRNAs in which CPEB binds to eIF4E1b (a homolog of eIF4E) through 4E-T (4E-transporter) (Figure 4A) (Minshall et al., 2007).”

“Inhibition of cap-dependent translation in vitro causes an increase in IRES-dependent translation (Svitkin et al., 2005).”

“, UUG) start codons by allowing premature eIF1 dissociation (Cheung et al., 2007), whereas overexpressing eIF1 suppresses UUG initiation in relaxed-fidelity (Sui−) yeast mutants.”

“Remarkably, the IRES domain that occupies the P-site mimics precisely the anticodon stem loop of tRNAi and an AUG start codon (Costantino et al., 2008) (Figure 3B).”

“Stalling at the stop codon of the uORF controlling translation of yeast CPA1 (encoding an arginine biosynthetic enzyme) is dependent on arginine and, interestingly, the stalled ribosome activates nonsense-mediated decay to also reduce CPA1 mRNA levels (Gaba et al., 2005).”

“Vasa (Vas) is a DEAD-box helicase that localizes during oogenesis to the posterior and that binds to eIF5B (Carrera et al., 2000).”

“, 2004) and is targeted by the protein TAV (transactivator/viroplasmin) that enables efficient reinitiation on polycistronic mRNAs of cauliflower mosaic virus (Park et al., 2001).”

“The transforming activity of eIF4E can be explained by its ability to promote translation of a subset of mRNAs encoding proteins involved in regulating growth, proliferation, and apoptosis, most likely in a combinatorial fashion (Larsson et al., 2007; Mamane et al., 2007).”

“Similarly, d4E-HP binds to a protein complex containing Nanos at the 3′UTR of hunchback mRNA to inhibit its translation at the posterior (Cho et al., 2006).”

“Domain II is also crucial for eIF5-dependent GTP hydrolysis by TC (in the eIF2-dependent mode of initiation) and subunit joining (Doudna and Sarnow, 2007; Locker et al., 2007; Pestova et al., 2008), suggesting that it also facilitates the conformational change(s) elicited by perfect codon-anticodon pairing in the cano…”

“In vas null oocytes, grk translation is greatly reduced, an effect also observed in oocytes that express only a form of Vas (VasΔ617) that is specifically compromised for eIF5B binding (Johnstone and Lasko, 2004).”

“Studies in the nematode Caenorhabditis elegans demonstrated that inhibition of several components of the eIF4F complex including eIF4E and eIF4G or lowering their levels extends life span (Pan et al., 2007; Syntichaki et al., 2007; Curran and Ruvkun, 2007; Hansen et al., 2007; Henderson et al., 2006).”

“Domain II is also crucial for eIF5-dependent GTP hydrolysis by TC (in the eIF2-dependent mode of initiation) and subunit joining (Doudna and Sarnow, 2007; Locker et al., 2007; Pestova et al., 2008), suggesting that it also facilitates the conformational change(s) elicited by perfect codon-anticodon pairing in the cano…”

“Screening natural compound libraries yielded potent inhibitors of eIF4A (Bordeleau et al., 2006; Pelletier and Peltz, 2007).”

“Recently, Fox and colleagues (Mukhopadhyay et al., 2008) showed that the zipper-interacting protein kinase (ZIPK) phosphorylates L13a on a single site and, in turn, is activated by phosphorylation of a second IFNγ-induced kinase, death-associated protein kinase-1.”

“There is now evidence that the 5′ enhancer sequences interact with the eIF3a-NTD (N-terminal domain), presumably as they emerge from the mRNA exit pore, to promote retention of post-termination 40S subunits on the mRNA (Szamecz et al., 2008).”

“Moreover, IF1 inhibits subunit joining to the 30S IC when these mRNA signals are absent (Milon et al., 2008), reminiscent of the role played by the eIF1A in blocking non-AUG selection during scanning.”

“Interestingly, the j-subunit of eIF3 can bind near the A-site and mRNA entry channel of the 40S subunit and impede mRNA binding in the absence of TC, presumably to ensure that TC loading precedes 40S binding to mRNA (Fraser et al., 2007).”

“Its C-terminal region promotes continued scanning at non-AUG codons, whereas its N-terminal extension acts in the opposite way to arrest scanning and promote eIF1 release at AUG codons (Fekete et al., 2007) (Figure 2A).”

“, 2006) where translation begins after a “pseudotranslocation” event moves the alanyltRNA decoding the GCU triplet into the P-site (Doudna and Sarnow, 2007; Jan et al., 2003).”

“cognate elongator tRNAs at the expense of Met-tRNAi (Antoun et al., 2006).”

“IF3 and eIF1 can even substitute for one another in vitro, suggesting that they elicit similar conformational changes in the PIC according to codon-anticodon pairing in the P-site (Lomakin et al., 2006).”

“Remarkably, only a small portion of one subunit (ε) of eIF2B is sufficient for GEF function (Gomez et al., 2002), and three of the remaining subunits provide a binding site for phosphorylated eIF2α that inhibits GEF function (Hinnebusch et al.”

“Dosage compensation is eliminated in females by translational repression of MSL-2 mRNA by Sex-lethal (SXL) protein, expressed only in females, by a combination of two mechanisms: SXL binds to the 3′UTR of the msl-2 mRNA together with the RNA-binding protein, UNR, and inhibits recruitment of the 43S PIC to the mRNA, wh…”

“Finally, Vaccinia virus promotes eIF4F assembly and also recruits initiation factors to cytoplasmic replication compartments, effectively increasing their local concentration (Katsafanas and Moss, 2007; Walsh et al., 2008).”

“Interaction of eIF5B with the extreme C terminus of eIF1A stimulates both subunit joining and the GTP hydrolysis that triggers eIF5B release from the initiation complex (Acker et al., 2006; Shin et al., 2002).”

“eIF3 also stimulates reinitiation after translation of a long uORF in a polycistronic mRNA of feline calicivirus (FCV) by binding to a sequence at the 3′ end of the uORF (Poyry et al., 2007).”

“In addition, viral gene products, such as the ICP6 of Herpes simplex virus, which binds to eIF4G, enhance eIF4F assembly (Walsh and Mohr, 2006).”

“This is important for acute virus replication in quiescent cells and is also observed upon reactivation of latent infections (Arias et al., 2009).”

“, 2007), and sequences capable of Shine-Delgarno-like pairing with rRNA (Dresios et al., 2006).”

“Activation of grk mRNA translation at the anterodorsal cortex of the developing oocyte is mediated by poly(A) binding protein 55D (PABP55D) in association with the large cytoplasmic protein Encore (Clouse et al., 2008).”

“For the uORF that inhibits translation of the cytomegalovirus UL4 gene, the uORF-encoded peptidyl-tRNA interacts with release factor eRF1 to block polypeptide hydrolysis and stall the ribosome at the stop codon (Janzen et al., 2002).”

“Its interaction with eIF1A helps to recruit eIF5B to the 48S PIC for subunit joining while eIF5B, in turn, promotes release of eIF1A from the 80S initiation complex to open up the A-site for the first aminoacyl-tRNA (Fringer et al., 2007).”

“Aging is associated with decreased protein synthesis (Norsgaard et al., 1996).”

“Moreover, there is genetic evidence that certain rRNA contacts with the P-site tRNA in 70S complexes are functionally conserved in eukaryotic PICs (Dong et al., 2008).”