Genetic analysis of translation initiation in bacteria: An initiator tRNA-centric view

Translation of messenger RNA (mRNA) in bacteria occurs in the steps of initiation, elongation, termination, and ribosome recycling. The initiation step comprises multiple stages and uses a special transfer RNA (tRNA) called initiator tRNA (i-tRNA), which is first aminoacylated and then formylated using methionine and N10 -formyl-tetrahydrofolate (N10 -fTHF), respectively. Both methionine and N10 -fTHF are produced via one-carbon metabolism, linking translation initiation with active cellular metabolism. The fidelity of i-tRNA binding to the ribosomal peptidyl-site (P-site) is attributed to the structural features in its acceptor stem, and the highly conserved three consecutive G-C base pairs (3GC pairs) in the anticodon stem. The acceptor stem region is important in formylation of the amino acid attached to i-tRNA and in its initial binding to the P-site. And, the 3GC pairs are crucial in transiting the i-tRNA through various stages of initiation. We utilized the feature of 3GC pairs to investigate the nuanced layers of scrutiny that ensure fidelity of translation initiation through i-tRNA abundance and its interactions with the components of the translation apparatus. We discuss the importance of i-tRNA in the final stages of ribosome maturation, as also the roles of the Shine-Dalgarno sequence, ribosome heterogeneity, initiation factors, ribosome recycling factor, and coevolution of the translation apparatus in orchestrating a delicate balance between the fidelity of initiation and/or its leakiness to generate proteome plasticity in cells to confer growth fitness advantages in response to the dynamic nutritional states.

Translation initiation site of mRNA is selected through dynamic interaction with the ribosome

SignificanceRibosomes translate the genetic codes of messenger RNA (mRNA) to make proteins. Translation must begin at the correct initiation site; otherwise, abnormal proteins will be produced. Here, we show that a short ribosome-specific sequence in the upstream followed by an unstructured downstream sequence is a favorable initiation site. Those mRNAs lacking either of these two characteristics do not associate tightly with the ribosome. Initiator transfer RNA (tRNA) and initiation factors facilitate the binding. However, when the downstream site forms structures, initiation factor 3 triggers the dissociation of the accommodated initiator tRNA and the subsequent disassembly of the ribosome-mRNA complex. Thus, initiation factors help the ribosome distinguish unfavorable structured sequences that may not act as the mRNA translation initiation site.

Quantification of tissue-specific protein translation in whole C. elegans using O-propargyl-puromycin labeling and fluorescence microscopy

The regulation of gene expression via protein translation is critical for growth, development, and stress response. While puromycin-based techniques have been used to quantify protein translation in C. elegans, they have been limited to using lysate from whole worms. To achieve tissue-specific quantification of ribosome activity in intact C. elegans, we report the application of O-propargyl-puromycin in a cuticle defective mutant followed by conjugation of an azide fluorophore for detection using fluorescent confocal microscopy. We apply this technique to quantify translation in response to heat shock, cycloheximide, or knockdown of translation factors. Furthermore, we demonstrate that O-propargyl-puromycin can be used to quantify translation between tissues or within a tissue like the germline. This technique is expected to have a broad range of applications in determining how protein translation is altered in different tissues in response to stress or gene knockdowns or with age.

Elevated expression of eukaryotic translation initiation factor 3H is associated with proliferation, invasion and tumorigenicity in human hepatocellular carcinoma

Aim

We studied the role of eukaryotic translation initiation factor 3 subunit H (EIF3H) in hepatocellular carcinoma (HCC) progression.

Results

High EIF3H expression was observed in 50.23% patients. Upregulation of EIF3H is an independent predictor for greater rates of cancer recurrence and shorter overall survival in HCC patients. Knockdown of EIF3H expression in HCC cells promoted apoptosis, and inhibited cell growth, colony formation, migration, as well as xenograft growth. TGF-βand MAPK pathways are potentially targeted by EIF3H.

Methods

EIF3H mRNA expression was measured in HCC tissue samples and paired non-tumor samples (N=60) and results were validated in another dataset of 215 HCC patients. Then EIF3H expression and clinical outcomes were correlated. Malignant phenotypes were studied after EIF3H expression was knocked down with siRNA in HCC cell lines. EIF3H targeted pathways were identified by microarray analysis.

Conclusion

EIF3H is frequently upregulated and is an independent prognostic marker for HCC patients and EIF3H inhibition mitigates the malignant phenotype. Our data provide novel insight into the function of EIF3H in HCC progression, and suggest that EIF3H may be a potentially valuable biomarker for HCC.

The Regulation of Translation in Alphavirus-Infected Cells

Sindbis virus (SINV) contains an RNA genome of positive polarity with two open reading frames (ORFs). The first ORF is translated from the genomic RNA (gRNA), rendering the viral non-structural proteins, whereas the second ORF is translated from a subgenomic mRNA (sgRNA), which directs the synthesis of viral structural proteins. SINV infection strongly inhibits host cell translation through a variety of different mechanisms, including the phosphorylation of the eukaryotic initiation factor eIF2α and the redistribution of cellular proteins from the nucleus to the cytoplasm. A number of motifs have been identified in SINV sgRNA, including a hairpin downstream of the AUG initiation codon, which is involved in the translatability of the viral sgRNA when eIF2 is inactivated. Moreover, a 3′-UTR motif containing three stem-loop structures is involved in the enhancement of translation in insect cells, but not in mammalian cells. Accordingly, SINV sgRNA has evolved several structures to efficiently compete for the cellular translational machinery. Mechanistically, sgRNA translation involves scanning of the 5′-UTR following a non-canonical mode and without the requirement for several initiation factors. Indeed, sgRNA-directed polypeptide synthesis occurs even after eIF4G cleavage or inactivation of eIF4A by selective inhibitors. Remarkably, eIF2α phosphorylation does not hamper sgRNA translation during the late phase of SINV infection. SINV sgRNA thus constitutes a unique model of a capped viral mRNA that is efficiently translated in the absence of several canonical initiation factors. The present review will mainly focus in the non-canonical mechanism of translation of SINV sgRNA.

Meal Distribution of Dietary Protein and Leucine Influences Long-Term Muscle Mass and Body Composition in Adult Rats

BACKGROUND

Protein quantity and quality at a meal affect muscle protein synthesis (MPS); however, long-term effects of protein distribution at individual meals on adult muscle mass remain unknown.

OBJECTIVE

We used a precise feeding protocol in adult rats to determine if optimizing postmeal MPS response by modifying the meal distribution of protein, and the amino acid leucine (Leu), would affect muscle mass.

METHODS

Two studies were conducted with the use of male Sprague-Dawley rats (∼300 g) trained to consume 3 meals/d, then assigned to diet treatments with identical macronutrient contents (16% of energy from protein, 54% from carbohydrates, and 30% from fat) but differing in protein quality or meal distribution. Study 1 provided 16% protein at each meal with the use of whey, egg white, soy, or wheat gluten, with Leu concentrations of 10.9%, 8.8%, 7.7%, and 6.8% (wt:wt), respectively. Study 2 used whey protein with 16% protein at each meal [balanced distribution (BD)] or meals with 8%, 8%, and 27% protein [unbalanced distribution (UD)]. MPS and translation factors 4E binding protein 1 (4E-BP1) and ribosomal protein p70S6 (S6K) were determined before and after breakfast meals at 2 and 11 wk. Muscle weights and body composition were measured at 11 wk.

RESULTS

In study 1, the breakfast meal increased MPS and S6K in whey and egg treatments but not in wheat or soy treatments. Gastrocnemius weight was greater in the whey group (2.20 ± 0.03 g) than the soy group (1.95 ± 0.04 g) (P < 0.05) and was intermediate in the egg and wheat groups. The wheat group had >20% more body fat than the soy, egg, or whey groups (P < 0.05). Study 2, postmeal MPS and translation factors were 30-45% greater in the BD group than the UD group (P < 0.05), resulting in 6% and 11% greater (P < 0.05) gastrocnemius and soleus weights at 11 wk.

CONCLUSION

These studies show that meal distribution of protein and Leu influences MPS and long-term changes in adult muscle mass.

Altered Machinery of Protein Synthesis in Alzheimer's: From the Nucleolus to the Ribosome

Ribosomes and protein synthesis have been reported to be altered in the cerebral cortex at advanced stages of Alzheimer's disease (AD). Modifications in the hippocampus with disease progression have not been assessed. Sixty-seven cases including middle-aged (MA) and AD stages I-VI were analyzed. Nucleolar chaperones nucleolin, nucleophosmin and nucleoplasmin 3, and upstream binding transcription factor RNA polymerase I gene (UBTF) mRNAs are abnormally regulated and their protein levels reduced in AD. Histone modifications dimethylated histone H3K9 (H3K9me2) and acetylated histone H3K12 (H3K12ac) are decreased in CA1. Nuclear tau declines in CA1 and dentate gyrus (DG), and practically disappears in neurons with neurofibrillary tangles. Subunit 28 ribosomal RNA (28S rRNA) expression is altered in CA1 and DG in AD. Several genes encoding ribosomal proteins are abnormally regulated and protein levels of translation initiation factors eIF2α, eIF3η and eIF5, and elongation factor eEF2, are altered in the CA1 region in AD. These findings show alterations in the protein synthesis machinery in AD involving the nucleolus, nucleus and ribosomes in the hippocampus in AD some of them starting at first stages (I-II) preceding neuron loss. These changes may lie behind reduced numbers of dendritic branches and reduced synapses of CA1 and DG neurons which cause hippocampal atrophy.

Eukaryotic translation initiation factor 6 is a novel regulator of reactive oxygen species-dependent megakaryocyte maturation

BACKGROUND

Ribosomopathies constitute a class of inherited disorders characterized by defects in ribosome biogenesis and function. Classically, bone marrow (BM) failure is a clinical symptom shared between these syndromes, including Shwachman-Bodian-Diamond syndrome (SBDS). Eukaryotic translation initiation factor 6 (eIF6) is a critical translation factor that rescues the quasilethal effect of the loss of the SBDS protein.

OBJECTIVES

To determine whether eIF6 activity is necessary for BM development.

METHODS

We used eIF6(+/-) mice and primary BM megakaryocytes to investigate the involvement of eIF6 in the regulation of hematopoiesis.

RESULTS

We provide evidence that reduced eIF6 expression negatively impacts on megakaryopoiesis. We show that inhibition of eIF6 leads to a reduction in cell size and mean ploidy level of megakaryocytes and a delay in megakaryocyte maturation by blocking the G1 /S transition. Consistent with this phenotype, only few megakaryocyte-forming proplatelets were found in eIF6(+/-) cells. We also discovered that, in eIF6(+/-) cells, the steady-state abundance of mitochondrial respiratory chain complex I-encoding mRNAs is decreased, resulting in decreased reactive oxygen species (ROS) production. Intriguingly, connectivity map analysis showed that eIF6-mediated changes overlap with specific translational inhibitors. eIF6 is a translation factor acting downstream of insulin/phorbol 12-myristate 13-acetate (PMA) stimulation. PMA treatment significantly restored eIF6(+/-) megakaryocyte maturation, indicating that activation of eIF6 is essential for the rescue of the phenotype.

CONCLUSIONS

Taken together, our results show a role for eIF6-driven translation in megakaryocyte development, and unveil the novel connection between translational control and ROS production in this cell subset.

Initiation codon selection is accomplished by a scanning mechanism without crucial initiation factors in Sindbis virus subgenomic mRNA

Translation initiation of alphavirus subgenomic mRNA (sgmRNA) can occur in the absence of several initiation factors (eIFs) in infected cells; however, the precise translation mechanism is still poorly understood. In this study, we have examined the mechanism of initiation and AUG selection in Sindbis virus (SINV) sgmRNA. Our present findings suggest that sgmRNA is translated via a scanning mechanism, since the presence of a hairpin structure before the initiation codon hampers protein synthesis directed by this mRNA. In addition, translation is partially recovered when an in-frame AUG codon is placed upstream of this hairpin. This scanning process takes place without the participation of eIF4A and active eIF2. These results, combined with our findings through modifying the SINV sgmRNA leader sequence, do not support the possibility of a direct initiation from the start codon without previous scanning, or a shunting mechanism. Moreover, studies carried out with sgmRNAs containing two alternative AUG codons within a good context for translation reveal differences in AUG selection which are dependent on the cellular context and the phosphorylation state of eIF2α. Thus, initiation at the additional AUG is strictly dependent on active eIF2, whereas the genuine AUG codon can start translation following eIF2α inactivation. Collectively, our results suggest that SINV sgmRNA is translated by a scanning mechanism without the potential participation of crucial eIFs. A model is presented that explains the mechanism of initiation of mRNAs bearing two alternative initiation codons.

The role of the poly(A) binding protein in the assembly of the Cap-binding complex during translation initiation in plants

Translation initiation in eukaryotes requires the involvement of multiple initiation factors (eIFs) that facilitate the binding of the 40 S ribosomal subunit to an mRNA and assemble the 80 S ribosome at the correct initiation codon. eIF4F, composed of eIF4E, eIF4A, and eIF4G, binds to the 5'-cap structure of an mRNA and prepares an mRNA for recruitment of a 40 S subunit. eIF4B promotes the ATP-dependent RNA helicase activity of eIF4A and eIF4F needed to unwind secondary structure present in a 5'-leader that would otherwise impede scanning of the 40 S subunit during initiation. The poly(A) binding protein (PABP), which binds the poly(A) tail, interacts with eIF4G and eIF4B to promote circularization of an mRNA and stimulates translation by promoting 40 S subunit recruitment. Thus, these factors serve essential functions in the early steps of protein synthesis. Their assembly and function requires multiple interactions that are competitive in nature and determine the nature of interactions between the termini of an mRNA. In this review, the domain organization and partner protein interactions are presented for the factors in plants which share similarities with those in animals and yeast but differ in several important respects. The functional consequences of their interactions on factor activity are also discussed.

Why is start codon selection so precise in eukaryotes?

Translation generally initiates with the AUG codon. While initiation at GUG and UUG is permitted in prokaryotes (Archaea and Bacteria), cases of CUG initiation were recently reported in human cells. The varying stringency in translation initiation between eukaryotic and prokaryotic domains largely stems from a fundamental problem for the ribosome in recognizing a codon at the peptidyl-tRNA binding site. Initiation factors specific to each domain of life evolved to confer stringent initiation by the ribosome. The mechanistic basis for high accuracy in eukaryotic initiation is described based on recent findings concerning the role of the multifactor complex (MFC) in this process. Also discussed are whether non-AUG initiation plays any role in translational control and whether start codon accuracy is regulated in eukaryotes.

Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy

Weak protein-protein interactions are critical in numerous biological processes. Unfortunately, they are difficult to characterize due to the high concentrations required for the production and detection of the complex population. The inherent sensitivity of NMR spectroscopy to the chemical environment makes it an excellent tool to tackle this problem. NMR permits the exploration of interactions over a range of affinities, yielding essential insights into dynamic biological processes. The conversion of messanger RNA to protein is one such process that requires the coordinated association of many low-affinity proteins. During start codon recognition, eukaryotic initiation factors assemble into high-order complexes that bind messanger RNA and bring it to the ribosome for decoding. Many of the structures of the eukaryotic initiation factors have been determined; however, little is known regarding the weak binary complexes formed and their structure-function mechanisms. Herein, we use start codon recognition as a model system to review the relevant NMR methods for the characterization of weak interactions and the development of small molecule inhibitors.

Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation

Start codon recognition is a crucial event in the initiation of protein synthesis. To gain insight into the mechanism of start codon recognition in eukaryotes, we used a yeast reconstituted initiation system to isolate the step of Met-tRNA(i)*eIF2*GTP ternary complex (TC) binding to the 40S subunit. We examined the kinetics and thermodynamics of this step in the presence of base changes in the mRNA start codon and initiator methionyl tRNA anticodon, in order to investigate the effects of base pairing and sequence on the stability of the resulting 43S*mRNA complex. We observed that the formation of three base pairs, rather than their identities, was the key determinant of stability of TC binding, indicating that nothing is inherently special about the sequence AUG for this step. Surprisingly, the rate constant for TC binding to the 40S subunit was strongly codon dependent, whereas the rate constant for TC dissociation from the 43S*mRNA complex was not. The data suggest a model in which, after the initial diffusion-limited encounter of TC with the 40S subunit, the formation of three matching start codon/anticodon base pairs triggers a conformational change that locks the complex into a stable state. This induced-fit mechanism supports the proposal that initiation codon recognition by the 43S complex induces a conformational change from an open state to a closed one that arrests movement along the mRNA.

Regulation of poly(A) binding protein function in translation: Characterization of the Paip2 homolog, Paip2B

The 5' cap and 3' poly(A) tail of eukaryotic mRNAs act synergistically to enhance translation. This synergy is mediated via interactions between eIF4G (a component of the eIF4F cap binding complex) and poly(A) binding protein (PABP). Paip2 (PABP-interacting protein 2) binds PABP and inhibits translation both in vitro and in vivo by decreasing the affinity of PABP for polyadenylated RNA. Here, we describe the functional characteristics of Paip2B, a Paip2 homolog. A full-length brain cDNA of Paip2B encodes a protein that shares 59% identity and 80% similarity with Paip2 (Paip2A), with the highest conservation in the two PABP binding domains. Paip2B acts in a manner similar to Paip2A to inhibit translation of capped and polyadenylated mRNAs both in vitro and in vivo by displacing PABP from the poly(A) tail. Also, similar to Paip2A, Paip2B does not affect the translation mediated by the internal ribosome entry site (IRES) of hepatitis C virus (HCV). However, Paip2A and Paip2B differ with respect to both mRNA and protein distribution in different tissues and cell lines. Paip2A is more highly ubiquitinated than is Paip2B and is degraded more rapidly by the proteasome. Paip2 protein degradation may constitute a primary mechanism by which cells regulate PABP activity in translation.

Preferential translation of cold-shock mRNAs during cold adaptation

Upon temperature downshift below the lower threshold of balanced growth (approximately 20 degrees C), the Escherichia coli translational apparatus undergoes modifications allowing the selective translation of the transcripts of cold shock-induced genes, while bulk protein synthesis is drastically reduced. Here we were able to reproduce this translational bias in E. coli cell-free extracts prepared at various times during cold adaptation which were found to display different capacities to translate different types of mRNAs as a function of temperature. Several causes were found to contribute to the cold-shock translational bias: Cold-shock mRNAs contain cis-elements, making them intrinsically more prone to being translated in the cold, and they are selective targets for trans-acting factors present in increased amounts in the translational apparatus of cold-shocked cells. CspA was found to be among these trans-acting factors. In addition to inducing a higher level of CspA, cold shock was found to cause a strong (two- to threefold) stoichiometric imbalance of the ratio between initiation factors (IF1, IF2, IF3) and ribosomes without altering the stoichiometric ratio between the factors themselves. The most important sources of cold-shock translational bias is IF3, which strongly and selectively favors translation of cold-shock mRNAs in the cold. IF1 and the RNA chaperone CspA, which stimulate translation preferentially in the cold without mRNA selectivity, can also contribute to the translational bias. Finally, in contrast to a previous claim, translation of cold-shock cspA mRNA in the cold was found to be as sensitive as that of a non-cold-shock mRNA to both chloramphenicol and kanamycin inhibition.

Reversal of pactamycin inhibition of methionyl-puromycin synthesis and 80S initiation complex formation by a ribosomal joining factor

A crude mixture of polypeptide chain initiation factors (0.5 M KCl ribosomal wash) from reticulocyte ribosomes was fractionated by DEAE-cellulose column chromatography. Among several initiation factors obtained from the column, one factor eluting at 0.22-0.25 M KCl showed a remarkable ability to overcome the inhibition of Met-puromycin and 80S initiation complex formation caused by the antibiotic, pactamycin. Earlier experiments had shown that pactamycin does not prevent the binding of Met-tRNA(f) to the small ribosomal subunit but does interfere with the joining of the 60S ribosomal subunit to form the 80S initiation complex. A Lineweaver-Burk plot of initial rates of Met-puromycin formation showed that the interaction of the factor and pactamycin was of a competitive type. In the absence of the factor, [(35)S]Met-puromycin was not synthesized and [(35)S]Met-tRNA(f) bound only to the small ribosomal subunit. The amount of [(35)S]Met-tRNA(f) bound to 80S ribosomes bearing endogenous mRNA and the amount of [(35)S]Met-puromycin formed were directly related to the amount of factor added. Thus, this factor can be termed a "joining factor," and a simple assay of its activity can be devised based on its ability to overcome the pactamycin inhibition of the puromycin reaction.

Sequence of events in initiation of translation: a role for initiator transfer RNA in the recognition of messenger RNA

It is shown that initiation of translation involves several steps. (i) Binding of fMet-tRNA(fMet) to the bacterial 30S ribosomal subunit in the absence of messenger RNA, yielding a 34S complex. This binding is rapid and dependent on initiation factor 2 but not on initiation factor 3. (ii) Binding of messenger RNA to the 34S complex. This binding is slower and depends on initiation factor 3. If R17 RNA is used as messenger, the resulting complex sediments at 46 S. (iii) Joining of a 50S subunit to yield a complete initiation complex. Binding of fMet-tRNA(fMet) not only precedes, but is necessary for, correct binding of messenger RNA to ribosomes. Thus, initiator tRNA may play an active role in the selection of initiation sites in messenger RNA.

Met-tRNAfMet binding to 40S ribosomal subunits: a site for the regulation of initiation of protein synthesis by hemin

On incubation of reticulocyte lysates at 30 degrees in the absence of added hemin, protein synthesis declines sharply within 4-6 min, due to the action of a translational inhibitor. Partially purified preparations of this inhibitor, in concentrations that inhibit protein synthesis in the lysate, cause reduced binding of Met-tRNA(f) (Met) to derived 40S ribosomal subunits in a ribosomal-salt-wash-dependent assay system. Neither the association of salt wash proteins with the subunits nor the level of Met-tRNA(f) (Met) bound in preformed 40S complexes is reduced by the inhibitor. No Met-tRNA(f) (Met) deacylase activity could be detected in the inhibitor preparation. Protein synthesis in reticulocyte lysates lacking added hemin or containing exogenous inhibitor is maintained by addition of small amounts of an initiation preparation factor, "F-MP," which may be involved in the binding of Met-tRNA(f) (Met) to 40S subunits. This binding constitutes a site for control of protein synthesis by hemin in reticulocytes.

Translational control induced by bacteriophage T7

Phage T7 discontinues host gene expression by translational and transcriptional control mechanisms. Translational control is exerted by the T7 translational-repressor. This protein inhibits the synthesis of beta-galactosidase (EC 3.2.1.23) in vivo and in vitro and the synthesis of the T3 enzyme S-adenosylmethioninehydrolase (EC 3.3.1.-). The translational-repressor does not interfere with T7-specific enzyme synthesis. The T7 translational-repressor purifies with the initiation factors. The repressor interacts with the initiation of translation of host enzymes. The translational-repressor gene is close to the promotor for RNA polymerase of Escherichia coli.

A specific inhibitor of polypeptide-chain initiation in Escherichia coli

An inhibitor of polypeptide-chain initiation was isolated from E. coli cells. This protein inhibits formation of the 30S or 70S initiation complex with either fMet-tRNA(f) as initiator and AUG, MS2 RNA, or late T4 RNA as messenger, or acPhe-tRNA as initiator and poly(U) as messenger. Chain elongation, e.g., poly(U) translation at high Mg(2+) concentration, is not inhibited. The inhibitor is rendered ineffective when active aminoacylation of tRNA is taking place, e.g., during natural mRNA translation. This inhibitor is distinct from the so-called interference (i) factors, which interfere exclusively with the action of initiation factor 3. Since the new inhibitor can apparently be turned on and off, it may have a regulatory function in translation.

Translation of rabbit hemoglobin meessenger RNA in vitro with purified and partially purified components from brain or liver of different species

Two mammalian systems have been developed for efficient in vitro translation of exogenous messenger RNA (rabbit globin mRNA). One system is completely derived from guinea pig brain, and the other is from liver of different species. Both systems consist of purified 60S and 40S ribosomal sununits, unseparated initiation factors partially purified by ammonium sulfate precipitation and DEAE-cellulose chromatography, and pH 5 enzyme fractions as sources of elongation and termination factors, aminoacyl-tRNA synthetases, and transfer RNA. Translation depends completely upon exogenous mRNA and initiation factors. Extraction of initiation factors from microsomes or ribosomes has been improved for these tissues by inclusion of Mg(++) ions in the 0.5 M KCl extraction solution. Both systems synthesize complete rabbit alpha- and beta-globin chains, but in variable ratios. The overall efficiencies of the two systems are about 60% (liver) and 40% (brain) of a comparable system with rabbit reticulocyte initiation factors.

Inhibition of reticulocyte peptide-chain initiation by pactamycin: accumulation of inactive ribosomal initiation complexes

Pactamycin does not inhibit the overall initiation factor- and GTP-dependent binding of [(35)S]Met-tRNA(f) to rabbit reticulocyte ribosomes but does prevent the formation of Met-puromycin, provided that the antibiotic is present during the course of the binding reaction. These data indicate that pactamycin blocks the synthesis of a functional peptide-chain initiation complex. Sucrose density gradient centrifugation analysis of binding reactions shows that pactamycin causes the accumulation of an initiation complex on the smaller ribosomal subunit (smaller initiation complex), to which the 60S ribosomal subunit either cannot join or with which it forms a larger inactive 80S initiation complex that falls apart under the conditions used for isolation. The smaller initiation complex formed in the presence of pactamycin differs from the normal intermediate in peptide-chain initiation in being much more resistant to degradation by pancreatic RNase. In the presence of pactamycin, the inactive smaller complex can also form on mRNA to which an unaffected ribosomal couple is already attached, forming an oligoribosome lacking a larger ribosomal subunit or a "1.5 mer." These effects of pactamycin can be overcome to a considerable degree by elevation of the Mg(2+) concentration.

In vitro synthesis of procollagen on polysomes

The major collagenous products synthesized in a cell-free polysome preparation are pro-alpha1 and pro-alpha2, formed in a ratio of 2:1. They are the precursor forms of alpha1 and alpha2 chains of normal connective-tissue collagen that are also formed in small amounts. A procollagen peptidase activity has been demonstrated in the supernatant fraction that can account for the formation of alpha1 and alpha2 chains from their precursors. The polysomal system is activated by a salt extract of reticulocyte ribosomes and is inhibited by aurintricarboxylic acid, suggesting that the polysomes are able to initiate protein synthesis.

Calf crystallin synthesis in frog cells: the translation of lens-cell 14S RNA in oocytes

14S RNA isolated from calf-lens polyribosomes was injected into oocytes of the frog Xenopus laevis. Oocytes injected with 14S RNA and buffer contained a protein resembling the A2 chain of calf alpha-crystallin; oocytes injected with buffer alone contained no crystallin-like material. alphaA2 crystallin polypeptides were identified by various criteria: urea-gel electrophoresis under acidic and basic conditions, gel electrophoresis in sodium dodecyl sulfate, N-terminal analysis, and paper chromatography of methionine-containing tryptic peptides. It is concluded that when it is injected into a living frog oocyte, the 14S RNA from lens tissue is reasonably stable and has the properties of an alphaA2 crystallin messenger. The messenger requires no lens cell-specific components for translation within the oocyte, and the translational machinery of the frog cell will accept messenger RNA from a totally different cell type from another species. The A2 chains of alpha-crystallin extracted from lens tissue possess an acetylated N-terminal methionine residue; the N-terminal methionine of alphaA2 chains derived from frog oocytes injected with 14S RNA was also acetylated.

Increased efficiency of exogenous messenger RNA translation in a Krebs ascites cell lysate

Addition of a 0.5 M KCl wash fraction from rabbit reticulocyte ribosomes causes a 3- to 10-fold increase in the extent of translation of natural mRNAs by Krebs-cell lysates. In the presence of the wash fraction, 1 pmol of rabbit or mouse 10S RNA directs the incorporation of 80 pmol of leucine into rabbit globin. The addition of human 10S RNA results in the synthesis of equal amounts of human alpha and beta chains, identified by column chromatography. The stimulation by the wash fraction is almost completely dependent on added mammalian tRNA. In contrast to the wash fraction from rabbit reticulocytes, the wash fraction isolated from Krebs-cell ribosomes is inhibitory to both endogenous and exogenous mRNA translation. The stimulation by the wash fraction from rabbit ribosomes is not specific for globin mRNAs, but also increases endogenous, phage Qbeta, and viral RNA-directed protein synthesis.

Initiation of hemoglobin synthesis: comparison of model reactions that use artificial templates with those using natural messenger RNA

PARTIAL REACTIONS DESIGNED TO STUDY THE INDIVIDUAL STEPS IN THE INITIATION OF PROTEIN SYNTHESIS MAY BE DIVIDED INTO TWO GROUPS: artificial models using artificial mRNA templates and natural models using naturally occurring mRNA. The requirements for each of the reticulocyte initiation factors, IF-M(1), IF-M(2), and IF-M(3), and for GTP are examined using these models in order to determine if either type of model is a valid representation of the events occurring in natural initiation. Binding of the initiator tRNA, Met-tRNA(F), to endogenous mRNA requires IF-M(1), IF-M(2), and GTP. A requirement for hydrolysis of GTP is not found when the artificial template ApUpG is used since GDPCP may be substituted for GTP. Met-tRNA(F) bound to the template ApUpG by IF-M(1) + IF-M(2) can form a peptide bond with the aminoacyl-tRNA analog, puromycin. Met-tRNA(F) bound by IF-M(1) + IF-M(2) to the initiator codon of natural globin mRNA, however, cannot form a peptide bond with either puromycin or valine-tRNA unless IF-M(3) is also present. The requirements for Met(F)-valine synthesis on exogenous globin mRNA are the same as the requirements on endogenous mRNA. Synthesis of the initial tripeptides of the alpha and beta chains of rabbit globin, Met(F)-Val-Leu and Met(F)-Val-His, requires, in addition, leucyl-tRNA and histidyl-tRNA. It appears, therefore, that model systems that use natural messenger RNA can duplicate the factor and energy requirements of natural initiation, but that the model systems thus far studied that use artificial messengers as templates do not.

A ribosome dissociation factor from rabbit reticulocytes (fluoride-E. coli ribosomes-initiation factors)

A ribosome dissociation factor has been detected in an extract of ribosomal particles from rabbit reticulocytes. This factor dissociates free ribosomes from reticulocytes and also from Escherichia coli; it does not dissociate ribosomes complexed with peptidyl-tRNA and mRNA. The reaction appears to be stoichiometric rather than catalytic; it reaches completion in one minute at 37 degrees C, but is very slow at 0 degrees C, and it is antagonized and reversed by Mg(++). Reticulocyte dissociation factor thus closely resembles that from E. coli. However, the activity has been found primarily associated with the native large subunits rather than the small subunits in lysates.

Translation of exogenous messenger RNA for hemoglobin on reticulocyte and liver ribosomes

The ribosome and initiation factor requirements for translation of rabbit-reticulocyte hemoglobin mRNA on rabbit reticulocyte ribosomes, reticulocyte ribosomal subunits, and liver ribosomes have been studied. Excellent synthesis of globin chains from exogenous mRNA in the fractionated cell-free system has been achieved. There is a near absolute requirement for each of the initiation factors, M(1), M(2), and M(3) (as well as for the supernatant proteins) for the translation of exogenous mRNA. Liver microsomal wash will partially replace reticulocyte factors M(1) and M(2), but will not replace the requirement for reticulocyte factor M(3). Rabbit liver ribosomes and rabbit reticulocyte ribosomes are equally active in their ability to support the translation of exogenous hemoglobin mRNA.

Requirement for GTP in the initiation process on reticulocyte ribosomes and ribosomal subunits

The requirement for GTP in the initiation process on reticulocyte ribosomes and ribosomal subunits has been examined by studying Met-tRNA(F) binding, ribosome-dependent [gamma-(32)P]GTP hydrolysis, and peptide-bond formation with puromycin. Met-tRNA(F) binding can be obtained with the methylene analogue, 5'-guanylylmethylene diphosphonate, as well as GTP, and it is not inhibited by fusidic acid or several other inhibitors of protein synthesis. This reaction can be performed with the 40S subunit and has the same requirements as the Met-tRNA(F)-binding reaction with washed ribosomes. Ribosome-dependent [gamma-(32)P]GTP hydrolysis can be obtained with the initiation factor M(2A) using either washed ribosomes or the 40S subunit. This reaction is also not significantly inhibited by fusidic acid. Peptide-bond formation between puromycin and Met-tRNA(F), however, is inhibited by fusidic acid, and does not occur if the methylene analogue of GTP is substituted for GTP. These data suggest that the binding of the initiator tRNA to the 40S subunit does not require the hydrolysis of GTP, but that at least one GTP hydrolysis event must occur after Met-tRNA(F) binding in order for the first peptide bond to be formed.

Translocation of messenger RNA and "accommodation" of fMet-tRNA

Messenger RNA is moved a distance of approximately three nucleotides in the 5' direction relative to the ribosome during the translocation of peptidyl-tRNA from the A to the P site. This movement is catalyzed by G factor and is dependent on the hydrolysis of GTP. In contrast, mRNA is not moved during the f(2)-catalyzed hydrolysis of GTP that is involved in the activation of ribosome-bound fMet-tRNA. This second type of GTP-dependent reaction has been named "Accommodation".

Initial dipeptide formation in hemoglobin biosynthesis

Initiation factors M(1) + M(2) from reticulocyte ribosomes bind Met-tRNA(F) to rabbit reticulocyte ribosomes containing endogenous hemoglobin mRNA. The initial binding of Met-tRNA(F) appears to be to the small ribosomal subunit. The Met-tRNA(F) is able to participate in what is presumed to be the first peptide bond in the formation of hemoglobin, namely the synthesis of a methionyl-valine dipeptide. The formation of this methionyl-valine dipeptide requires Met-tRNA(F), initiation factors M(1), M(2), and M(3), as well as Val-tRNA and T(1). No synthesis of methionyl-valine dipeptide takes place if Met-tRNA(F) is replaced by Met-tRNA(M), or if initiation factor M(3) is omitted. Thus, Met-tRNA(F) appears to be the initiator tRNA for hemoglobin biosynthesis and M(3), although required for the synthesis of the first peptide bond of hemoglobin, does not appear to be necessary, under the experimental conditions studied, for Met-tRNA(F) binding.