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Results for “Codon, Initiator”

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PubMed2004

[Antisense oligonucleotide inhibition of coxsackievirus B3 gene expression in HeLa cells and dose-response experiments].

OBJECTIVE: In this study, the authors investigated inhibition of coxsackievirus B (CVB) gene expression using antisense oligonucleotides complementary to the 5' NCR, translation initiation codon and structural protein coding sequences and also observed the dose-response of the sequence specific inhibition of CVB plaque formation by antisense oligonucleotides. METHODS: Antiviral activities of these oligonucleotides were evaluated by using plaque reduction assay, yield reduction assay, cytopathic effect (CPE) and Western blot analysis. The cells were treated with random oligonucleotides as a specificity control. RESULTS: At a screening concentration of 5 micromole, 6 of the phosphorothioate oligonucleotide demonstrated some reduction of virus replication relative to untreated cells. 70%-90% inhibition of virus at 0.1 MOI (multiplicity of infection), 50% inhibition of virus infection at 10 MOI. The levels of the VP1 were reduced in CVB-infected cells treated with Scb561 and Scb733. VP1 was significantly reduced after treatment with 0.625 micromole Scb561 and almost undetectable in cells treated with 2.5 micromole Scb561. Dose response experiments implied that sequence specific oligonucleotide doses were related to effect on inhibition of CVB3 infection. When oligonucleotide doses were increased from 1.25 to 5 micromole, 75% to 90% inhibition were observed with Scb561 and 65% to 80% inhibition with Scb733, whereas random control failed to inhibit CVB replication (8% inhibition for each). CONCLUSION The present studies showed that antisense oligonucleotides against internal ribosome entry site (IRES) and translation initiation codon were capable of specifically inhibiting the synthesis of viral protein and subsequent productive CVB replication.The selective inhibition using antisense oligonucleotide might lead to development of an effective antiviral agent for future clinical evaluation.

5' Untranslated Regions↗

PubMed1986

Amino-terminal structure of spoOA protein and sequence homology with spoOF and spoOB proteins.

The previously reported nucleotide sequence of the spoOA coding region of Bacillus subtilis suggested that the protein is initiated with either of two possible initiation codons, ATG and GTG, 84 base pairs apart. To determine which codon is utilized as an initiator in B. subtilis, we constructed a fusion gene in which the promoter and NH2-terminal region of the spoOA gene was connected to the chloramphenicol acetyltransferase gene (cat gene). After introduction of the plasmid carrying the spoOA-cat fusion gene into B. subtilis cells, the fusion protein was purified by affinity chromatography. The sequence of NH2-terminal amino acids of the fusion protein was determined and the result established that the GTG codon is utilized as an initiator in B. subtilis. Comparison of the amino acid sequences revealed a marked homology between the spoOA (NH2-terminal half) and spoOF proteins. A less striking but significant homology was also found between the spoOA (COOH-terminal half) and spoOB proteins. This suggests the presence of a common functional domain structure for these proteins that are supposed to play key regulatory roles in sporulation.

Acetyltransferases↗

PubMed2003

Effects of additional sequences directly downstream from the AUG on the expression of GFP gene.

We have studied the expression of the green fluorescent protein (GFP) gene to gain more understanding of the effects of additional nucleotide triplets (codons) downstream from the initiation codon on the translation of the GFP mRNA in CHO and Cos1 cells. A leader sequence of six consecutive identical codons (GUG, CUC, AGU or UCA) was introduced into a humanized GFP (hm gfp) gene downstream from the AUG to produce four GFP gene variants. Northern blot and RT-PCR analysis indicated that mRNA transcription from the GFP gene was not significantly affected by any of the additional sequences. However, immunoblotting and FACS analysis revealed that AGU and UCA GFP variants produced GFP at a mean level per cell 3.5-fold higher than the other two GFP variants and the hm gfp gene. [35S]-Methionine labeling and immunoprecipitation demonstrate that GFP synthesis was very active in UCA variant transfected-cells, but not in GUG variant and hm gfp transfected-cells. Moreover, proteasome inhibitor MG-132 treatment indicated that the GFPs encoded by each of the GFP variants and the hm gfp were equally stable, and this together with the comparable mRNA levels observed for each construct suggested that the different steady-state GFP concentrations observed reflected different translation efficiencies of the various GFP genes. In addition, the CUC GFP variant, when transiently transfected into CHO or COS-1 cells, did not produce any GFP expressing cells (fully green cells), and the GUG variant produced GFP expressing cells less than 10%, while AGU and UCA GFP variants up to 30-35% in a time course study from 8 to 36 h posttransfection. Analysis of the potential secondary structure of the GFP variant mRNAs especially in the translation initiation region suggested that the secondary structure of the GFP mRNAs was unlikely to explain the different translation efficiencies of the GFP variants. The present findings indicate that a change of the initiation context of the GFP gene by addition of extra coding sequence can alter the translation efficiency of GFP mRNA, providing a means of more efficient expression of GFP in eukaryotic cells.

Animals↗

PubMed1992

Mitochondrial rps14 is a transcribed and edited pseudogene in Arabidopsis thaliana.

We have isolated and analysed a 2 kb region of the mitochondrial genome of Arabidopsis thaliana (Columbia) showing a high level of nucleotide identity with the mitochondrial (mt) rps14 small-subunit ribosomal protein gene from Oenothera berteriana and Vicia faba, as well as with an open reading frame (ORF) located upstream of the nad3 locus in O. berteriana. The rps14 locus is present as a single copy in the A. thaliana mt genome and has a translational stop codon located near the initiation codon, as well as a deletion of one nucleotide that disturbs the coding sequence. The cloning and sequencing of nine amplified mt rps14 cDNAs clearly demonstrated that this gene is transcribed and that the mRNA precursors are edited at three positions, all involving C-to-U conversions. No editing events changing the stop codon and restoring the correct coding sequence were witnessed within the 9 individual cDNA clones. Therefore, we conclude that the single rps14 sequence of the mitochondrial genome from A. thaliana is in fact a pseudogene that is transcribed and edited but not translated.

Amino Acid Sequence↗

PubMed1991

The chloroplast gene for ribosomal protein CL23 is functional in tobacco.

Chloroplast rpl23 loci potentially coding for a polypeptide homologous to the E. coli L23 ribosomal protein are frame-shifted in spinach and several other plants, indicating that these loci are pseudogenes. In tobacco, rpl23 constitutes a continuous open reading frame of 93 codons and its transcript initiates at least 66 bp upstream from the initiation codon. The N-terminal amino acid sequence of a 13 kDa protein from the 50 S subunit of tobacco chloroplast ribosomes matches that derived from the tobacco rpl23 locus. This shows that rpl23 is a functional gene in tobacco.

Amino Acid Sequence↗

PubMed1986

Role of the adenovirus early region 1B tumor antigens in transformation and lytic infection.

We have investigated the contribution of each of the two adenovirus type 5 (Ad5) major early region 1b (E1b) proteins in cell transformation and in lytic infection. An Ad5 E1 plasmid, in which the reading frame for the 19-kDa E1b protein was abolished by a stop codon close to the initiation codon, transformed primary baby rat kidney (BRK) cells with an efficiency of about half of that of a wild type Ad5 E1 plasmid, whereas a plasmid with a mutation in the gene for the 58-kDa E1b protein transformed the same primary cells with only one-third of the wild type efficiency. Plasmids containing region E1a only or a plasmid carrying mutations in the genes for major E1b proteins all transformed primary cells with an efficiency of approximately 5% of wild type. To test the effect of the E1b mutations in virion-mediated cell transformation, the mutant E1b regions were introduced into intact viral genomes by overlap recombination and were subsequently used in a transformation assay on BRK cells. The 19 and 58-kDa mutant viruses were found to transform BRK cells with 11 and 25% of the efficiency of wild type virus, respectively. These results suggest that the 19-kDa E1b protein is essential for virus-mediated cell transformation, in agreement with results of others, but not for plasmid-mediated cell transformation. In lytic infection, the 19-kDa mutant virus was some 30-fold reduced in yield on HeLa cells, whereas the 58-kDa mutant virus was 3000-fold reduced in its ability to grow on HeLa cells at low multiplicity of infection, but showed a marked multiplicity-dependent leakiness. The 58-kDa mutant virus was not defective when its growth was assayed on human embryonic kidney (HEK) cells. This may indicate that cellular proteins are expressed in HEK cells that are functionally homologous to the 58-kDa E1b protein.

Adenovirus Early Proteins↗

PubMed2000

The eIF1A solution structure reveals a large RNA-binding surface important for scanning function.

The translation initiation factor eIF1A is necessary for directing the 43S preinitiation complex from the 5' end of the mRNA to the initiation codon in a process termed scanning. We have determined the solution structure of human eIF1A, which reveals an oligonucleotide-binding (OB) fold and an additional domain. NMR titration experiments showed that eIF1A binds single-stranded RNA oligonucleotides in a site-specific, but non-sequence-specific manner, hinting at an mRNA interaction rather than specific rRNA or tRNA binding. The RNA binding surface extends over a large area covering the canonical OB fold binding site as well as a groove leading to the second domain. Site-directed mutations at multiple positions along the RNA-binding surface were defective in the ability to properly assemble preinitiation complexes at the AUG codon in vitro.

Amino Acid Sequence↗

PubMed2004

The 5'-untranslated region of the tobacco alcohol dehydrogenase gene functions as an effective translational enhancer in plant.

The alcohol dehydrogenase gene (NtADH) was previously isolated from tobacco BY2 suspension cultured cell. Expression of this gene was dramatically increased only during the early stationary phase, and the 5'-untranslated region (5'-UTR) was hypothesized to be involved in the stimulatory effect at the post-transcriptional level. In this paper, we investigated whether the NtADH 5'-UTR possesses the ability to positively enhance gene expression at the translational level. For easily estimating translational efficiency, we used beta-glucuronidase (GUS) gene as a reporter and tobacco BY2 cell, Arabidopsis thaliana T87 cell, and rice Oryza sativa suspension cultured cells as host cells in a transient assay system. Compared with the control plasmid pBI221, insertion of the NtADH 5'-UTR enhanced GUS expression levels about 30- to 100-fold and 30- to 60-fold in transiently transformed BY2 and T87 cells, respectively. However, in transiently transformed O. sativa cells, expression was barely enhanced. In comparison with the 5'-UTR of tobacco mosaic virus (Omega sequence), a known translational enhancer, the NtADH 5'-UTR enhanced translation to a similar level. Meanwhile, the translational efficiency was affected by the sequence context around the AUG initiation codon at the translational initiation step. Moreover, this NtADH 5'-UTR also worked in stable tobacco transformants. Therefore, it is expected that this 5'-UTR will serve as a powerful tool for enhancing foreign gene expression.

Journal Article↗

PubMed1994

Thermodynamic characterization of the cooperativity of 40S complex formation during the initiation of eukaryotic protein synthesis.

The first step in mammalian protein synthesis is the formation of the 40S initiation complex, composed of the 40S ribosomal subunit (R), mRNA (M, here, a 10-mer oligoribonucleotide analogue containing the initiation codon), and the quaternary complex (Q, composed of eIF-2, GTP, Met-tRNA(fMet), and the ancillary protein factor Co-eIF-2C). The interdependence of the binding of R, M, and Q in forming the 40S complex is currently unclear. We have determined the thermodynamic parameters that characterize these interactions. The binary constants for R+M and Q+M were determined spectroscopically, measuring changes in the anisotropy of the fluorescence emission of 3'-fluorescein labeled M. The other binary constant, for Q+R, and the ternary constant were determined from Millipore filtration assays using radiolabeled Met-tRNA(fMet). The association constants for the binary reactions were as follows: Ka(Q,M) < or = 0.14 x 10(6) M-1, Ka(R,M) = 1.78 x 10(6) M-1, and Ka(Q,R) = 0.94 x 10(6) M-1. The binding of Q to R.M was markedly greater than that of Q to R [Ka(Q,R.M)/Ka(Q,R) > 62]. High cooperativity for this interaction occurs in either a single-site model or in lattice models for the binding of M to R. Data obtained using five other RNA 10-mers, each with the sequence altered at the AUG codon, suggest that this cooperativity is AUG dependent. The data are consistent with a scheme in which mRNA and Q bind independently to the 40S ribosome, but when the AUG codon is properly aligned with Q, a conformational change results in a 2.4 kcal/mol stabilization of the complex.

Animals↗

PubMed2001

Absence of effect of varying Thr-Leu codon pairs on protein synthesis in a T7 system.

The over-represented threonine-leucine (Thr-Leu) codon pair ACG CUG has been previously reported to be inhibitory to translation compared to the synonymous under-represented Thr-Leu codon pair ACC CUG, in an E. coli system in which the codon pairs were located either 3 and 4, or 6 and 7, or 9 and 10 codons downstream from the initiating codon for the message [Irwin, B., Heck, J. D., and Hatfield, G. W. (1995) J. Biol. Chem. 270, 22801-22806]. In the work reported here, these synonymous codon pairs were tested in a T7 system, with the codon pairs located either 14 and 15, or 6 and 7 codons downstream from the AUG start codon. In contrast to the reported findings in the E. coli system, there was no difference found in translation between mRNAs containing the respective codon pairs in the T7 system. The reasons for the different findings remain unclear, but presumably are a consequence of differences between the E. coli and T7 systems used to assay gene expression. Nevertheless, as a result of this work, it appears that the effect of varying codon pairs reported in the E. coli system is not due to a difference in translational step times through the respective codon pairs, as previously proposed.

Bacteriophage T7↗

PubMed1997

Isolation and characterization of cDNA for a plant mitochondrial phosphate translocator (Mpt1): ozone stress induces Mpt1 mRNA accumulation in birch (Betula pendula Roth).

We have isolated by DDRT-PCR (differential-display reverse-transcription polymerase chain reaction) and cDNA library screening a 1.3 kb cDNA corresponding to a strongly ozone-inducible transcript from birch (Betula pendula Roth). Nucleotide sequence analysis suggests that it encodes a mitochondrial phosphate translocator protein (Pic), the first one isolated from plants. The isolated birch mitochondrial phosphate translocator cDNA (designated Mpt1) contains an open reading frame of 1092 bases encoding a 364 amino acid polypeptide. The deduced protein is 66% similar to bovine Pic isoform B. Comparison of the N-terminal amino acid sequence to known mammalian Pic proteins and the existence of an in-frame stop codon upstream of the initiation codon suggest that the isolated cDNA is full-length. Southern hybridization analysis of birch genomic DNA shows that Mpt1 is a single-copy gene. Accumulation of Mpt1 mRNA during oxidative stress imposed by ozone is detectable already at 2 h and it is at maximum ca. 12 h after the beginning of an 8 h ozone exposure (150 ppb). A second O3 peak at 48-56 h did not increase transcript levels further. O3 exposure for 2 h was sufficient for Mpt1 induction. Birch Mpt1 transcript levels remain at moderately low level during leaf development and is lower in roots and leaves when compared to young shoots undergoing wood formation and lignification.

Amino Acid Sequence↗

PubMed2004

The role of the initiation surveillance complex in promoting efficient protein synthesis.

Initiation is most often the rate-limiting step of translation. Translation initiation requires the involvement of numerous factors that assist binding of the 40 S ribosomal subunit to an mRNA and the assembly of the 80 S ribosome at the correct initiation codon. Recruitment of an initiation surveillance complex is required for translation and serves to identify mRNAs that are structurally and functionally competent for translation. For most cellular mRNAs, recruitment of the surveillance complex requires the 5'-cap and 3'-poly(A) tail. However, some cellular and viral mRNAs that naturally lack either of these have evolved alternatives that serve to recruit the complex. The initiation surveillance complex functions to stabilize eIF4F (where eIF stands for eukaryotic initiation factor), the cap-binding complex, to the cap; promote eIF4A helicase activity to remove secondary structure in the 5'-leader that might otherwise reduce 40 S ribosomal subunit scanning; promote eIF4B binding to increase eIF4A/eIF4F function and stabilize binding of the poly(A)-binding protein to the poly(A) tail. The surveillance complex is regulated through changes in phosphorylation in response to environmental conditions or by developmental signals as a means to regulate globally protein synthesis. Thus the initiation surveillance complex ensures that only intact mRNAs are recruited for translation and serves to regulate protein synthesis.

Phosphorylation↗

PubMed1997

Cross-talk to the genes for Bacillus anthracis capsule synthesis by atxA, the gene encoding the trans-activator of anthrax toxin synthesis.

The two major virulence factors of Bacillus anthracis are the tripartite toxin and the polyglutamate capsule, which are encoded by genes on the large plasmids, pXO1 and pXO2, respectively. The genes atxA, located on pXO1, and acpA, located on pXO2, encode positive trans-acting proteins that are involved in bicarbonate-mediated regulation of toxin and capsule production, respectively. A derivative strain cured of pXO1 produced less capsular substance than the parent strain harbouring both pXO1 and pXO2, and electroporation of the strain cured of pXO1 with a plasmid containing the cloned atxA gene resulted in an increased level of capsule production. An acpA-null mutant was complemented by not only acpA but also the atxA gene. The cap region, which is essential for encapsulation, contains three genes capB, capC, and capA, arranged in that order. The atxA gene stimulated capsule synthesis from the cloned cap region. Transcriptional analysis of cap by RNA slot-blot hybridization and primer-extension analysis revealed that atxA activated expression of cap in trans at the transcriptional level. These results indicate that cross-talk occurs, in which the pXO1-located gene, atxA, activates transcription of the cap region genes located on pXO2. We identified two major apparent transcriptional start sites, designated P1 and P2, located at positions 731 bp and 625 bp, respectively, upstream of the translation-initiation codon of capB. Transcription initiated from P1 and P2 was activated by both atxA and acpA, and activation appeared to be stimulated by bicarbonate. Deletion analysis of the upstream region of the cap promoter revealed that activation by both atxA and acpA required a DNA segment of 70 bp extending upstream of the P1 site. These results suggest that cross-talk by atxA to the genes encoding capsule synthesis is caused by the interaction of the atxA gene product with a regulatory sequence upstream of cap.

Antigens, Bacterial↗

PubMed1990

[Antisense oligonucleotides: tools of molecular genetics and therapeutic agents].

The binding of an oligodeoxynucleotide, so-called anti-sense, to the complementary sequence of a messenger RNA can prevent the synthesis of the encoded protein. This approach constitutes a very efficient and specific means to artificially regulate gene expression. Numerous chemical modifications have been introduced into synthetic oligos in order to provide them with properties that unmodified molecules do not display. For instance, oligos built up with methylphosphonate, phosphorothioate and alpha-anomer units lead to molecules that are resistant to DNases. Acridine-linked oligos exhibit an increased affinity for the target sequence due to the intercalation of the dye into the oligo/RNA duplex. Two different mechanisms account for translation inhibition by antisense oligos. Inhibition of the elongation step results only from the induced cleavage of the target RNA by RNase-H. In contrast, oligos targeted upstream of the AUG initiation codon can block the initiation step through an RNase-H independent mechanism. As a consequence, methylphosphonate- and alpha-oligos, which do not elicit RNase-H activity, targeted to the 5' region, are efficient antisense; but they are inactive if targeted to the coding sequence. Experiments performed with antisense oligos in cell-free extracts supported the notion that the mini-exon sequence, acquired by trans-splicing, was present on every message in trypanosomatids and on some of them in nematodes. Furthermore, an acridine-linked oligo complementary to the mini-exon sequence of Trypanosoma brucei induced a lethal effect on cultured procyclics. Therefore these compounds constitute promising tools in molecular genetics and could open new routes to rationally tailor therapeutic agents.

Animals↗

PubMed1981

Nucleotide sequence of cloned cDNAs encoding human preproparathyroid hormone.

We have cloned cDNA copies of human preproparathyroid hormone in Escherichia coli after insertion of double-stranded DNA into the Pst I site of plasmid pBR322 using the poly(dG) . poly(dC) homopolymer extension technique. Recombinant plasmids coding for preproparathyroid hormone were identified by filter hybridization assay using as a probe 32P-labeled bovine preproparathyroid cDNA. Nucleotide sequence analysis of five recombinant plasmids permitted the assignment of 74 nucleotides of the 5' noncoding region, the entire coding region of 345 nucleotides, and the entire 3' noncoding region of 348 nucleotides of the mRNA. The coding sequence predicts the previously unknown "pre" amino acid sequence and clarifies the hormone's amino acid sequence, which has been disrupted. The 5' noncoding region contains an AUG codon followed by a UGA stop codon before the authentic initiator codon. The 3' noncoding region is 120 nucleotides longer than in bovine preproparathyroid mRNA and contains two A-A-U-A-A-A sequences, potential signals for polyadenylation.

Base Sequence↗

PubMed1997

Structure of the 32-kDa galectin gene of the nematode Caenorhabditis elegans.

Galectins are a family of soluble beta-galactoside-binding lectins distributed in both vertebrates and invertebrates and, more recently, found also in fungus. The 32-kDa galectin isolated from the nematode Caenorhabditis elegans (Hirabayashi, J., Satoh, M., and Kasai, K. (1992) J. Biol. Chem. 267, 15485-15490) was the first "tandem repeat-type" galectin, containing two homologous carbohydrate-binding sites. Here, we report the structure of the nematode 32-kDa galectin gene. Physical mapping by yeast artificial chromosome polytene filter hybridization revealed that the 32-kDa galectin gene is located on chromosome II. Analysis of the transcript (1.4 kilobases) showed the presence at its 5'-end of a 22-nucleotide trans-spliced leader sequence (SL1). The entire genomic structure spanning >5 kilobase pairs (kbp), including the 5'-noncoding region, two intervening sequences (introns 1 and 2), and the 3'-noncoding region, was completely determined by the combination of genomic polymerase chain reaction and conventional colony hybridization. Intron 1 was relatively long (2.4 kbp) and was found to be inserted after the ninth codon (TAC) from the initiation codon. This position proved to be almost homologous to the conserved first intron insertion position in the vertebrate galectin genes (i. e. genes of mammalian galectin-1, -2, and -3 and chick 14-kDa galectin). On the other hand, intron 2 was much shorter (0.6 kbp), and it was inserted into the central region of the second carbohydrate-binding site. Although such an insertion pattern has never been observed in the vertebrate galectin genes, it seems to be common in C. elegans tandem repeat-type galectin genes, as predicted by the C. elegans genome project (Coulson, A., and the C. elegans Genome Consortium (1996) Biochem. Soc. Trans. 24, 289-291). Based on extensive sequence comparison, the origin and molecular evolution of the tandem repeat-type galectins are discussed.

Amino Acid Sequence↗

PubMed1985

A former amino terminal signal sequence engineered to an internal location directs translocation of both flanking protein domains.

To determine whether a functional amino terminal signal sequence can be active at an internal position, a hybrid gene was constructed in which the entire coding region of bovine preprolactin cDNA was inserted into chimpanzee alpha-globin cDNA 109 codons downstream from the initiation codon of globin. When RNA synthesized in vitro from this plasmid (pSPGP1) was translated in the rabbit reticulocyte cell-free system, a 32-kD protein was produced that was both prolactin and globin immunoreactive. When microsomal membranes were present during translation (but not when added posttranslationally), a 26-kD and a 14-kD product were also observed. By immunoreactivity and electrophoretic mobility, the 26-kD protein was identical to mature prolactin, and the 14-kD protein appeared to be the globin domain with the prolactin signal sequence attached at its carboxy terminus. From (a) posttranslational proteolysis in the presence and absence of detergent, (b) sedimentation of vesicles in the presence and absence of sodium carbonate pH 11.5, and (c) N-linked glycosylation of the globin-immunoreactive fragment after insertion of an Asn-X-Ser N-linked glycosylation site into the globin coding region of pSPGP1, it appears that all of the 26-kD and some of the 14-kD products, but none of the 32-kD precursor, have been translocated to the lumen of the membrane vesicles. Thus, when engineered to an internal position, the prolactin signal sequence is able to translocate both flanking protein domains. These data have implications for the understanding of translocation of proteins across the membrane of the endoplasmic reticulum.

Amino Acid Sequence↗

PubMed2000

Recognition of 5'-terminal TAR structure in human immunodeficiency virus-1 mRNA by eukaryotic translation initiation factor 2.

TAR, a 59 nt 5'-terminal hairpin in human immuno-deficiency virus 1 (HIV-1) mRNA, binds viral Tat and several cellular proteins. We report that eukaryotic translation initiation factor 2 (eIF2) recognizes TAR. TAR and the AUG initiation codon domain, located well downstream from TAR, both contribute to the affinity of HIV-1 mRNA for eIF2. The affinity of TAR for eIF2 was insensitive to lower stem mutations that modify sequence and structure or to sequence changes throughout the remainder that leave the TAR secondary structure intact. Hence, eIF2 recognizes structure rather than sequence in TAR. The affinity for eIF2 was severely reduced by a 3 nt change that converts the single A bulge into a 7 nt internal loop. T1 footprinting showed that eIF2 protects nucleotides in the loop as well as in the strand opposite the A bulge. Thus, eIF2 recognizes the TAR loop and lower part of the sub-apical stem. Though not contiguous, these regions are brought into proximity in TAR by a bend in the helical structure induced by the UCU bulge; binding of eIF2 opens up the bulge context and apical stem. The ability to bind eIF2 suggests a function for TAR in HIV-1 mRNA translation. Indeed, the 3 nt change that reduces the affinity of TAR for eIF2 impairs the ability of reporter mRNA to compete in translation. Interaction of TAR with eIF2 thus allows HIV-1 mRNA to compete more effectively during protein synthesis.

Base Sequence↗