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PubMed1999

Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules.

Translation initiation factor IF3, one of three factors specifically required for translation initiation in Escherichia coli, inhibits initiation on any codon other than the three canonical initiation codons, AUG, GUG, or UUG. This discrimination against initiation on non-canonical codons could be due to either direct recognition of the two last bases of the codon and their cognate bases on the anticodon or to some ability to "feel" codon-anticodon complementarity. To investigate the importance of codon-anticodon complementarity in the discriminatory role of IF3, we constructed a derivative of tRNALeuthat has all the known characteristics of an initiator tRNA except the CAU anticodon. This tRNA is efficiently formylated by methionyl-tRNAfMettransformylase and charged by leucyl-tRNA synthetase irrespective of the sequence of its anticodon. These initiator tRNALeuderivatives (called tRNALI) allow initiation at all the non-canonical codons tested, provided that the complementarity between the codon and the anticodon of the initiator tRNALeuis respected. More remarkably, the discrimination by IF3, normally observed with non-canonical codons, is neutralised if a tRNALIcarrying a complementary anticodon is used for initiation. This suggests that IF3 somehow recognises codon-anticodon complementarity, at least at the second and third position of the codon, rather than some specific bases in either the codon or the anticodon.

Anticodon↗

PubMedDate not supplied

Reversed genetics: a new approach to the elucidation of structure--function relationship.

Methods for generating point mutations at predetermined sites of RNA or DNA genomes have been developed. With Qbeta RNA as a template, minus strands were synthesized in vitro in a stepwise, substrate-controlled reaction. The nucleotide analogue N4-hydorxyCMP was introduced in the desired position, the minus strands were completed with the four standard triphosphates and used as templates to synthesize plus strands; about 30% of the progeny plus strands showed a base transition at the position corresponding to the nucleotide analogue. Two mutant RNAs with extracistronic nucleotide substitutions have been generated; one of these was viable, albeit with a reduced propagation rate, while the other was non-infectious. Furthermore, mutants with changes at the initiation codon of the coat cistron were prepared. An analysis of ribosome binding to such mutant RNAs revealed the importance of the A-U-G region for the formation of the initiation complex. With a similar approach applied to the beta-globin complementary DNA (CDNA) plasmid PbetaG, point mutations have been introduced at the positions corresponding to amino acids 121 to 123.

Base Sequence↗

PubMed1988

Structure of the Aspergillus nidulans pyruvate kinase gene.

The complete nucleotide sequence of the Aspergillus nidulans pyruvate kinase gene, including its flanking sequences, is presented. The gene has a 1,578 bp coding sequence that encodes a protein of 526 amino acids; the latter is strongly homologous to the pyruvate kinases found in Saccharomyces cerevisiae (66%) and mammals (53%). The gene is interrupted by seven introns, three of which are in a conserved position compared to those present in the mammalian pyruvate kinase genes sequenced thus far. A fourth intron within the mononucleotide binding fold domain is in a conserved position with respect to the position of an intron within the NAD+ binding region of maize ADH I. The transcription start site has been determined; a major site of transcription was found 80 bp before the translation initiation codon. The promoter region of the A. nidulans pyruvate kinase gene contains no direct homologies with the TATA or CCAAT sequences in the expected region (30-70 bp) before the transcription initiation site. However, extended CT-enriched regions are found in the promotor region, similar to what has been observed in genes that are highly expressed in Saccharomyces cerevisiae and filamentous fungi.

Amino Acid Sequence↗

PubMed1983

The messenger RNA for alcohol dehydrogenase in Drosophila melanogaster differs in its 5' end in different developmental stages.

Alcohol dehydrogenase (EC 1.1.1.1) of Drosophila melanogaster is coded by a single structural gene, active in both larvae and adults. The major larval and adult transcripts of Adh differ in their 5'-untranslated regions. The major larval mRNA is about 1100 bases long, some 50 bases shorter than the major adult transcript. The 5' end of the larval mRNA is colinear with the genomic sequence immediately adjacent to the coding region, starting 70 base pairs (bp) upstream of the initiation codon. By contrast, the adult mRNA shares only 36 of its 123 5'-untranslated bases with the larval mRNA; the remaining 87 are encoded by a sequence 654 bp upstream. Both initiation sites are preceded by a TATA box some 24 bp upstream. The developmental specificity of Adh expression is seen, therefore, to have a counterpart in the specificity of transcription initiation at the two separate promoter regions.

Alcohol Dehydrogenase↗

PubMed1987

Nucleotide sequence and characterization of toxR: a gene involved in exotoxin A regulation in Pseudomonas aeruginosa.

We have previously reported the discovery and subsequent cloning of a regulatory gene, designated toxR, which appears to regulate the expression of the exotoxin A (ETA) structural gene toxA. Subsequent work by this laboratory has resulted in the subcloning of the toxR gene and its transfer to a high copy number plasmid (pGW28). Functional analysis of the toxR gene using a Tn5 insertion along with toxR deletions indicates that inactivation of toxR results in a dramatic reduction of ETA production. Nucleotide sequence analysis of pGW28 has revealed a 675 bp major open reading frame (225 codons) which could encode for a protein of 24,626 daltons. Using S1 nuclease mapping, the toxR RNA transcript has been shown to originate 20 bp upstream of the presumptive translation initiation codon. Experiments using a toxA specific probe have revealed the the toxR gene product appears to regulate the expression of ETA at the transcriptional level.

ADP Ribose Transferases↗

PubMed1991

A comparison of the genes which encode non-structural protein NS3 of different orbiviruses.

The segment 10 (S10) genes of African horsesickness virus (AHSV), Palyam virus and epizootic haemorrhagic disease virus were translated in vitro in a rabbit reticulocyte lysate system. Each of the S10 genes encoded two proteins NS3 and NS3A, which were shown to be related by peptide mapping. Cloned copies of the S10 genes of two AHSV serotypes (AHSV-3 and AHSV-9) and Palyam virus were sequenced and compared to each other and to the nucleotide sequence of bluetongue virus (BTV) gene S10. Two in-phase ATG translation initiation codons reported for the S10 genes of BTV-10 and BTV-1 were conserved in the S10 genes of AHSV-3, AHSV-9 and Palyam virus, and would be able to initiate synthesis of NS3 and NS3A respectively. Comparison of the amino acid sequences of NS3 of AHSV-3 and AHSV-9 identified two areas of approximately 45 amino acids which displayed high (98%) similarity. One of these areas corresponded to the only region which displayed more than 50% amino acid similarity between NS3 of BTV, AHSV and Palyam virus. This region could represent an important structural or catalytic site of the protein. The overall amino acid similarity outside this conserved region was between 13% and 29%.

Amino Acid Sequence↗

PubMed1987

Use of the Escherichia coli gene for asparagine synthetase as a selective marker in a shuttle vector capable of dominant transfection and amplification in animal cells.

A new dominant amplifiable selective system for use in bacterium-animal cell shuttle vectors was developed by the insertion of a 2-kilobase genomic fragment containing the cloned Escherichia coli gene for asparagine synthetase (AS) into the pBR322-simian virus 40 recombinant vector pSV2 so as to place the translational initiator codon for the bacterial AS about 1,000 base pairs downstream from the simian virus 40 early promoter. This new construct, pSV2-AS, retains bacterial sequences for transcriptional and translational initiation and so can express AS in bacteria. The construct can also complement AS- mutants of mammalian cells, giving AS+ transfectants capable of growth in medium lacking asparagine, with relatively high efficiency (about 300 colonies per microgram of DNA per 10(6) cells exposed). The vector can be amplified up to 100-fold in such AS+ transfectants by selection in asparagine-free medium containing increasing concentrations of the AS inhibitor beta-aspartyl hydroxamate. AS+ transfectants were found to be much more resistant to a second AS inhibitor, Albizziin, than were normal AS+ animal cell lines. This difference, which may indicate a strong resistance of the bacterial AS enzyme to Albizziin, was exploited to develop an effective selection for bacterial AS transfectants of a number of wild-type AS+ cell lines of rat, Chinese hamster, mouse, and human origin. LR-73 cells, a Chinese hamster AS+ cell line, were transfected with pSV2-AS with an efficiency of about 1,000 colonies per 0.5 microgram of DNA per 10(6) cells. The integrated construct in these cells was amplified by incubation of the transfectants in increasing concentrations of beta-aspartyl hydroxamate. Advantages and disadvantages of this new dominant, selectable, and amplifiable marker over markers commonly used in shuttle vectors are discussed.

Amino Acids, Diamino↗

PubMed2006

Alteration of protein subcellular location and domain formation by alternative translational initiation.

Alternative translation is an important cellular mechanism contributing to the generation of proteins and the diversity of protein functions. Instead of studying individual cases, we systematically analyzed the alteration of protein subcellular location and domain formation by alternative translational initiation in eukaryotes. The results revealed that 85.7% of alternative translation events generated biological diversity, attributed to different subcellular localizations and distinct domain contents in alternative isoforms. Analysis of isoelectric point values revealed that most N-terminal truncated isoforms significantly lowered their isoelectric point values targeted at different subcellular localizations, whereas they had conserved domain contents the same as the full-length isoforms. Furthermore, Fisher's exact test indicated that the two ways-targeting at different cellular compartments and changing domain contents-were negatively associated. The N-term truncated isoforms should have only one way to diversify their functions distinct from the full-length ones. The peculiar consequence of subcellular relocation as well as change of domain contents reflected the very high level of biological complexity as alternative usage of initiation codons.

Animals↗

PubMed2006

Highly expressed proteins have an increased frequency of alanine in the second amino acid position.

BACKGROUND: Although the sequence requirements for translation initiation regions have been frequently analysed, usually the highly expressed genes are not treated as a separate dataset. RESULTS: To investigate this, we analysed the mRNA regions downstream of initiation codons in nine bacteria, three archaea and three unicellular eukaryotes, comparing the dataset of highly expressed genes to the dataset of all genes. In addition to the detailed analysis of the nucleotide and codon frequencies we compared the N-termini of highly expressed proteins to the N-termini of all proteins coded in the genome. CONCLUSION: The most conserved pattern was observed at the amino acid level: strong alanine over-representation was observed at the second amino acid position of highly expressed proteins. This pattern is well conserved in all three domains of life.

Adenosine↗

PubMedDate not supplied

Effects of liposomal antisense oligonucleotides on mRNA and protein levels of the HPV 16 E7 oncogene.

Despite the known association of human papillomavirus (HPV) infection with cervical cancer there is no specific antiviral treatment for HPV infection. Antisense oligode-oxynucleotides (AS-ODNs) may offer an effective way to treat HPV infections as the stability and delivery have been improved using modified ODNs or carrier systems. In this study we investigated the effects of liposomal AS-ODNs (0.1, 1 and 5 microM) on HPV 16 E7 mRNA and protein levels in CaSki cells. We used cationic liposomes (10 microM) containing dimethyldioctadecylammonium bromide (DDAB) or 2,3-dioleyloxy-N-[2(sperminecar-boxamido)ethyl]-N, N-dimethyl-1-propanaminium trifluoroacetate (DOSPA). Both these liposomes had dioleoylphosphatidyl-ethanolamine (DOPE) as a helper lipid. The target of the AS-ODNs was E7 protein because it is the one of the two oncoproteins of HPV 16. Only liposomal AS-ODNs which were targeted to the initiation codon of E7, had an effect on E7 mRNA expression; two shorter transcripts were detected, suggesting that RNase H degradation was activated. Liposomal random ODN or liposomal ODN targeted downstream from the initiation site of E7 did not affect the mRNA pattern. However, no change was found in the E7 protein levels detected by immunoprecipitation. Further studies showed that AS-ODNs inhibited the translation of E7 mRNA in a rabbit reticulocyte lysate assay. This data, together with the changes in mRNA levels, proved that the AS-ODNs reached the target mRNA. One possible explanation for the unchanged protein level of E7 in CaSki cells might be that immunoprecipitation is not sensitive enough to detect minor changes in protein levels. However, further progress is still needed in the field of carrier systems and modifications of AS-ODNs before non-sequence specific effects can be avoided.

Antiviral Agents↗

PubMed1999

Facile characterization of translation initiation via nonsense codon suppression.

A new strategy for studying the mechanism of translation initiation in eukaryotes has been developed. The strategy involves the use of an in vitro translation system to incorporate a non-natural fluorescent amino acid into a protein from a suppressor tRNAPheCUA misacylated with that amino acid. It is thereby possible to monitor translation initiation efficiency at an AUG codon in different contexts; this is illustrated for three constructs encoding Escherichia coli dihydrofolate reductase mRNA with different translation initiation regions. Fluorescence measurements after in vitro translation of the mRNAs in rabbit reticulocyte lysate reflected differences in the position and efficiency of translation initiation and, therefore, can be used for characterization of the translation initiation process.

Amino Acid Sequence↗

PubMed1990

Translation initiation in Escherichia coli: old and new questions.

We discuss the features of Escherichia coli mRNAs which determine where and how efficiently translation is initiated. We have shown that DNA fragments comprising 60-80 nucleotides that bracket the initiation codon of real genes generally promote translation when inserted within a foreign mRNA, while those not corresponding to an authentic gene start do not do so even if they include a Shine-Dalgarno-like element followed by AUG or GUG. Therefore, the information that pinpoints the correct start sites, while extending beyond the mere presence of these elements, remains essentially local. The possible nature of this information is discussed. Next, we point out that, in order to remain accessible, translational starts must escape long-range base-pairing within large mRNAs, and we argue that the tight coupling between translation and transcription plays an important role in achieving this. Finally, we discuss two intriguing situations in which the initiation frequency should be dependent upon the rate of translation elongation.

Codon↗

PubMed2000

Mutation analysis of the GALT gene in Czech and Slovak galactosemia populations: identification of six novel mutations, including a stop codon mutation (X380R).

A study of the galactose-1-phosphate uridyltransferase (GALT) gene from 37 unrelated galactosemia families is reported here. A total of 16 sequence variations in eleven mutated alleles was found. The two most common molecular defects were the mutations Q188R (46.0%) and K285N (25.7%). Six novel mutations in the GALT gene, X380R, Y209S, E340K, L74fsdelCT, Q169K and L256/P257delGCC, were detected. Three mutations, V151A, L195P and R204X that were previously described in other populations, were also found. The mutation X380R, which breaks the stop codon of the GALT gene, causes elongation of the GALT enzyme's protein chain. A deletion of four nucleotides in the 5' promoter region, in a position 116 - 119 nucleotides upstream from the initiate codon (5'UTR-119delGTCA), was revealed in Duarte (D2) alleles, in addition to N314D, IVS4nt-27g-->c, IVS5nt+62g-->a, and IVS5nt-24g-->a. An unusual molecular genotype was observed on 2 types of classical galactosemia alleles, with six variations from the normal nucleotide sequence presented in cis (mutation V151A or E340K plus five Duarte (D2) characteristic variations). In summary, galactosemia is a heterogeneous disorder at the molecular level, and mutation N314D, appears to be an ancient genetic variant of the GALT gene. Hum Mutat 15:206, 2000.

Amino Acid Substitution↗

PubMed1998

Yellow fever 5' noncoding region as a potential element to improve hepatitis C virus production through modification of translational control.

The lengthy 5' noncoding region (5' NCR) of hepatitis C virus (HCV) RNA forms a highly ordered secondary structure, very conserved among different strains. It includes an internal ribosome entry site (IRES) element, responsible for the cap-independent translation initiation of HCV RNA. Similarly to the IRES of hepatitis A virus (HAV), another human hepatitis virus, HCV IRES, activity in internal initiation of translation is weak. Furthermore, both viruses exhibit a poor growth phenotype that may result at least partially from an inhibitory control of translation. To enhance HCV translation, as a preliminary step in designing constructs for improvement in viral production, we sought to evaluate a chimeric construct containing the yellow fever virus (YFV) 5' NCR fused to the initiation codon of the HCV coding sequence. YF viral RNA, as the majority of eukaryotic messenger RNAs, is translated by a ribosome scanning mechanism in a cap-dependent manner. The efficiency of translation initiation of the parental HCV construct was compared in vitro in rabbit reticulocyte lysates with that of the chimeric construct containing YFV 5' NCR. Surprisingly, the related distanced YFV 5' NCR was fivefold more active than was the wild-type HCV IRES in directing that function. Furthermore, chimeric transcripts were shown to be effective in vivo after transfection of eukaryotic cells. Taken together, these results raise the following question: why has the HCV genus evolved to the acquisition of an IRES element within its 5' NCR among the Flaviviridae family?

5' Untranslated Regions↗

PubMed2002

Structure, upstream promoter region, and functional domains of a mouse and human Mix paired-like homeobox gene.

Mix/Bix proteins represent a vertebrate subgroup of paired-like homeodomain proteins which are known to function around the time of gastrulation. Here we report the structures of the genomic and upstream promoter regions of a mouse and human Mix-like gene. Both genes map to syntenic regions of chromosome 1 and contain two coding exons, with the paired-type homeodomain split between the exons within helix 3. Differentiating mouse embryonic stem cells transcribe a messenger RNA of approximately 2.6 kb. The first exon encodes the translation initiation codon and a 5' untranslated region of approximately 90 bp. Sequence analysis of the 960 bp upstream of the transcription start site of the mouse Mix gene revealed the presence of a putative initiator region and TATA box as well as potential Smad, FoxH1/FAST, T-box, COUP-TF, C/EBP, GATA, HNF3 binding sites and retinoic acid response elements. A number of these sites are conserved in the human Mix promoter. We find that most paired-related homeodomain proteins, including mouse and human Mix, contain a proline-rich region within their amino termini which may interact with other proteins. Mouse and human Mix proteins contain highly conserved carboxy-terminal polar/acidic regions with the potential to form an amphipathic helix and the ability to activate transcription in yeast. Mouse Mix expressed in COS cells or in vitro binds a DNA consensus sequence identified previously for paired class homeodomain proteins. These studies suggest that a number of features of paired-like protein structure and function are conserved across diverse species and provide a useful framework for studying the function and regulation of the mouse Mix gene.

Amino Acid Sequence↗

PubMed2002

Structural basis of translational control by Escherichia coli threonyl tRNA synthetase.

Escherichia coli threonyl-tRNA synthetase (ThrRS) represses the translation of its own messenger RNA by binding to an operator located upstream of the initiation codon. The crystal structure of the complex between the core of ThrRS and the essential domain of the operator shows that the mRNA uses the recognition mode of the tRNA anticodon loop to initiate binding. The final positioning of the operator, upon which the control mechanism is based, relies on a characteristic RNA motif adapted to the enzyme surface. The finding of other thrS operators that have this conserved motif leads to a generalization of this regulatory mechanism to a subset of Gram-negative bacteria.

Anticodon↗

PubMed1997

Molecular characterization and expression of Onchocerca volvulus glutathione reductase.

Glutathione metabolism represents a potential target for anti-parasite drug design. The central role of glutathione reductase (GR) in maintenance of the thiol redox state and in anti-oxidative defence has to be evaluated in more detail in order to establish the essential function of this enzyme for the survival of the filarial parasite Onchocerca volvulus. The O. volvulus GR (OvGR) gene was cloned and sequenced. The gene is composed of 13 exons and 12 introns and spans 4065 bp. The first intron is located within the 5'-untranslated region of the gene, 16 nucleotides upstream of the translation initiation codon. Southern-blot analysis and structural characterization of the genomic sequence indicate that OvGR is encoded by a single-copy gene. Isolation of various cDNA clones revealed a polymorphism of polyadenylation initiation with no consensus polyadenylation sites in any of the cDNAs analysed. The entire cDNA is 1977 bp long and carries the nematode-specific spliced leader sequence SL1 at its 5' end, 236 nucleotides upstream of the first in-frame methionine. The cDNA codes for a polypeptide of 462 amino acids with 53.5% sequence identity with human GR (HsGR). A total of 18 out of 19 residues contributing to glutathione binding are identical in OvGR and HsGR. However, one of the arginine residues (Arg-224 in HsGR) involved in discrimination between NADPH and NADH in all known GRs is substituted by tryptophan (Trp-207 in OvGR). The coding region of OvGR was expressed in Escherichia coli as a histidine-fusion protein, and it was established that the parasite protein still favours the binding of NADPH (Km 10.9 microM) over NADH (Km 108 microM). The histidine-fusion protein has a subunit size of 54 kDa and is active as a homodimer of 110 kDa.

Amino Acid Sequence↗

PubMed2004

Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA.

Protein synthesis in all cells begins with recruitment of the small ribosomal subunit to the initiation codon in a messenger RNA. In some eukaryotic viruses, RNA upstream of the coding region forms an internal ribosome entry site (IRES) that directly binds to the 40S ribosomal subunit and enables translation initiation in the absence of many canonical translation initiation factors. The hepatitis C virus (HCV) IRES RNA requires just two initiation factors, eukaryotic initiation factor (eIF) 2 and eIF3, to form preinitiation 48S ribosomal complexes that subsequently assemble into translation-competent ribosomes. Using an RNA-based affinity purification approach, we show here that HCV IRES RNA facilitates eIF2 function through its interactions with eIF3 and the 40S ribosomal subunit. Although the wild-type IRES assembles normally into 48S and 80S ribosomal complexes in human cell extract, mutant IRES RNAs become trapped at the 48S assembly stage. Trapped 48S complexes formed by IRES mutants with reduced eIF3 binding affinity nonetheless contain eIF3, consistent with inherent eIF3-40S subunit affinity. Intriguingly, however, one of these IRES mutants prevents stable association of both eIF3 and eIF2, preventing initiator tRNA deposition and explaining the block in 80S assembly. In contrast, an IRES mutant unable to induce a conformational change in the 40S subunit, as observed previously by single-particle cryoelectron microscopy, blocks 80S formation at a later stage in assembly. These data suggest that the IRES RNA coordinates interactions of eIF3 and eIF2 on the ribosome required to position the initiator tRNA on the mRNA in the ribosomal peptidyl-tRNA site (P site).

Eukaryotic Initiation Factor-2↗