Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Codon, Initiator”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources
PubMed1985

Characterization of the lep operon of Escherichia coli. Identification of the promoter and the gene upstream of the signal peptidase I gene.

The DNA sequence flanking the gene (lep) encoding signal peptidase I of Escherichia coli has been determined. The upstream flanking sequence contains a gene (lepA) that encodes a polypeptide of 598 amino acid residues and terminates 18 base pairs from the initiation codon of the lep gene. The position of the lep promoter was determined by both gene fusion with the lacZ gene as well as by S1 nuclease mapping of the lep mRNA to be 73 base pairs upstream from the initiation codon of the lepA gene. The lepA gene was cloned into a high expression vector (pIN-III), and its gene product was identified to be a protein of apparent molecular weight of 76,000. This gene product was preferentially localized in the cytoplasmic membrane and periplasmic fractions upon subcellular fractionation. The DNA sequence immediately downstream of the lep gene contains features consistent with a rho factor-independent transcriptional termination site, indicating that the lep operon encodes only two proteins (lepA and lep).

Amino Acid Sequence↗
PubMed1984

Translationally associated helix-destabilizing activity in rabbit reticulocyte lysate.

Helix-destabilizing activity associated with mRNA translation was detected in rabbit reticulocyte lysate by assessing the ability of the ribosome to read through mRNA/cDNA duplexes. Hybridization of globin mRNA to cDNA fragments which extend into the 5' nontranslated region fully block the translation of the hybridized message. However, hybridization of the mRNA to cDNA fragments which cover regions 3' to the initiation codon has no adverse effect on its translation. The translation of mRNA hybridized to this second category of cDNA fragments occurs without the total removal of cDNA. These results imply that the ribosomal complex, once fully assembled at the AUG initiation codon, can locally destabilize secondary structures as it moves along the message. This activity may be critical for translational elongation by the ribosome.

Adult↗
PubMed1991

In vivo transcriptional pattern in the infC operon of Bacillus stearothermophilus.

By Northern blot and primer extension analyses it was shown that in Bacillus stearothermophilus the genes infC, rpmI and rplT constitute a single transcriptional unit; the promoter and the transcriptional start-point used in vivo were identified and the half-life of the transcript (1.2 min) was determined. No indication of multiple initiation sites nor of differential stability of different regions of the transcript was found. The results suggest that Escherichia coli and B. stearothermophilus have a different pattern of transcription around the infC gene cluster and that differential translational efficiency within the infC-rpmI-rplT transcriptional unit accounts for the different levels of IF3, L35 and L20 expression. The rare AUU initiation codon is the only strictly conserved element of the several peculiar transcriptional and translational features found in E. coli infC. Upon changing this codon to AUG, we found a ca. 30-fold increased expression of B. stearothermophilus infC, which is similar to that previously found with E. coli infC (i.e. 40-fold), and provided evidence that regulation of infC expression through its rare AUU initiation codon might be a general phenomenon in bacteria.

Amino Acid Sequence↗
PubMed1986

Characterization of the human beta-crystallin gene Hu beta A3/A1 reveals ancestral relationships among the beta gamma-crystallin superfamily.

We report here the detailed structure of a human beta-crystallin gene, designated Hu beta A3/A1, which was isolated and characterized using homologous mouse and bovine beta-crystallin cDNAs. Hu beta A3/A1 consists of six exons, spanning approximately 8 kilobases. The first two exons code for an N-terminal extension of 32 amino acid residues, while the other four encode the four similar structural motifs of the predicted polypeptide. Sequence homologies among the latter four exons and their intron-exon junctions support a model of gene evolution based on two successive exon duplications. Transcription of Hu beta A3/A1 in the eye lens initiates 24 base pairs downstream of a putative TATA box and just 7 nucleotides upstream of a potential initiation codon, generating a single mRNA of approximately 1 kilobase. Comparison of Hu beta A3/A1 with the homologous bovine cDNA and the translation products of the corresponding bovine gene suggests that translation of Hu beta A3/A1 commences at either of two potential initiation codons located in the first and second exons. Differential use of these two codons predicts two polypeptides differing by the presence or absence of 17 amino acid residues at their N-termini.

Amino Acid Sequence↗
PubMed1990

RNA editing in transcripts of the mitochondrial genes of the insect trypanosome Crithidia fasciculata.

With the aid of cDNA and RNA sequence analysis, we have determined to what extent transcripts of mitochondrial maxicircle genes of the insect trypanosome Crithidia fasciculata are altered by RNA editing, a novel mechanism of gene expression which operates via the insertion and deletion of uridine residues. Editing of cytochrome c oxidase (cox) subunit II and III transcripts and of maxicircle unidentified reading frame (MURF) 2 RNA is limited to a small section and results in the creation of a potential AUG translational initiation codon (coxIII, MURF2) or the removal of a frameshift (coxII). No differences with the genomic sequences were observed in the remainder of these RNAs. Surprisingly, NADH dehydrogenase subunit I transcripts were completely unedited in the coding region, implying that an AUG translational initiation codon is absent. The partial ribosomal RNA sequences determined also conform to the gene sequences. Together these results lead to the conclusion that the unusual sequences predicted by the protein and rRNA genes must indeed be present in the gene products. Editing also occurred in the poly(A) tail of RNAs from all protein genes, including those that are unedited in the coding region. The tails display a large variation in AU sequence motifs. Finally, some cDNAs contained sequences absent from both the DNA and the edited RNA. Some of these may represent intermediates in the RNA editing process. We argue, however, that long runs of T may be artefacts of cDNA synthesis.

Animals↗
PubMed1995

Cloning and sequencing of the catechol 2,3-dioxygenase gene of Alcaligenes sp. KF711.

The catechol 2,3-dioxygenase is an aromatic ring-fission enzyme catalyzing the conversion of catechol to 2-hydroxymuconic semialdehyde. A catechol 2,3-dioxygenase gene has been cloned from chromosomal DNA of Alcaligenes sp. KF711, and its sequence was determined. The catechol 2,3-dioxygenase gene was consisted of 927 nucleotides with ATG initiation codon and TGA termination codon, which can encode a polypeptide of molecular weight 35 kDa containing 308 amino acid residues. G+C content of the gene was 58 mol%, and a putative ribosome-binding sequence was identified at about 10 nucleotides upstream from the ATG initiation codon. The sequence of catechol 2,3-dioxygenase from Alcaligenes sp. KF711 exhibited 81-92% homology at nucleotide level and 84-92% homology at amino acid level with those of corresponding enzymes encoded in xylE of TOL plasmid, nahH of NAH7 plasmid, and dmpB of Pseudomonas CF600.

Alcaligenes↗
PubMed1998

Expression of the rice yellow mottle virus P1 protein in vitro and in vivo and its involvement in virus spread.

Rice yellow mottle sobemovirus (RYMV) is responsible for the yellow mottle disease on rice in Africa. The expression and function of the protein P1 (17.8 kDa) encoded by the first open reading frame (ORF) of RYMV was investigated. Using an antibody raised against purified P1, two proteins with apparent molecular masses of 18 and 19 kDa were identified in in vitro translation reactions of transcripts of the full-length cDNA of RYMV. Likewise, gene products with similar molecular mass were detected in inoculated and systemically infected rice leaves and in infected rice protoplasts. A mutant from which ORF1 nucleotides 88 to 547 were deleted and a frameshift mutant that resulted in truncation of 83 amino acids from the C terminus of P1 were incapable of replicating in protoplasts. In contrast, a mutant that does not express P1 due to a mutation at the initiation codon replicated efficiently in protoplasts but at a reduced level (about 0.5- to 2-fold less) compared to replication of wild-type RNA. None of these mutants caused systemic infection in rice plants. Transgenic rice plants that express P1 complemented the initiation codon mutant, but not the deletion mutants, and produced systemic infection. These experiments demonstrate that P1 of RYMV is dispensible for virus replication, although nucleotide deletions or additions in ORF1 are apparently lethal for virus replication. Furthermore, P1 of RYMV is required for the infection of plants and is important for virus spread.

Animals↗
PubMed1987

Structure and expression of pea mitochondrial F1ATPase alpha-subunit gene and its pseudogene involved in homologous recombination.

We have characterized four pea mitochondrial DNA segments carrying the F1ATPase alpha-subunit coding sequences. These four types share a common 1.7-kb repeat sequence flanked by four combinations of two different left- and right-hand sequences. These results suggest that the alpha-subunit genes locate at the homologous recombination sites in the pea mitochondrial genome and that homologous recombination between two of these loci generates the other two types of structures. The uninterrupted alpha-subunit coding sequence of 1,521 bp is present in two of these loci. A rearrangement of 965 bp 3' to the ATG initiation codon generates two copies of pseudogenes where the C-terminal two-thirds of the alpha-subunit coding sequence is replaced with an unidentified coding frame. The other border of sequence divergence is located 733 bp upstream of the ATG initiation codon. Although multiple forms of alpha-subunit gene transcripts are present in mitochondria, the pseudogenes do not seem to express any alpha-subunit-related polypeptide.

Amino Acid Sequence↗
PubMed1994

Cloning and sequencing of the spherulin gene, the occlusion body major polypeptide of the Melolontha melolontha entomopoxvirus (MmEPV).

In the late stage of infection, virions of the Melolontha melolontha entomopoxvirus (MmEPV) are occluded into cytoplasmic paracrysalline proteinaceous occlusion bodies designated spherules (A. Amargier, C. Vago, G. Meynadier, 1964, Mikroskopie 19, 309-315). We have cloned and sequenced a 4-kpb DNA fragment of the MmEPV genome encompassing the spherule major protein gene named spherulin. The spherulin gene contains an open reading frame able to code for a 942-amino-acid (aa) polypeptide (MW 109 kDa), consistent with a size above 100 kDa determined by SDS-PAGE for purified spherulin. The MmEPV spherulin showed more than 40% as homology with the Amsacta moorei EPV (AmEPV) spheroidin and shared homologies with the partially sequenced Choristoneura biennis EPV (CbEPV) spheroidin, indicating that this biologically important polypeptide is well conserved among EPVs infecting phylogenetically as distant groups of insects as lepidoptera and coleoptera. Western blot analyses confirmed the relationships between the three polypeptides. In contrast, no homology was detected between the MmEPV spherulin and EPV fusolins or vertebrate poxvirus A-type inclusion proteins. The 45 bases upstream from the ATG initiation codon of spherulin shared 60% homology with the vaccinia virus late promoters including the highly conserved TAAATG consensus sequence. Furthermore, the 5' extremity of the spherulin mRNA consisted of a poly(A) tract of about 20 nucleotides just upstream from the AUG translational initiation codon. These are characteristic features of vertebrate poxvirus late mRNAs suggesting similar modalities of gene expression for vertebrate and insect poxvirus genomes.

Amino Acid Sequence↗
PubMed1992

RNA packaging signal of human immunodeficiency virus type 1.

Cells infected with a recombinant vaccinia virus carrying the gag and pol regions of the human immunodeficiency virus type 1 genome (Vac-gag/pol) released human immunodeficiency virus (HIV)-like particles containing HIV-specific RNA. However, cells infected with another recombinant vaccinia, Vac-gag/pol-dP, derived through the deletion of an 85-base region (nucleotide positions 679-763) of the HIV genome between the primer binding site and the gag initiation codon of Vac-gag/pol, produced HIV-like particles devoid of the HIV-specific RNA. This 85-base deletion was suggested to cause the collapse of a stable stem-loop structure of 46 bases (751-796) around the gag initiation codon. To examine the role of the stem-loop structure in the packaging of RNAs, we constructed a vaccinia vector plasmid that carried this 46-base sequence followed by the Sendai virus nucleocapsid (NP) gene. When both Vac-gag/pol-dP and this plasmid were introduced into cells, HIV-like particles released from the cells contained the NP gene RNA. However, another vaccinia vector plasmid, which carried the 46-base sequence in the midst of the NP gene, could not supply RNA for incorporation into HIV-like particles. Computer analysis of this plasmid sequence suggested that the 46-base sequence cannot form the stem-loop structure. These findings suggest that the stem-loop structure formed by the 46-base sequence is crucial as a packaging signal.

Base Sequence↗
PubMed2000

Characterization of the cystatin B gene promoter harboring the dodecamer repeat expanded in progressive myoclonus epilepsy, EPM1.

Mutations in the gene encoding cystatin B (CSTB) are responsible for the primary defect in progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1). A novel and unique type of disease-causing mutation, an unstable dodecamer repeat expansion, accounts for the majority of EPM1 patients world-wide. This minisatellite repeat expansion, located in the putative promoter of CSTB 175 bp upstream from the translation initiation codon, appears to downregulate CSTB gene expression in vivo. We report here the characterization of the CSTB promoter using different promoter-luciferase gene constructs. Transient transfections of cultured mammalian cells suggest that the region from -670 to -1 bp from the translation initiation codon functions as the CSTB promoter. Active binding to five Sp1 and four AP1 sites as well as weak binding to an androgen response element (ARE) half site was demonstrated by electrophoretic mobility shift assays. The effect of the minisatellite expansion on the promoter activity was evaluated by comparing the activity of constructs containing wild-type and expanded alleles. An increase in the number of dodecamer units from three to 19 repeats lowered transcription in vitro by 10-fold. Northern analysis of lymphoblastoid RNA from individuals with 'premutation' length dodecamer repeat (12-17 copies) expansions showed decreased levels of CSTB mRNA expression. These data indicate that expansion of the dodecamer repeat located in the proximal promoter of CSTB severely disrupts the function of the promoter and thereby reduces transcription of CSTB.

Animals↗
PubMed2001

The Cold Box stem-loop proximal to the 5'-end of the Escherichia coli cspA gene stabilizes its mRNA at low temperature.

The 5'-end region of cspA mRNA contains a Cold Box sequence conserved among several cold-shock mRNAs. This region forms a stable stem-loop structure followed by an AU-rich sequence. Here we show that the Cold Box region is essential for the normal scale of cspA mRNA induction after cold shock because a deletion of the stem-loop significantly destabilizes the mRNA and reduces the cold shock-induced cspA mRNA amount by approximately 50%. The AU-rich track, however, slightly destabilizes the mRNA. The integrity of the stem is essential for the stabilizing function, whereas that of the loop sequence is less important. Overexpression of a mutant cspA mRNA devoid of both the AUG initiation codon and the coding sequence results in a severe growth inhibition at low temperature along with a derepression of the chromosomal cspA expression. Furthermore, the overexpressed RNA is stably associated with the 30 S and 70 S ribosomes. Our results demonstrate that the AUG initiation codon and the coding region containing the downstream box are not required for cspA mRNA to bind ribosomes and that the 5'-untranslated region by itself has a remarkable affinity to ribosomes at low temperature.

5' Untranslated Regions↗
PubMed1995

Cloning and characterization of the promoter for the rat insulin-like growth factor-binding protein-3 gene.

Insulin-like growth factor-binding protein-3 (IGFBP-3), the major IGFBP in the adult circulation, is produced by a wide range of cell and tissue types. IGFBP-3 appears to be regulated by transcriptional and/or posttranslational mechanisms in a species-, cell-, and development-specific manner. In vitro and in vivo studies suggest that a number of factors (e.g. cAMP, GH, insulin-like growth factor-I, epidermal growth factor, TSH, and FSH) can act as transcriptional regulators of IGFBP-3 in particular cell types. To address the mechanistic basis for these observations, we isolated the rat IGFBP-3 gene and began characterization and analysis of the hormonal regulation of its promoter. The rat IGFBP-3 gene is located within 2 adjacent EcoRI fragments spanning about 10 kilobases. Southern analysis indicated a single copy gene. A 1.18-kilobase fragment 5' to the translation initiation codon has been sequenced and showed 65% homology with the corresponding human IGFBP-3 sequence. The region between -100 and -1 bp relative to the transcription start site showed 85% homology. The transcription start site was 118 basepairs (bp) up-stream of the initiation codon, and a TATA box consensus was located 27 bp 5' to this CAP site. No CAAT box was present, but a CpG island was identified. Consensus sequences for a number of putative response elements (e.g. activating protein-2, insulin, TSH/insulin-like growth factor, and GH) were present within -700 bp of the CAP site. A series of 5'-truncated chloramphenicol acetyltransferase reporter constructs has been transfected into both COS-1 cells and the rat thyroid cell line FRTL-5. Both basal and hormonally responsive (TSH and phorbol ester) promoter activities have been localized within the first 472 bases of the promoter region. These data indicate that suitable transfected cell systems can be established in which additional investigations can be undertaken into the mechanisms of cell- and species-specific hormonal regulation of IGFBP-3 gene expression.

Animals↗
PubMed2000

Translation by ribosome shunting on adenovirus and hsp70 mRNAs facilitated by complementarity to 18S rRNA.

Translation initiation on eukaryotic mRNAs involves 40S ribosome association with mRNA caps (m(7)GpppN), mediated by initiation factor eIF4F. 40S eukaryotic ribosomes and initiation factors undergo 5' scanning to the initiation codon, with no known role for complementarity between eukaryotic 18S rRNA and the 5' noncoding region of mRNAs. We demonstrate that the 5' noncoding region of human adenovirus late mRNAs, known as the tripartite leader, utilizes a striking complementarity to 18S rRNA to facilitate a novel form of translation initiation referred to as ribosome shunting, in which 40S ribosomes bind the cap and bypass large segments of the mRNA to reach the initiation codon. Related elements are also shown to promote ribosome shunting in adenovirus IVa2 intermediate phase mRNA during virus infection and in human heat shock protein 70 (hsp70) mRNA for selective translation during heat shock. The importance of mRNA complementarity to 18S rRNA suggests that ribosome shunting may involve either specific RNA structural features or a prokaryotic-like interaction between mRNA and rRNA.

Adenoviruses, Human↗
PubMed1989

Nucleotide sequence and transcriptional analysis of the Streptomyces griseus gene (afsA) responsible for A-factor biosynthesis.

The nucleotide sequence of the Streptomyces griseus afsA gene, possibly encoding a key enzyme for A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) biosynthesis, was determined. The translational initiation codon was identified by introducing out-of-frame mutations at appropriate positions by oligonucleotide-directed mutagenesis. The afsA gene was thus found to code for a protein of 301 amino acid residues and 32.6 kilodaltons whose codon usage pattern was in agreement with the general tendency of Streptomyces genes with an extremely high guanine-plus-cytosine content. High-resolution S1 nuclease mapping indicated that the transcriptional start point was the A residue, the first position of the ATG translational initiation codon.

4-Butyrolactone↗
PubMed1991

Nucleotide sequence and expression of the capsid protein gene of feline calicivirus.

The sequence of the 3'-terminal 2,486 bases of the feline calicivirus (FCV) genome was determined. This region of the FCV genome, from which the 2.4-kb subgenomic RNA is derived, contained two open reading frames. The larger open reading frame, found in the 5' end of the subgenomic mRNA, contained 2,004 bases encoding a polypeptide of 73,467 Da. The smaller open reading frame, encoded in the 3' end of the mRNA, was composed of 318 bases, encoding a polypeptide of 12,185 Da. The AUG initiation codon of the second open reading frame overlapped the UGA termination codon of the first, with the sequence AUGA. The nucleotide sequence of the region containing this overlap resembles the -1 frameshift sequences of the retroviruses. The 5' end of the 2.4-kb subgenomic RNA was mapped by primer extension analysis. There were two apparent transcription initiation points, both of which were 5' to the AUG initiation codon of the large open reading frame. Transcription from these sites yielded RNA transcripts with 5' nontranslated leader regions of 17 and 18 bases. The total length of the 2.4-kb subgenomic RNA was 2,375 bases (from the 5'-most start site) excluding the poly(A) tail. Edman degradation of the purified capsid protein of FCV showed that the capsid protein was encoded by the large open reading frame. Western immunoblot analysis of FCV-infected cells using a feline anti-FCV antiserum demonstrated that translation of the capsid protein was detectable at 3 h postinfection and continued to accumulate until 8 h postinfection, the last time examined.

Amino Acid Sequence↗
PubMed1985

Inhibition of rabbit globin mRNA translation by sequence-specific oligodeoxyribonucleotides.

Oligodeoxyribonucleotides 8-12 nucleotides in length whose sequences are complementary to the 5' end, the initiation codon regions, or the coding regions of rabbit globin mRNA were tested for their ability to inhibit translation in a rabbit reticulocyte lysate and in a wheat germ extract. The oligomers interact specifically with their target mRNAs as shown by their ability to serve as primers with reverse transcriptase. In the reticulocyte lysate, oligomers complementary to the 5' end or the initiation codon regions inhibit translation of both alpha- and beta-globin mRNA, whereas oligomers complementary to the coding regions have little or no effect. This suggests that reticulocyte ribosomes are able to displace the oligomers from the mRNA during the elongation but not the initiation step of translation. In the wheat germ system, translation was effectively inhibited by all oligomers regardless of their binding site on the message. In contrast to their behavior in the reticulocyte system, the oligomers inhibited alpha- and beta-globin synthesis in a specific manner. This observation suggests that control of alpha- and beta-globin mRNA translation is coordinated in the reticulocyte lysate system but not in the wheat germ extract. The results of our studies indicate that oligodeoxyribonucleotides may be useful probes for studying control of mRNA translation in cell-free systems.

Animals↗
PubMed1977

The nucleotide sequences of the untranslated 5' regions of human alpha- and beta-globin mRNAs.

The complete sequences of the untranslated 5' regions of human alpha- and beta-globin mRNAs were determined by sequence analysis of full-length cDNAs. The single-stranded cDNAs were digested with the restriction endonuclease Hae III, and the two 3'-terminal fragments of 75 and 132 nucleotides, complementary to the 5' termini of the alpha- and beta-globin mRNAs, respectively, were isolated and sequenced. Including the initiation codon AUG, the untranslated 5' regions of human alpha- and beta-globin mRNAs contain 41 and 54 nucleotides, respectively, and exhibit striking homologies with the corresponding sequences in the rabbit. Human alpha- and beta-globin mRNAs have five bases in the region of the initiation codon that may form base pairs with the 3' terminus of 18S rRNA. Stable secondary structures with hairpin loops can be constructed in the untranslated 5' regions.

Base Sequence↗