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Results for “Codon, Initiator”

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PubMed1983

Gene structure of a phenobarbital-inducible cytochrome P-450 in rat liver.

The gene structure of a phenobarbital-inducible rat liver cytochrome P-50 was elucidated by sequence analysis of two isolated genomic clones. The total length of the gene was approximately 14 kilobases and was separated into nine exons by eight intervening sequences. Nucleotide sequences of all exon/intron boundaries follow the G-T/A-G rule. A putative transcription initiation site was assigned to an A, 30 base pairs upstream from the initiation codon by S1 nuclease protection mapping. A possible "TATA" equivalent sequence, C-A-T-A-A-A, was found 27 base pairs further upstream from this initiation site. A poly(A) attachment site was determined to be 386 or 387 base pairs downstream from the termination codon by comparison with the cDNA sequence. Detailed comparison with two cDNA sequences determined previously showed the coding nucleotide sequence of the genomic clones to concur with that of the pcP-450pb2 cDNA clone coding for cytochrome P-450e except for three neutral base substitutions. Therefore, we conclude that the gene sequence determined here is for the cytochrome P-450e gene or a similar gene. On the other hand, 40 base substitutions were found in about 1,900 base pairs compared between the sequences of the genomic clone and the other cDNA clones (pcP-450pbl and 4) coding for cytochrome P-450b, and 15 of them result in 14 amino acid replacements in the total 491 amino acid residues. These base substitutions occur in relatively limited regions of the sequences. Most of them are found in exons 6, 7, 8, and 9; most frequently in exon 7.

Amino Acid Sequence↗

PubMed1994

Molecular cloning of the human AH receptor gene promoter.

A lambda phage clone containing a promoter region of the human Ah receptor gene was isolated. This clone spanned 13.8 kb and contained the 1st exon, the sequence of which completely matched the reported Ah receptor cDNA. Using RNase protection assay and primer extension analysis, the transcription initiation sites were determined to be 643 and 615 bp upstream of the translational initiation codon ATG. This promoter did not contain a TATA box, while multiple GC boxes were present close to the determined transcription initiation sites. Comparison of the 5' flank sequence of the human Ah receptor with its murine equivalent showed several well conserved regions, containing binding sites for known transcription factors, such as Sp1. The promoter activity was confirmed by transient transfection of chimeric constructs of the Ah receptor gene and reporter gene luciferase into hepatoma HepG2 cells.

Animals↗

PubMed1990

The role of the 5' nontranslated regions of the fusion protein mRNAs of canine distemper virus and rinderpest virus.

The mRNAs which code for the fusion proteins of the morbilliviruses (measles virus, canine distemper virus, and rinderpest virus) have unusually long 5' untranslated regions (UTRs) which are GC-rich and are capable of folding into extensive secondary structures. In measles virus the first AUG codons in the fusion (F) protein mRNA are in close proximity at nucleotide positions 574 and 583 and protein translation is initiated at the second position. In the canine distemper virus (CDV) and rinderpest virus (RPV) F gene transcripts the analogous initiation codons are preceded by several other AUG codons many nucleotides upstream either in the same reading frame or at the beginning of other short open reading frames. We have studied the effect of deleting these upstream regions on the production of the fusion proteins of both CDV and RPV from cDNA constructs. Within the cells the presence of these regions enhances the production of the F protein while, in contrast, the production of the authentic F protein from in vitro translations using RNA transcripts is inhibited by these sequences.

Animals↗

PubMed2006

A unified view of the initiation of protein synthesis.

The mechanism of the initiation of protein synthesis is discussed in terms of two different hypotheses in which each emphasized a different possible element of the process: the Shine-Dalgarno (SD) hypothesis ascribed an essential role to recognition of the SD segment by the ribosomal RNA; it is supported by a variety of experiments but conflicting evidence negates its obligatory nature. In contrast, our hypothesis highlighted the role of the structure of the mRNA and proposes that the initiation codon is selected by virtue of its unique accessibility. The rationale for the importance of accessibility in the selection of the initiation site is discussed. An analysis and a recapitulation of the initiation process and ribosomal specificity are presented. The apparent conflicts with the SD hypothesis are resolved in a unified mechanism where accessibility is the dominant factor.

Models, Biological↗

PubMed2002

Development and characterization of a reconstituted yeast translation initiation system.

To provide a bridge between in vivo and in vitro studies of eukaryotic translation initiation, we have developed a reconstituted translation initiation system using components from the yeast Saccharomyces cerevisiae. We have purified a minimal set of initiation factors (elFs) that, together with yeast 80S ribosomes, GTP, and initiator methionyl-tRNA, are sufficient to assemble active initiation complexes on a minimal mRNA template. The kinetics of various steps in the pathway of initiation complex assembly and the formation of the first peptide bond in vitro have been explored. The formation of active initiation complexes in this system is dependent on ribosomes, mRNA, Met-tRNAi, GTP hydrolysis, elF1, elF1A, elF2, elF5, and elF5B. Our data indicate that elF1 and elF1A both facilitate the binding of the elF2 x GTP x Met-tRNAi complex to the 40S ribosomal subunit to form the 43S complex. elF5 stimulates a step after 43S complex formation, consistent with its proposed role in activating GTP hydrolysis by elF2 upon initiation codon recognition. The presence of elF5B is required for the joining of the 40S and 60S subunits to form the 80S initiation complex. The step at which each of these factors acts in this reconstituted system is in agreement with previous data from in vivo studies and work using reconstituted mammalian systems, indicating that the system recapitulates fundamental events in translation initiation in eukaryotic cells. This system should allow us to couple powerful yeast genetic and molecular biological experiments with in vitro kinetic and biophysical experiments, yielding a better understanding of the molecular mechanics of this central, complex process.

Eukaryotic Cells↗

PubMed1989

cDNA sequence, gene organization, and progesterone induction of mRNA for uteroferrin, a porcine uterine iron transport protein.

The complete nucleotide sequence of porcine uteroferrin mRNA was determined by analysis of overlapping cDNA and genomic clones. The uteroferrin mRNA is 1,424 nucleotides in length and encodes a precursor protein of 338 amino acids, of which 20 residues subsequently are cleaved to form the mature peptide. The uteroferrin gene spans 3.5 kb and consists of three exons and two introns. The first intron separates the 5' untranslated sequences from the translation initiation codon ATG while the other intron interrupts the coding region of the mature protein. Primer extension analysis localized the presumptive transcription initiation site of the mRNA 94 nucleotides 5' of the ATG. No canonical TATA or CAAT sequences were apparent upstream from the mRNA cap site. However, sequences within the 5'-flanking region of the gene exhibit similarities to defined regulatory sequences for iron- and steroid hormone-responsive genes. The steady-state level of uteroferrin mRNA is enhanced by progesterone but not by estrogen alone, although the extent of progesterone induction is lower than at midgestation. The simple organization of the uteroferrin gene, which contrasts with those of the transferrin gene family, and the progesterone induction of uteroferrin mRNA expression suggest that, although this protein may have evolved in a manner distinct from other iron binding proteins, its regulation by steroid hormones may be similar.

Acid Phosphatase↗

PubMed1989

Crystallin gene expression during rat lens development.

The analysis of the developmental pattern of the alpha A-, alpha B-, beta B1-, beta B2-, beta B3-, beta A3/A1-, and beta s-crystallin genes during fetal and postnatal development of the rat shows that the differential regulation of crystallin synthesis relies on differential gene shutdown rather than differential gene activation; that is, all crystallin genes are active during early development but turn off at different stages. The only two exceptions to this rule are the alpha B- and beta s-crystallin genes. The alpha B-crystallin gene transcript becomes first detectable at 18 days of fetal development, while the beta s-crystallin gene appears to be active only in the postnatal period. We also determined the absolute numbers of the alpha A-, alpha B-, beta B1-, beta B2-, beta B3-, beta A3/A1-, beta s-, and gamma-crystallin gene transcripts present in the lens at various times after birth. Comparison of these RNA data with the published protein data shows that the alpha B- and beta B2-crystallin RNAs are relatively overrepresented, suggesting the possibility that these two RNA species are not used as efficiently as other crystallin mRNAs. Examination of the known (hamster) alpha B-crystallin sequence and elucidation of the (rat) beta B2-crystallin sequence yielded no evidence for aberrant codon usage. These two RNAs have one sequence motif in common: they are the only crystallin mRNAs in which the translation initiation codon is preceded by CCACC.

Age Factors↗

PubMed1991

Tissue-specific promoters regulate aromatase cytochrome P450 gene expression in human ovary and fetal tissues.

The formation of estrogens from C19 steroids is catalyzed by a specific form of cytochrome P450, aromatase cytochrome P450 (P450AROM; the product of the CYP19 gene). Previous studies have demonstrated that aromatase activity in human adipose and ovarian granulosa cells is subject to complex multifactorial regulation and that changes in activity are correlated with changes in the levels of mRNA encoding P450AROM. We have previously isolated the human CYP19 gene. Two unique untranslated first exons (exons I.1 and I.2) have been identified in mRNA specific for P450AROM in human placenta. Although the proportion of transcripts encoding exon I.2 is very small, genomic clones encoding the sequences of both exons I.1 and I.2 have recently been isolated. The corpus luteum of human ovary differs in that promoters I.1 and I.2 are completely inactive. Sequence analysis of the DNA immediately 5' of exon II (which contains the start site of translation) demonstrates the presence of a TATAA sequence beginning 149 basepairs 5' of the ATG initiation codon identified in placental exon II. Using a combination of primer extension and S1 nuclease protection analysis, it appears that the initiation site of ovarian P450AROM transcripts aligns 26 basepairs down-stream of the sequence TATAA. It appears, therefore, that the expression of P450AROM-specific mRNA in corpus luteum is regulated by an additional promoter (promoter II), which is located just 5' of exon II. Consistent with these observations, Northern analysis of poly(A)+ RNA isolated from placenta and corpus luteum demonstrates that the major promoter of placental P450AROM is promoter I.1, while the major promoter in the corpus luteum is promoter II.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1991

Characterization of immunoglobulin heavy chain genes from an acute lymphocytic leukemia with four rearrangements.

Approximately 25% of acute leukemias of the B-cell lineage demonstrate more than two rearranged immunoglobulin heavy chain genes when examined by Southern blot analysis. The origin of the extra bands was investigated by molecular cloning and sequencing of four rearranged genes from one patient's leukemic cells. All four rearrangements were apparently derived independently. Two of the rearrangements used the VH6 variable region, attached to different diversity and joining regions. One of the two rearrangements contained a mutation in the coding sequence leading to the generation of a nonsense codon. This rearranged gene also differed from the other VH6 containing gene starting at about 330 bp upstream of the ATG initiation codon. The third rearranged gene used a member of the VH2 variable gene family. A DH-JH rearrangement was found in the fourth rearranged gene. The data indicate that the leukemia probably arose as a result of the transformation of an early B-cell progenitor that lacked rearranged immunoglobulin genes but retained some differentiation potential.

Blotting, Southern↗

PubMed1990

High-level expression of complementary DNA encoding rat calmodulin in Escherichia coli.

We report the production and characterization of a rat calmodulin made in Escherichia coli. To express the rat calmodulin cDNA in E. coli, we have employed an expression vector containing the E. coli trp promoter and trpA terminator. The cDNA was modified so as to delete the 5' nontranslated sequence and to incorporate a consensus sequence for the E. coli ribosome-binding site. Several codons for the N-terminal amino acids were selected to fit the E. coli consensus nucleotide sequence around the translational initiation codon. After induction of expression in E. coli, rat calmodulin accounted for over 30% of total cellular proteins. About 100 mg of recombinant rat calmodulin, purified to over 90% homogeneity by extraction from bacterial lysate followed by phenyl-Sepharose column chromatography, was obtained from 1 liter of E. coli culture. This recombinant calmodulin activated rat brain cyclic AMP phosphodiesterase to the same extent as the native calmodulin purified from rat brain. These results indicate that the overproduction system of the recombinant calmodulin in E. coli facilitates the study of the structure-function relationship by site-specific mutagenesis.

Amino Acid Sequence↗

PubMed1997

Evidence that translation reinitiation abrogates nonsense-mediated mRNA decay in mammalian cells.

Nonsense codons upstream of and including position 192 of the human gene for triosephosphate isomerase (TPI) have been found to reduce the abundance of TPI mRNA to approximately 25% of normal. The reduction is due to the decay of newly synthesized TPI mRNA that co-purifies with nuclei. TPI mRNA that co-purifies with cytoplasm is immune to nonsense-mediated decay. Until now, a nonsense codon at position 23 has been the 5'-most nonsense codon that has been analyzed. Here, we provide evidence that a nonsense codon at position 1, 2 or 10 reduces the abundance of nucleus-associated TPI mRNA to an average of only 84% of normal because translation reinitiates at the methionine codon at position 14. First, converting codon 14 to one for valine increased the effectiveness with which an upstream nonsense codon reduces mRNA abundance. Second, when TPI gene sequences, including codon 14, were fused upstream of and in-frame to the translational reading frame of an Escherichia coli chloramphenicol acetyl transferase (CAT) gene that lacked an initiation codon, a nonsense codon at TPI position 1 or 2 allowed for the production of TPI-CAT that was an estimated 14 amino acids smaller than TPI-CAT produced by a nonsense-free gene, whereas a nonsense codon at TPI position 23 precluded the production of TPI-CAT. These and related findings lend credence to the concept that the nonsense-mediated reduction in the half-life of nucleus-associated TPI mRNA involves cytoplasmic ribosomes.

Animals↗

PubMed1996

att, a target for regulation by tra2 in the testes of Drosophila melanogaster, encodes alternative RNAs and alternative proteins.

We have identified a gene, alternative testis transcripts (att), which is alternatively expressed, at both the RNA and protein levels, in testes and somatic tissues. The testis-specific RNA differs from somatic RNAs in both promoter usage and RNA processing and is dependent on the function of the transformer 2 gene. The differences between the somatic and testis RNAs have substantial consequences at the protein level. The somatic RNAs encode a protein with homology to the mammalian Graves' disease carrier proteins. The testis RNA lacks the initiation codons used in somatic tissue and encodes two different proteins. One of these begins in a testis-specific exon, uses a reading frame different from that for the somatic protein, and is completely novel. The other protein initiates translation in the frame of the somatic RNA at a Len CUG codon which is within the open reading frame for the somatic protein. This produces a novel truncated version of the Graves' disease carrier protein-like protein that lacks all sequences N terminal to the first transmembrane domain.

Alternative Splicing↗

PubMed1995

Translation of the second gene of peanut clump virus RNA 2 occurs by leaky scanning in vitro.

The two 5'-proximal open reading frames of peanut clump virus RNA 2, which encode the coat protein of 23 kDa and a protein of 39 kDa (P39), are both translated in vitro from genomic RNA 2. We have studied the translational strategy involved in the initiation at the second AUG of RNA 2, which is the initiation codon of P39. Mutation experiments with synthetic transcripts corresponding to the 5'-half of RNA 2 ruled out mechanisms of P39 translation initiation involving termination-reinitiation and internal ribosomes entry. The results were consistent, however, with a leaky scanning mechanism for P39 initiation, in which about one-third of the ribosomes fail to initiate translation of coat protein and scan along the template to initiate translation at the AUG of the P39 gene, more than 1000 residues in from the 5'-terminus of the RNA 2.

Arachis↗

PubMed1979

Nucleotide sequence analysis of the leader segments in a cloned copy of adenovirus 2 fiber mRNA.

Fiber mRNA of adenovirus 2 has been used as a template for RNA-dependent DNA polymerase. The resulting cDNA/RNA hybrids have been inserted at the Pst I site of the plasmid vector pBR322 after A:T tailing. One recombinant plasmid, pJAW 43, has been characterized in detail and shown to contain sequences from the main body of fiber mRNA, the three leaders common to most late adenoviral mRNAs and a fourth leader found in some species of fiber mRNA. The complete DNA sequence of the leader region has been determined and does not contain the initiation codon AUG, although this codon does occur immediately downstream from the junction between the fourth leader and the main body of the fiber mRNA. The first leader (map coordinate 16.6) is 41 nucleotides long, the second (from 19.6) is 71 nucleotides, the third (from 26.6) is 88 nucleotides and the fourth (from 78.5) is 181 nucleotides. The location of junctions between viral leaders and intervening sequences has been determined by reference, where possible, to sequences of the adenovirus 2 genome. Although the presence of short repeated sequences at the boundaries of intervening sequences and leaders makes it impossible to locate the splice point unambiguously, all of the leader-intervening sequence junctions can be arranged to stress a common feature--the presence of the dinucleotides GT and AG at the 5' and 3' ends, respectively, of the intervening sequences. This prototype sequence, which has also been recognized at or near the splice points in other eucaryotic systems, is possibly part of a larger unit which serves as a recognition site for specific excision-ligation events that ultimately lead to the production of mature mRNAs.

Adenoviruses, Human↗

PubMed1989

Nucleotide sequence of a novel kanamycin resistance gene, aphA-7, from Campylobacter jejuni and comparison to other kanamycin phosphotransferase genes.

A novel kanamycin phosphotransferase gene, aphA-7, was cloned from a 14-kb plasmid obtained from a strain of Campylobacter jejuni and the nucleotide sequence of the gene was determined. The presumed open reading frame of the aphA-7 structural gene was 753 bp in length and encoded a protein of 251 amino acids with a calculated weight of 29,691 Da. A 29-kDa protein was demonstrated in Escherichia coli maxicells containing the cloned aphA-7 gene. A ribosomal binding site corresponding to 5 of 8 bases of the 3' end of the E. coli 16S rRNA was 8 bp upstream of the start codon. Sequences corresponding to the -35 and -10 regions of the consensus promoter sequences of E. coli were upstream of the presumed initiation codon of the gene. The DNA sequence was most closely related to the aphA-3 gene from Streptococcus faecalis, showing 55.4% sequence similarity. There was 45.6% identity at the amino acid level between the aphA-3 and the aphA-7 proteins. Of the three conserved regions noted previously in phosphotransferase genes, the aphA-7 amino acid sequence was identical to the six conserved amino acids in motif 3, but differed in one of the five conserved amino acids in motif 1 (if gaps are permitted) and 3 of the 10 conserved residues in motif 2. The 32.8% G + C ratio in the open reading frame of the aphA-7 kanamycin resistance gene, which is similar to that of the C. jejuni chromosome, suggests that the aphA-7 may be indigenous to Campylobacters.

Amino Acid Sequence↗

PubMed1996

Genomic organization and glucocorticoid transcriptional activation of the rat Na+/H+ exchanger Nhe3 gene.

The activity of the apical membrane Na+/H+ exchanger NHE3 isoform of renal or intestinal epithelial cells is chronically regulated by a wide variety of stimuli, including acidosis, cAMP, glucocorticoids, and thyroid hormone. To understand the molecular mechanisms responsible for long term regulation of this cation transporter, we have isolated and determined the structure of this gene from a rat genomic library. The Nh3 gene spans > 40 kilobases and contains 17 exons that are flanked by typical splice donor and acceptor sequences at the exon-intron boundaries. The transcription initiation site was mapped by S1 nuclease protection analyses of mRNA from rat kidney and intestine. Multiple start sites were clustered between nucleotides -100 and -96 relative to the translation initiation codon. An atypical TATA-box and CCAAT-box are centered 30 and 147 nucleotides, respectively, upstream of the predominant transcription initiation site. Sequence analysis of approximately 1.4 kilobases of the 5'-flanking promoter region also revealed the presence of other putative cis-acting elements recognized by various transcription factors (e.g. AP-1, AP-2, C/EBP, NF-I, OCT-1/OTF-1, PEA3, Sp1, glucocorticoid, and thyroid hormone receptors), some of which may participate in the chronic regulation of this gene. The glucocorticoid responsiveness of the Nhe3 gene was assessed by fusing its 5' regulatory region to the firefly luciferase reporter gene and then by measuring the expression of the chimeric gene in transiently transfected renal epithelial OK and LLC-PK1 cells. Glucocorticoid treatment significantly increased the luciferase activity of the chimeric gene in both cell lines, thereby indicating that glucocorticoid regulation of Nhe3 is mediated primarily by a transcriptional mechanism.

Amino Acid Sequence↗

PubMed1992

Structure of the human DNA repair gene HAP1 and its localisation to chromosome 14q 11.2-12.

Apurinic/apyrimidinic (AP) sites are pre-mutagenic DNA lesions which occur spontaneously and following exposure of cells to ionising radiation or chemical mutagens. HAP1 (Human AP endonuclease 1), the major enzyme in human cells initiating repair of AP sites, shows strong sequence homology to DNA repair enzymes from bacteria, Drosophila and other mammalian species. We have cloned the HAP1 gene and determined its complete nucleotide sequence. The site of transcription initiation has been mapped to 452 bp upstream of the ATG initiation codon in the genomic DNA. The HAP1 gene consists of five exons and is unusually small (less than 2.6 kb from transcription initiation site to polyadenylation sequence) with 54% of the protein coding region and the entire 3' untranslated region contained within a single exon. The first exon is non-coding. Regions of three exons show sequence homology to the E.coli xth (exonuclease III) gene. Using in situ hybridisation, the HAP1 gene has been localised to human chromosome 14q 11.2-12.

Base Sequence↗

PubMed1988

Structure and complete nucleotide sequence of the gene encoding chicken cytosolic adenylate kinase.

The gene encoding cytosolic adenylate kinase (AK1) was isolated from a chicken genomic DNA library by using its cDNA as a hybridization probe. The chicken AK1 gene spanned about 6 kilobase pairs and consisted of 7 exons. Analyses of the 5'-flanking region sequence and S1 nuclease mapping revealed that the transcription initiation site is located at 84 base pairs upstream from the ATG initiation codon. The TATA box and the putative CAT box were located 29 base pairs and 97 base pairs upstream from the transcription initiation site, respectively. A total of 7 GC boxes were found in the 5'-flanking region, the exon 1, and the intron 1. The GC boxes were surrounded by the sequences with extremely high G+C contents. When projected on the three-dimensional structure of the AK1 protein molecule, introns fell either between or near the ends of alpha-helices and beta-strands, and most of the coding exons encoded at least one alpha-helix and one beta-strand. The dot matrix plot analysis between chicken AK1 and bovine mitochondrial adenylate kinase (AK2) suggested that the AK1 gene might have evolved from the AK2 gene by deletion of one or more exon(s).

Adenylate Kinase↗