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PubMed1997

Cloning and characterization of the promoter region of a gene encoding a 67-kDa glycoprotein.

A rat genomic library constructed in lambda-EMBL3 (SP6/T7) vector () was screened using 32P-labeled rat p67 cDNA. A clone containing a segment of 5'-upstream region of p67 genomic DNA was obtained. The DNA (about 1.7 kilobase pairs) was isolated and characterized. Sequence analysis of this DNA fragment showed that the 898 base pairs at the 5'-end of the upstream region was identical to several long interspersed nucleotide sequences. One hundred forty-eight base pairs at the 3'-end contained the beginning of the first exon including the ATG initiator codon. The remaining 652 base pairs in between contained two AT-rich regions and several regulatory sequences. The mRNA initiation site was identified at 89 base pairs upstream from the translation start codon. The DNA fragment was also analyzed by transient transfection. When linked to a firefly luciferase reporter gene, this fragment enhanced transcription in a rat hepatoma cell line (KRC-7). Using a series of deletions in the DNA, the minimum essential promoter region (from -177 to -60) was identified. The promoter activity was also enhanced by treatment with phorbol 13-myristate 12-acetate (PMA). This enhancement required an AP-1 sequence (-298 to -292; 5'-TGACTCA-3') and a similar sequence (-97 to -88; 5'-ATGACATCAT-3'). Deletion of either of these sequences significantly reduced PMA enhancement. Deletion of both of these sequences almost completely eliminated PMA enhancement.

Aminopeptidases↗

PubMed1990

Isolation and characterization of the human hepatic lipase gene.

Overlapping bacterial phage and cosmid genomic clones were isolated spanning an area of approximately 60 kilobases that contains the human hepatic lipase (HL) gene. It is composed of 9 exons spanning approximately 35 kilobases of DNA. The entire coding regions, the 5'-flanking sequences, and the exon-intron junctions were sequenced. The intron positions correspond to those of human lipoprotein lipase and canine pancreatic lipase, supporting the concept that these genes constitute a dispersed gene family of lipases and have evolved by duplication of a common ancestral gene. A region of the HL gene, which displays a significant homology with various other lipolytic enzymes and contains the putative catalytic site serine residue of HL, was encoded by exon 4. A major transcription start site of the human HL gene was located by primer extension analysis, 43 nucleotides upstream of the translation initiation codon. Two possible promoter elements were located 25 and 63 nucleotides upstream of the transcription initiation site: a "TATA" box-like sequence, TAATA, and a sequence found in the promoter region of many liver-specific genes, AGGTTAATTATTAAT. In addition, sequences homologous to glucocorticoid and cAMP-responsive elements were identified in the 5'-nontranscribed region.

Amino Acid Sequence↗

PubMed1990

Translation initiation at a downstream AUG occurs with increased efficiency when the upstream AUG is located very close to the 5' cap.

The major late 16S mRNA species of simian virus 40 encodes both a 61-amino-acid protein, LP1, and the major virion protein, VP1. Although the initiation signal GCCAUGG is usually utilized at high efficiency, at least one-third of 40S ribosomal subunits bypass it when it is present on the major 16S mRNA of simian virus 40 (S. A. Sedman, P. J. Good, and J. E. Mertz, J. Virol. 63:3884-3893, 1989). The LP1 translation initiation codon is situated 10 bases from the 5' end of this mRNA. To determine whether the short length of the untranslated leader of this mRNA affects the efficiency of translation initiation at the LP1 initiation signal, monkey cells were transfected with plasmids which encode major late 16S-like mRNAs with 5' untranslated regions (UTRs) of 6 or 44 bases. Decreasing the length of the 5' UTR from 44 to 6 bases resulted in a 30% decrease in translation initiation at the LP1 AUG and a threefold increase in synthesis of VP1. When the VP1 open reading frame was replaced with the chloramphenicol acetyltransferase open reading frame, the reduction in 5' UTR length resulted in a 70% decrease in translation initiation at the LP1 AUG and a 30% increase in chloramphenicol acetyltransferase synthesis. Therefore, ribosomes bypass an AUG codon more efficiently when it is located very close to the 5' end of the mRNA.

Animals↗

PubMed1986

The 5' flanking region of the ornithine transcarbamylase gene contains DNA sequences regulating tissue-specific expression.

Ornithine transcarbamylase (OTCase) is a mitochondrial matrix enzyme that catalyzes the 2nd step in the mammalian urea cycle. The gene encoding OTCase is located on the X chromosome and expression of OTCase is limited almost exclusively to hepatocytes. We have characterized a lambda phage recombinant, isolated from a mouse genomic library, that spans the first two exons of the mouse OTCase gene. Nuclease S1 mapping and primer extension analysis of this clone allowed us to determine that the transcription start site is 136 base pairs (bp) upstream from the translation initiation codon. Two TATA-like sequences were found 25 and 153 bp from the transcription initiation point. An 800-bp fragment containing the 5' flanking region of the OTCase gene was fused upstream to the coding sequence of the chloramphenicol acetyltransferase gene to assay promoter activity. This plasmid was introduced into mouse fibroblast NIH 3T3 cells and human hepatoma Hep G2 cells by the calcium phosphate co-precipitation method. After DNA transfection chloramphenicol acetyltransferase activity was observed only in Hep G2 cells. We conclude that this 800-bp fragment contains sufficient information to control OTCase gene expression in a tissue-specific manner, probably by interacting with trans-acting factor(s) which are not present in the other cell line.

Acetyltransferases↗

PubMed1995

High-level expression of the human tumor necrosis factor-alpha.

Five expression plasmids for a total chemically synthesized gene of tumor necrosis factor-alpha (TNF-alpha) were constructed, which differ in two aspects: 1) distance (D) between the SD and the initiation codon ATG; 2) energy-delta G0f298 released to form the stable secondary structure in the translation initiation region. The plasmid with a (D) of 6bp has the lowest delta G0f298 (absolute value) and showed the highest expression level, up to 60% of the total bacterial proteins. Codons usage will impose much influence on expression level, so it is reasonable and understandable that the total chemically synthesized TNF-alpha gene with the codons preferable to E. coli use gave much higher expression level than the sc-TNF-alpha in which only partial N-terminal codons were modified.

Base Sequence↗

PubMed2002

Mass spectrometric analysis of the N terminus of translational initiation factor eIF4G-1 reveals novel isoforms.

In eukaryotes, translation initiation factor 4G (eIF4G) acts as the central binding protein for an unusually large number of proteins involved in mRNA metabolism. Several gene products homologous to eIF4G have been described, the most studied being eIF4G-1. By its association with other initiation factors, eIF4G-1 effects mRNA cap and poly(A) recognition, unwinding of secondary structure, and binding to the 43S initiation complex. Multiple electrophoretic isoforms of eIF4G-1 are observed, and multiple cDNAs have been reported, yet the relationship between the two is not known. We report here a new cDNA for eIF4G-1, present as a previously unidentified human expressed sequence tag, that extends the long open reading frame, provides a new in-frame initiation codon, and predicts a longer form of eIF4G-1 than reported previously. eIF4G isoforms from human K562 cells were cleaved with recombinant Coxsackievirus 2A protease and the N- terminal domains purified by m(7)GTP-Sepharose chromatography and polyacrylamide gel electrophoresis. Proteins were digested with proteolytic enzymes and peptides masses determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry. In selected cases, peptides were sequenced by electrospray-mass spectrometry fragmentation. This identified the N termini of the three most abundant eIF4G-1 isoforms, two of which had not previously been proposed. These proteins appear to have been initiated from three different AUG codons.

Amino Acid Sequence↗

PubMed1998

Genomic structure and chromosomal mapping of the mouse STOP gene (Mtap6).

The microtubule associated protein STOP (Stable Tubule Only Polypeptide) is a calmodulin-regulated protein able to induce a high degree of microtubule stability. STOP is abundant in neurons which contain large subpopulations of stable microtubules. Genomic clones spanning 67 kb and encompassing the mouse STOP gene (Mtap6) have been isolated and characterized. These clones derive from a single gene mapping to the E2-F1 region of mouse chromosome 7. The gene is composed of 4 exons that exhibit conventional vertebrate splicing sequences. Transcription of the gene initiate at multiple sites in a 85 nucleotide region located 530 bases upstream the translation initiation codon. Accordingly, the 5' flanking region of the gene lacks a TATA box or an initiator element at usual position. The protein encoded by the mouse STOP gene (Mtap6) is composed of 906 amino acids and presents a 91% identities with the rat brain STOP.

Amino Acid Sequence↗

PubMed1992

Convergent and overlapping transcripts of the Chlamydia trachomatis 7.5-kb plasmid.

Transcription of the 7.5-kb cryptic plasmid of Chlamydia trachomatis serovar L2 was investigated. Faint, diffuse transcripts of about 1.6 and 2.2 kb and intense short transcripts of about 250 and 430 bases were identified by Northern blot analysis. The short transcripts were found to have a common 5' end corresponding to bp 501 relative to the unique BamHI site of the plasmid and to terminate at different downstream sites. Putative promoter sequences of TTGCCA and TATATT, which closely resemble the consensus recognition site of Escherichia coli sigma 70, were identified at the -35 and -10 positions upstream from the 5' end of the short transcripts made in chlamydia. Transcripts of similar sizes were also expressed from this promoter in E. coli harboring a recombinant plasmid encoding the short transcripts. The short transcripts encode a common open reading frame (ORF) of 34 codons; however, a strong ribosome binding site was not found in the vicinity of the initiator codon, and it is not known whether the transcripts are translated in vivo. A large ORF of 330 codons, which has been shown to encode a hypothetical protein containing conserved domains of recombinase-like proteins, is antisense to the short transcripts. Transcripts encoding the large ORF could not be detected directly by Northern blot or primer extension analysis. However, transcripts were detected by polymerase chain reaction amplification of the large ORF cDNA and when Southern blots of single-stranded antisense DNA for the large ORF were probed with radiolabeled RNA synthesized by host-free chlamydial reticulate bodies. Thus, both strands of the chlamydial plasmid are transcribed in the region encoding the short transcripts. We propose that the short transcripts play a regulatory role as antisense RNAs.

Amino Acid Sequence↗

PubMed1989

Demonstration of an amino terminal La epitope recognized by human anti-La sera.

In order to study the antigenic properties of the La protein we have isolated a 1650 base pair (bp)-long human cDNA encoding an anti-La reactive protein. Restriction enzyme analysis and DNA sequencing was used to compare this clone with two published but inconsistent partial sequences. Our clone extends about 220 bp further towards the 5' end than the two clones previously studied and includes a putative initiation codon. When introduced into an expression vector, stable fusion proteins were made both from the initial clone and from two deletion clones. The recombinant proteins were tested by immunoblotting against a panel of anti-La sera. All reacted with the fusion protein produced by the 1650-bp clone. About half of the anti-La sera showed reactivity against the recombinant protein from the shortest deletion clone. This indicates the presence of an epitope in the amino terminal part of the La protein, encoded by sequences not present in previously published clones.

Amino Acid Sequence↗

PubMed2000

Preimplantation genetic diagnosis in two families at risk for recurrence of Herlitz junctional epidermolysis bullosa.

The Herlitz type of junctional epidermolysis bullosa (H-JEB) is a severe inherited bullous disease which leads to the early demise of the affected newborn. Mutations in the genes encoding the 3 polypeptides of the anchoring filament protein laminin 5 underlie this condition. We studied 2 families with affected children who previously died from H-JEB. Mutation screening using heteroduplex analysis and direct sequencing of the PCR products revealed a previously described hotspot mutation in LAMB3 (R635X), and a novel delayed termination codon in LAMB3 in the first proband. In the second proband, we found a novel initiation codon mutation in LAMB3, and a novel 2 bp deletion in LAMB3. For preimplantation genetic diagnosis (PGD) in these families, we developed nested multiplex PCR assays, amplifying the mutations and informative intragenic polymorphisms in the probands. Single embryonic cells were biopsied from 8-cell embryos using standard techniques, and subjected to the multiplex PCR assay followed by restriction enzyme digestion. Embryos found not to carry either mutation were transferred to the mothers, and a pregnancy was established in the second family as evidenced by the elevated level of HCG, although the pregnancy did not persist. This study illustrates the feasibility of PGD for an inherited skin disorder for the first time.

Base Sequence↗

PubMed1985

DNA sequence of the lactose operon: the lacA gene and the transcriptional termination region.

The lac operon of Escherichia coli spans approximately 5300 base pairs and includes the lacZ, lacY, and lacA genes in addition to the operator, promoter, and transcription termination regions. We report here the sequence of the lacA gene and the region distal to it, confirming the sequence of thiogalactoside transacetylase and completing the sequence of the lac operon. The lacA gene is characterized by use of rare codons, suggesting an origin from a plasmid, transposon, or virus gene. UUG is the translation initiation codon. A preliminary examination of 3' end of the lac messenger in the region distal to the lacA gene indicates several endpoints. A predominant one is located at the 3' end of a G + C-rich hairpin structure, which may be involved in termination of transcription or in post-transcriptional processing. An open reading frame of 702 base pairs is present on the complementary strand downstream from lacA.

Acetyltransferases↗

PubMed1987

Nucleotide sequence of cloned cDNA for human sphingolipid activator protein 1 precursor.

Two cDNA clones encoding prepro-sphingolipid activator protein 1 (SAP-1) were isolated from a lambda gt11 human hepatoma expression library using polyclonal antibodies. These had inserts of approximately 2 kilobases (lambda-S-1.2 and lambda-S-1.3) and both were both homologous with a previously isolated clone (lambda-S-1.1) for mature SAP-1. We report here the nucleotide sequence of the longer two EcoRI fragments of S-1.2 and S-1.3 that were not the same and the derived amino acid sequences of mature SAP-1 and its prepro form. The open reading frame encodes 19 amino acids, which are colinear with the amino-terminal sequence of mature SAP-1, and extends far beyond the predicted carboxyl terminus of mature SAP-1, indicating extensive carboxyl-terminal processing. The nucleotide sequence of cDNA encoding prepro-SAP-1 includes 1449 bases from the assigned initiation codon ATG at base-pair 472 to the stop codon TGA at base-pair 1921. The first 23 amino acids coded after the initiation ATG are characteristic of a signal peptide. The calculated molecular mass for a polypeptide encoded by 1449 bases is approximately 53 kDa, in keeping with the reported value for pro-SAP-1. The data indicate that after removal of the signal peptide (23 amino acids) mature SAP-1 (78 amino acids) is generated by removing an additional 7 amino acids from the amino terminus and approximately 373 amino acids from the carboxyl terminus. One potential glycosylation site was previously found in mature SAP-1. Three additional potential glycosylation sites are present in the processed carboxyl-terminal polypeptide, which we designate as P-2. The molecular mass of glycosylated pro-SAP-1 is estimated at approximately 69 kDa, assuming glycosylation of all four sites. The value is close to the reported 70-kDa value for glycosylated pro-SAP-1. A computer search failed to reveal homology between P-2 and the sequence of any other protein; its function is uncertain. The 3' untranslated region is composed of 90 base pairs and is incomplete, since it does not contain a polyadenylylation site or a poly(A) tail.

Amino Acid Sequence↗

PubMed2002

Localization of regulatory elements mediating constitutive and cytokine-stimulated plasminogen gene expression.

The activity of plasmin, the major enzyme responsible for dissolving fibrin clots, is regulated by plasminogen activators, plasminogen activator inhibitors, alpha(2)-antiplasmin, and inflammatory mediators. Recent studies suggest that plasmin activity can be regulated also at the level of plasminogen gene expression. In this study, we characterized the murine plasminogen promoter and 5'-flanking region. The major transcription start site was identified at -83 bp relative to the ATG translational initiation codon. A series of 5'-flanking sequences up to 2400 bp upstream of the transcription initiation site were fused to the luciferase reporter gene and transfected into hepatocytic cells. A 106-bp 5'-flanking region of the murine plasminogen gene demonstrated sufficient functional promoter activity in plasminogen-expressing cells. IL-6 treatment stimulated luciferase activity driven by the 5'-flanking region and an intact consensus IL-6-responsive element at -791, was required for maximal stimulation by this cytokine. These results indicate the presence of regulatory elements in the 5'-flanking region of the murine plasminogen promoter that may regulate murine plasminogen gene expression and, hence, plasmin activity.

Amino Acid Motifs↗

PubMed2002

5' stem-loop of collagen alpha 1(I) mRNA inhibits translation in vitro but is required for triple helical collagen synthesis in vivo.

The 5' stem-loop is a conserved sequence element found around the translation initiation site of three collagen mRNAs, alpha1(I), alpha2(I), and alpha1(III). We show here that the 5' stem-loop of collagen alpha1(I) mRNA is inhibitory to translation in vitro. The sequence 5' to the translation initiation codon, as a part of the 5' stem-loop, is also not efficient in initiating translation under competitive conditions. This suggests that collagen alpha1(I) mRNA may not be a good substrate for translation. Since the 5' stem-loop binds protein factors in collagen-producing cells, this binding may regulate its translation in vivo. We studied in vivo translation of collagen alpha1(I) mRNA after transfecting collagen alpha1(I) genes with and without the 5' stem-loop into Mov 13 fibroblasts. The mRNA with the alpha1(I) 5' stem-loop was translated into pepsin-resistant collagen, which was secreted into the cellular medium. This mRNA also produced more disulfide-bonded high molecular weight collagen found intracellularly. The mRNA in which the 5' stem-loop was mutated, but without affecting the coding region of the gene, was translated into pepsin-sensitive collagen and produced only trace amounts of disulfide-bonded collagen. This suggests that the 5' stem-loop is required for proper folding or stabilization of the collagen triple helix. To our knowledge this is the first example that an RNA element located in the 5'-untranslated region is involved in synthesis of a secreted multisubunit protein. We suggest that 5' stem-loop, with its cognate binding proteins, targets collagen mRNAs for coordinate translation and couples translation apparatus to the rest of the collagen biosynthetic pathway.

5' Untranslated Regions↗

PubMed1976

Nucleotide sequence of the restriction fragments hind L and hind M of SV40 DNA.

The nucleotide sequence of the two minor SV40 DNA restriction fragments Hind L and Hind M is here reported. For this purpose we used 5'-32p-labeled DNA fragments either partially digested with snake venom diesterase for analysis by the wandering spot method or partially degraded with the base specific reagents dimethylsulphate or hydrazine for direct sequence analysis on gel. In the former procedure the strands were separated before degradation, while in the latter the strands were separated after modification but before the degradation. Due to the presence of several termination codons, the region Hind L - Hind M cannot be translated in a polypeptide. Also, no initiation codons for protein synthesis are present in this region.

Base Sequence↗

PubMed1988

Cloning and nucleotide sequence of the brnQ gene, the structural gene for a membrane-associated component of the LIV-II transport system for branched-chain amino acids in Salmonella typhimurium.

The genetically defined gleR-brnQ region responsible for the branched-chain amino acid transport in Salmonella typhimurium was mapped in the 3.3-kilobase SalI-PstI segment of plasmid pOH56 by complementation analysis. By subcloning and genetic recombination analysis, the gleR and brnQ3 mutational sites were localized within the 0.85-kilobase SalI-EcoRV segment, and brnQ4 within the 0.8-kilobase EcoRV-HindIII segment. The nucleotide sequence of the brnQ gene and its flanking regions was determined. The brnQ gene is encoded by the sequence starting 24 base pairs upstream from the EcoRV site. Transcription of the brnQ gene starts at three sites separated by 171, 173 and 174 nucleotides, respectively, from the initiation codon. The promoter sequences can be seen in the immediate upstream region of the transcription initiation sites. There is a long silent region between the transcription initiation sites and a potential Shine-Dalgarno nucleotide sequence. The coding sequence of the brnQ gene, which is 1317 base pairs long, specifies a very hydrophobic protein of 439 amino acid residues.

Amino Acid Sequence↗

PubMed1989

Characterization of the human Na,K-ATPase alpha 2 gene and identification of intragenic restriction fragment length polymorphisms.

We have determined the structure of the gene that encodes the alpha 2 isoform of the human Na,K-ATPase. The gene contains 23 exons and spans approximately 25 kilobases. The amino acid sequence of the human alpha 2 isoform deduced from the genomic sequence exhibits 99% identity to the rat alpha 2 isoform. One of the nine amino acid differences between the human and rat sequences occurs at an amino acid position which is known to be involved in species differences in sensitivity of the alpha 1 isoform to cardiac glycosides. Approximately 1500 base pairs of sequence flanking the 5' end of the alpha 2 gene have been determined. This region contains numerous potential AP-1, AP-2, and NF-1-binding sites, a potential Sp1 recognition site, and several sequences that are similar to the glucocorticoid receptor-binding site. The transcription start site was mapped by primer extension and S1 nuclease protection analyses of RNA from human brain, skeletal muscle, and heart. Multiple transcription initiation sites are clustered between residues -104 to -99 relative to the translation initiation codon. A potential TATA box is located 29 base pairs upstream of the first transcription initiation site. Immediately 5' to the apparent TATA box is a 35-base pair polypurine.polypyrimidine tract containing an imperfect mirror repeat which resembles sequences that form triple-stranded structures. Two intragenic DNA probes which detect restriction fragment length polymorphisms associated with the alpha 2 gene have been identified. These probes will be useful in genetic linkage analyses designed to define the possible role of the Na,K-ATPase in certain hereditary disorders.

Amino Acid Sequence↗

PubMed1980

Structural comparison of two nontandemly repeated yeast glyceraldehyde-3-phosphate dehydrogenase genes.

A hybrid plasmid (pgap63) was isolated which contains a second yeast glyceraldehyde-3-phosphate dehydrogenase structural gene. The complete nucleotide sequence of this gene was determined and compared with the primary structure of a yeast glyceraldehyde-3-phosphate dehydrogenase gene (pgap49) which was reported previously (Holland, J.P., and Holland, M.J. (1979) J. Biol. Chem. 254, 9839-9845). Based on the restriction endonuclease cleavage maps of the isolated segments of yeast DNA which contain these genes, the two genes are nontandemly duplicated. Greater than 94% of the nucleotides within the coding regions of these genes are homologous and the polypeptides encoded by the two structural genes differ by only 15 amino acid residues. Both genes have the same, highly biased, codon usage pattern and neither contains intervening sequences. Approximately 100 nucleotides adjacent to the ATG initiation codons and 130 nucleotides beyond the TAA termination codons are greater than 70% homologous. Structures within the flanking sequences of the genes which are potentially relevant to transcriptional and translational control are described. Several sequences (8 to 15 nucleotides in length) are repeated in both the 5' and 3' flanking sequences of the genes in a noninverted fashion. Finally, a rapid procedure for the isolation of spontaneous deletions within hybrid plasmid DNAs is described, as is the isolation of a structural gene deletion in pgap49.

Amino Acid Sequence↗