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PubMed1991

Effect of eukaryotic initiation factor 4F on AUG selection in a bicistronic mRNA.

Artificial bicistronic mRNAs based on rabbit beta-globin and bacterial chloramphenicol acetyltransferase protein-coding sequences were tested for translation activity in a mouse astrocytoma cell-free extract. This cell extract exhibited an apparent preference for 5'-distal or internal initiation over 5'-proximal ("first AUG") initiation. 5'-Distal initiation appeared to be 5'-cap independent, suggesting that nonstandard initiation was responsible. This conclusion was based on a lack of inhibition of internal initiation by added cap analog and insensitivity of internal initiation to the presence or absence of a 5'-cap structure. Exogenous reticulocyte initiation factors were tested for effect on 5'-proximal initiation. The only factor with a significant effect was found to be eukaryotic initiation factor 4F, or the cap-binding protein. Addition of this factor promoted 5'-end initiation as evident by a general increase in 5'-proximal open reading frame (ORF) product relative to 5'-distal ORF product. The relative expression of 5'-proximal to 5'-distal ORFs in bicistronic or multicistronic mRNAs may very well be dependent on activity levels of eukaryotic initiation factor 4F and possibly other mRNA-dependent initiation factors.

Animals↗
PubMedDate not supplied

Monoclonal antibodies recognizing a recombinant portion of human alpha-fetoprotein with antigenic selectivity versus albumin.

Determination of serum alpha-fetoprotein is useful in the clinical management of liver cancer, but it has not been particularly helpful in the early diagnosis of this disease, since also non-neoplastic liver diseases may result in small increases of its serum concentration. To improve the clinical performance of this assay, we have previously developed an in vitro culture system, in which the expression of alpha-fetoprotein and albumin could be coordinately modulated by thyroid hormone. This system allowed large scale production and purification of native alpha-fetoprotein to be used as reference material. In addition, we synthesized and cloned in a bacterial expression vector a DNA sequence coding of human alpha-fetoprotein amino acid sequence 38-119. This alpha-fetoprotein sequence was chosen since it is the least homologous to albumin, being the amino acid sequence of the two proteins extremely similar with an overall identity of about 38%. Now we have obtained three hybridomas recognizing with high affinity and specificity both the recombinant fragment and native alpha-fetoprotein. These antibodies, which therefore recognize the native protein in the amino acid sequence 38-119, should allow the development of an immunoassay for alpha-fetoprotein with absolute selectivity versus albumin. This might result in more sensitive clinical determinations, avoiding the possibility of cross-reactions.

Albumins↗
PubMed1989

Somatostatin gene expression in pancreatic islet cells is directed by cell-specific DNA control elements and DNA-binding proteins.

Somatostatin is a peptide synthesized in the pancreatic islets, nervous system, gastrointestinal tract, and thyroid gland. Factors that control islet cell-specific expression of the somatostatin gene were analyzed by expression of fusion genes consisting of 5' rat somatostatin gene sequences linked to coding sequences of the receptor genes, bacterial chloramphenicol acetyltransferase, and human growth hormone. Fusion genes containing 900 and 250 base pairs (bp) of 5'-flanking DNA were preferentially expressed at 5-10-fold higher levels in somatostatin-producing islet cell lines, as compared with islet cell lines that produced insulin and glucagon, and in three non-islet cell lines. A deletional mutation consisting of only 65 bp of 5'-flanking sequence of the rat somatostatin gene expressed in all islet cell lines but not in non-islet lines, indicating the existence of a negative-acting islet cell-specific element located between nucleotides -250 and -65. The 65-bp sequence contains the octameric cAMP-responsive enhancer (CRE) TGACGTCA (nucleotides -48 to -41). Fine mapping of sequences responsible for islet-specific expression by substitution of synthetic oligonucleotide cassettes revealed full retention of expression by deletion to nucleotides -48 and complete loss of expression at nucleotides -42 of the CRE. Substitution of the 9 bp adjacent 3' to the CRE of the somatostatin gene (nucleotides -40 to -32) with the corresponding sequence located 3' to the CRE of the glucagon gene abolished expression. By gel mobility shift and DNaseI footprinting analyses, proteins in extracts of islet cells bound to the 24 bp including the CRE and downstream adjacent 9 bp (nucleotides -58 to -35). An additional upstream region of DNA was protected from DNase I digestion (nucleotides -110 to -80). Proteins from non-islet cells bound to the region from nucleotides -58 to -35, but patterns of DNase I protection differed from those using proteins from islet cells. These observations indicate that several DNA-binding proteins interact with cis-acting elements located between 35 and 58 bp upstream of the transcriptional start site of the rat somatostatin gene to determine islet cell-specific gene expression. CRE-binding protein(s) is ubiquitous among phenotypically different cells, and expression of the somatostatin gene in non-somatostatin-producing islet cells appears to be inhibited by a negative-acting element located upstream of the CRE.

8-Bromo Cyclic Adenosine Monophosphate↗
PubMed1988

A new lux gene in bioluminescent bacteria codes for a protein homologous to the bacterial luciferase subunits.

The nucleotide sequence of a new gene, luxF, located between the luxB and E genes in the bioluminescent system of Photobacterium phosphoreum has been determined. The luxF gene codes for a polypeptide of 231 amino acids which is homologous to the alpha and beta subunits of luciferase coded by the luxA and luxB genes, respectively. The degree of homology of the luxF protein is very high with the beta subunit of luciferase (approximately 30% identity) with greatest similarity to the Vibrio luxB proteins. the luxF gene appears to have evolved by duplication of the luxB gene followed by deletion of approximately 100 codons just penultimate to the 5'-terminal. The close homology with the luciferase beta subunit implicates the luxF protein in a function related to the light-emitting reaction.

Amino Acid Sequence↗
PubMed1968

Isolation and characterization of bacterial ribosomal RNA cistrons.

The DNA sequences which code for ribosomal DNA have been isolated and purified. The technique used has general application for RNA:DNA hybridization studies and enables the isolation of any gene for which sufficient gene product can be obtained. Experiments with isolated ribosomal RNA cistrons demonstrated that (a) the majority of the ribosomal cistrons are similar to one another; (b) the cistrons which are similar to one another are virtually identical to one another; (c) ribosomal cistrons of different bacterial species are closely related to one another.

Chromatography↗
PubMed1978

Structure of yeast phenylalanine-tRNA genes: an intervening DNA segment within the region coding for the tRNA.

Sixteen bacterial clones containing sequences complementary to yeast PhetRNA were isolated from a collection of hybrid plasmids containing BamHI restriction endonuclease-generated yeast DNA fragments inserted in the plasmid vector pBR315. Ten of these clones contained hybrid plasmids with distinct BamHI fragments. The sequence of the Phe-tRNA structural genes and adjacent regions of three of these clones is reported here. In the region flanking the tRNA gene, the sequence of two of the cloned DNAs is similar; the sequence of the third varies considerably. All three of the tRNA genes are bordered by A,T-rich regions. In particular, near the region coding for the 3' end of the tRNA there is a long sequence of As in the coding strand. This is reminiscent of the region of termination of transcription of the yeast 5S rRNA gene. The sequences coding for the Phe-tRNA contain an additional segment of 18 or 19 base pairs (depending upon the clone) not predicted by the yeast Phe-tRNA sequence. These intervening segments are nearly identical in the three clones and are located within the structural gene, two base pairs from the nucleotides coding for the tRNA anticodon.

Anticodon↗
PubMedDate not supplied

Expression of a bacterial repair gene in mammalian cells.

The coding sequence of the uvrA gene from Escherichia coli has been fused to the early promoter, enhancer and origin of replication of the simian virus SV40, and was supplemented with splicing and polyadenylation sites arising from the same virus. Introduction of this hybrid gene into simian cos-1 cells results in the synthesis of a full length UvrA protein (114 kD) which has retained its ability to bind to single-stranded DNA.

Animals↗
PubMed1988

Sequence analysis of the Streptococcus mutans fructosyltransferase gene and flanking regions.

The nucleotide sequence of the ftf gene from Streptococcus mutants GS-5 was determined. The deduced amino acid sequence indicates that the unprocessed fructosyltransferase gene product has a molecular weight of 87,600. A typical streptococcal signal sequence is present at the amino terminus of the protein. The processed enzyme is relatively hydrophilic and has a pI of 5.66. An inverted repeat structure was detected upstream from the ftf gene and may function in the regulation of fructosyltransferase expression. Sequencing of the regions flanking the gene revealed the presence of four other putative open reading frames (ORFs). Two of these, ORFs 2 and 3, appear to code for low-molecular-weight proteins containing amino acid sequences sharing homology with several gram-positive bacterial DNA-binding proteins. In addition, ORF 3 is transcribed from the ftf DNA coding strand. Partial sequencing of ORF 4 suggests that its gene product may be an extracellular protein.

Amino Acid Sequence↗
PubMed1992

Context rules of rightward overlapping reading.

We have investigated the mechanism and sequence context rules governing ribosome frameshifting promoted by aminoacyl-tRNA limitation. In the case of one shifty sequence, frameshifting promoted by lysyl-tRNA limitation occurs at the sequence AAG C and is due to rightward movement of the ribosome so as to read the AGC triplet overlapping the hungry codon from the right. The frequency of this event is unaffected by sequence elements more than three bases to the left (upstream) or two bases to the right (downstream) of the hungry codon, and only slightly affected by the identity of the base two bases to the right. It is strongly affected by the base immediately to the right of the hungry codon, which becomes the wobble base of the shifted triplet; and by the third base of the hungry codon, even though the two synonyms (AAG and AAA) call for the same aminoacyl-tRNA; and by the identity of the base immediately to the left of the hungry codon. The latter result suggests that the aminoacyl-tRNA in the P site affects the maintenance of reading frame at the adjacent A site of the ribosome. However, the DNA sequence makes it seem unlikely that the P-site tRNA shifts to the right in concert with the A-site tRNA, a mechanism that can account for leftward frameshifting (in the opposite direction) in retroviral translation. The specificity of sequence determinants of leftwing versus rightwing frameshifting is discussed.

Amino Acid Sequence↗
PubMed1992

Sequence and expression in Escherichia coli of the 40-kDa subunit of activator 1 (replication factor C) of HeLa cells.

Activator 1 (A1; also called replication factor C), in conjunction with proliferating-cell nuclear antigen (PCNA), is essential for the elongation of primed DNA templates by DNA polymerases delta and epsilon. A1 contains five distinct subunits of 145, 40, 38, 37, and 36.5 kDa. Here we describe the isolation, sequence, and bacterial expression of a cDNA coding for the 40-kDa subunit. In keeping with the presence of an ATP-binding motif, the bacterially expressed 40-kDa subunit binds ATP. The interaction between the 40-kDa subunit and ATP was reduced by the addition of PCNA. In addition, antibodies raised against the 40-kDa subunit abolished the A1- and PCNA-dependent synthesis of DNA catalyzed by polymerase delta. The putative amino acid sequence of the 40-kDa subunit of A1 revealed significantly homology with the bacteriophage T4 gene 44 protein and, to a lesser degree, with the tau and gamma subunits of Escherichia coli DNA polymerase III holoenzyme.

Adenosine Triphosphate↗
PubMed1988

Sequences contained within the promoter of the human thymidine kinase gene can direct cell-cycle regulation of heterologous fusion genes.

Recent evidence on the transcriptional regulation of the human thymidine kinase (TK) gene raises the possibility that cell-cycle regulatory sequences may be localized within its promoter. A hybrid gene that combines the TK 5' flanking sequence and the coding region of the bacterial neomycin-resistance gene (neo) has been constructed. Upon transfection into a hamster fibroblast cell line K12, the hybrid gene exhibits cell-cycle-dependent expression. Deletion analysis reveals that the region important for cell-cycle regulation is within -441 to -63 nucleotides from the transcriptional initiation site. This region (-441 to -63) also confers cell-cycle regulation to the herpes simplex virus thymidine kinase (HSVtk) promoter, which is not expressed in a cell-cycle manner. We conclude that the -441 to -63 sequence within the human TK promoter is important for cell-cycle-dependent expression.

Base Sequence↗
PubMed1992

Isolation and sequencing of the cDNA coding for spinach 10-formyltetrahydrofolate synthetase. Comparisons with the yeast, mammalian, and bacterial proteins.

The one-carbon metabolism enzymes 10-formyltetrahydrofolate synthetase (EC 6.3.4.3), 5,10-methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9), and 5,10-methylenetetrahydrofolate dehydrogenase (EC 1.5.1.5) can be found on a single trifunctional protein in the eukaryotes examined. The one exception is in spinach leaves where 10-formyltetrahydrofolate synthetase is monofunctional (Nour, J. M., and Rabinowitz, J. C. (1991) J. Biol. Chem. 266, 18363-18369). In the prokaryotes examined, 10-formyltetrahydrofolate synthetase is either absent or is monofunctional. A cDNA clone encoding spinach leaf 10-formyltetrahydrofolate synthetase was isolated through the use of antibodies to the purified enzyme. This clone had an open reading frame of 1914 base pairs and encoded for a protein containing 636 amino acids with a calculated M(r) of 67,727. The percentage identity between spinach 10-formyltetrahydrofolate synthetase and the synthetase domains in the four trifunctional eukaryotic enzymes and the two monofunctional prokaryotic enzymes that have been cloned and sequenced was: 64.9% human, 63.8% rat, 55.6% yeast cytoplasm, 53.8% yeast mitochondria, 47.8% Clostridium acidi-urici, and 47.9% Clostridium thermoaceticum. Clearly the spinach monofunctional protein had greatest homology with the mammalian proteins. The spinach protein is longer than the two other monofunctional prokaryotic proteins. Possible reasons for this are presented. The codon usage and the putative translation initiation sites are examined and compared with other spinach proteins.

Amino Acid Sequence↗
PubMed1986

Molecular cloning and sequencing of the region of the rubella virus genome coding for glycoprotein E1.

The sequence of the 1600 3' terminal nucleotides of the RNA of rubella virus was determined from cDNA synthesized from both virion and intracellular RNA using reverse transcriptase and an oligodeoxythymidine primer and cloned into a bacterial plasmid vector. This sequence contained the complete coding sequence for virion envelope protein E1 and a 57 nucleotide nontranslated region between the stop codon for E1 and the poly A tract. The predicted size for E1 was 481 amino acids and within this sequence were three potential N-linked glycosylation sites and a putative trans-membrane domain near the carboxy terminus. Immediately preceding the E1 coding region was a putative signal sequence. No homology was found at either the amino acid or nucleotide level between the region of the rubella virus genome sequenced and corresponding regions of the genomes of the alphaviruses, the other genus of the family Togaviridae for which sequence information has been obtained.

Amino Acid Sequence↗
PubMed1985

Efficient expression of the Escherichia coli leuB gene in yeast.

Efficient expression of the Escherichia coli leuB (beta-isopropylmalate dehydrogenase) gene occurred in yeast after in vitro DNase digestion and religation of plasmid bound leuB and the yeast HIS3 DNA which placed the 5' end of the yeast HIS3 gene immediately adjacent to the coding region of the E. coli leuB gene. Two structurally distinct classes of gene fusions were constructed, each involved portions of the yeast HIS3 gene which contributed DNA sequences responsible for leuB expression in yeast. The first class involved fusion of the HIS3 coding region to bacterial DNA resulting in the production of a fusion protein with beta-isopropylmalate dehydrogenase activity. The second class consisted of bacterial DNA, including the leuB coding region, fused to the HIS3 promotor region with the absence of any portion of the HIS3 coding region. In both constructions the HIS3 promotor region is required for transcription, however, translation of the class two fusion is initiated at a bacterial DNA coded AUG, and the 5' end of the mRNA coded by the leuB gene mapped predominantly at bacterial DNA sequences. The DNA sequence responsible for the 5' end of the HIS3 mRNAs remain in the class two gene fusions but this did not preclude the initiation of transcription at bacterial DNA sequences. The pattern of mRNA initiation at bacterial DNA suggests that DNA sequences at, or adjacent to, the site of transcription initiation are involved in the determination of the sites of initiation, and perhaps the frequency at which initiation occurs.

3-Isopropylmalate Dehydrogenase↗
PubMed1990

The promoter of the human proliferating cell nuclear antigen (PCNA) gene is bidirectional.

The proliferating cell nuclear antigen (PCNA) gene codes for a protein that is necessary for cellular DNA synthesis and cell cycle progression. A functional promoter has been identified in the 5' flanking region of the human PCNA gene. An abbreviated promoter (from the capsite to the PvuII restriction site at -395) was found to be equally efficient in directing transcription from a linked reporter, whether placed in the correct or reverse orientation in respect to the coding sequence. The reporter used was a cDNA of human thymidine kinase (TK), and the bidirectionality of the promoter was demonstrated by its ability to confer the TK+ phenotype to TK- ts 13 cells and by the amount of specific message in RNA blots. The PvuII promoter placed between two coding sequences (the TK cDNA and the bacterial gene for neoresistance) is capable of driving transcription simultaneously in both directions. Finally, in blots of RNA from human cells, two transcripts could be detected that hybridized to a sense riboprobe from the 5' flanking region of the human PCNA gene. We conclude that the locus for the human PCNA gene contains a bidirectional promoter producing diverging transcripts.

Cell Line↗
PubMed1986

An efficient chloramphenicol-resistance marker for Saccharomyces cerevisiae and Escherichia coli.

Chloramphenicol (Cm) was demonstrated to be a suitable selective agent for the plasmid-mediated transformation of haploid and polyploid strains of Saccharomyces cerevisiae. A yeast/Escherichia coli shuttle Cm-resistance (CmR) marker was constructed by inserting the CAT coding sequence from Tn9, and its associated bacterial ribosome-binding site, between a modified yeast ADC1 promoter and CYC1 terminator. When present on a 2 microns-based replicating plasmid, this marker transformed yeast as efficiently as the auxotrophic markers TRP1 and LEU2. When included in an integrating vector, single-copy transformants were formed as efficiently as with LEU2 and HIS3. Industrial yeast strains were transformed with both the replicating and integrating plasmids. The CmR marker could also efficiently transform E. coli. This versatile and efficient performance is currently unique for a yeast dominant marker.

Acetyltransferases↗
PubMedDate not supplied

[Convergent origin of repeats in genes coding for globular proteins. An analysis of the factors determining the presence of inverted and symmetrical repeats].

The factors, determining the presence of inverted and symmetrical repeats in genes coding for globular proteins, have been analysed. An interesting property of genetical code has been revealed in the analysis of symmetrical repeats: the pairs of symmetrical codons corresponded to pairs of amino acids with mostly similar physical-chemical parameters. This property may explain the presence of symmetrical repeats and palindromes only in genes coding for beta-structural proteins-polypeptides, where amino acids with similar physical-chemical properties occupy symmetrical positions. A stochastic model of evolution of polynucleotide sequences has been used for analysis of inverted repeats. The modelling demonstrated that only limiting of sequences (uneven frequencies of used codons) is enough for arising of nonrandom inverted repeats in genes.

Amino Acid Sequence↗