SEARCH · PubMed Health

Results for “bacterial coding sequence”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 649 records · Page 36Linked to original sources

PubMed1987

[Design of a hybrid gene coding for the leader sequence of Bacillus amyloliquefaciens alpha-amylase and for human proinsulin].

The chemically synthesized structure gene of human proinsulin was cloned in E. coli on the secretory vector containing regulatory elements of the Bacillus amyloliquefaciens alpha-amylase gene. The proinsulin gene was inserted by the EcoRI site located immediately after the DNA area encoding the alpha-amylase signal peptide. The E. coli cells transformed by such a plasmid produced hybrid protein consisting of the alpha-amylase signal peptide, five amino acid residues after the gene mating and human proinsulin. For accurate mating of the alpha-amylase gene leader sequence and proinsulin gene directed mutagenesis was performed on the filiform phage M13 mp9 with synthetic oligonucleotide. The hybrid gene was transferred to the vector molecule capable of replicating in Bacillus subtilis. It was shown that in the cells of both E. coli and B. subtilis there is synthesized protein interacting by the radio-immunological data with antibodies to porcine insulin, a large portion of immunologically active protein being detected in the periplasmic space of E. coli cells and in the culture fluid of B. subtilis cells which was indicative of proinsulin secretion directed by the alpha-amilase regulatory elements.

Amino Acid Sequence↗

PubMed1996

Genomic cloning of a human heat shock protein 40 (Hsp40) gene (HSPF1) and its chromosomal localization to 19p13.2.

The Hsp40 (heat shock protein with molecular size of approximately 40 kDa) is one of the mammalian homologues of bacterial DnaJ heat shock protein. We have isolated and characterized a genomic DNA clone encompassing the entire coding sequences of the human Hsp40 cDNA. The Hsp40 gene (HGMW-approved symbol HSPF1) is composed of three exons divided by two introns. The 5' region of the gene is highly GC rich, and there are multiple basal elements for transcription factors including typical heat shock elements. The Hsp40 gene has been assigned to chromosome 19 band p13.2 by in situ hybridization.

Binding Sites↗

PubMed1991

Cloning, sequencing and characterization of the Saccharomyces cerevisiae URA7 gene encoding CTP synthetase.

The URA7 gene of Saccharomyces cerevisiae encodes CTP synthetase (EC 6.3.4.2) which catalyses the conversion of uridine 5'-triphosphate to cytidine 5'-triphosphate, the last step of the pyrimidine biosynthetic pathway. We have cloned and sequenced the URA7 gene. The coding region is 1710 bp long and the deduced protein sequence shows a strong degree of homology with bacterial and human CTP synthetases. Gene disruption shows that URA7 is not an essential gene: the level of the intracellular CTP pool is roughly the same in the deleted and the wild-type strains, suggesting that an alternative pathway for CTP synthesis exists in yeast. This could involve either a divergent duplicated gene or a different route beginning with the amination of uridine mono- or diphosphate.

Amino Acid Sequence↗

PubMed1996

Epitope mapping of monoclonal antibodies raised to recombinant Mengo 3D polymerase.

The cDNA coding sequence of the RNA-dependent RNA polymerase (3Dpol) of Mengovirus was cloned and expressed in a bacterial system. Eleven monoclonal antibodies were raised against the recombinant Mengo 3Dpol (rM3D). All of them recognized the recombinant and the viral-induced form of the protein. The panel of monoclonals belonged to the IgG1 and IgG2a isotypes and were mapped to four different epitopes in the 3D molecule by competition assays. All monoclonals recognized Mengo 3Dpol in western blots and cross-reacted with the homologous polymerases of seven other cardioviruses but failed to react with 3Dpol from poliovirus type 1 and 3 or rhinovirus type 14 and 16.

Antibodies, Monoclonal↗

PubMed1991

Rabbit hemorrhagic disease virus--molecular cloning and nucleotide sequencing of a calicivirus genome.

The RNA genome of rabbit hemorrhagic disease virus (RHDV) was molecularly cloned. The 5' terminal sequence of the genomic RNA was determined after PCR amplification of a G-tailed first strand cDNA template. The cloned cDNA allowed determination of the first complete caliciviral sequence encompassing 7437 nucleotides without poly(A) tail. The RHDV genome contains one long open reading frame of 2344 codons which in the 5' region encodes the nonstructural proteins. Sequence comparison studies revealed significant homology between nonstructural proteins of the feline calicivirus (FCV) and RHDV. In analogy to FCV the deduced RHDV amino acid sequence contains a picornavirus 2C-like sequence, a hypothesized cysteine protease motif, and the conserved polymerase residues GDD. For the protein region containing the GDD motif, alignments of sequences from different viruses including the putative caliciviruses hepatitis E virus and Norwalk virus were performed; concerning the classification of the latter two viruses, a final judgement was not possible. Bacterial expression of sequences derived from the 3' part of the genomic RHDV RNA showed that this region codes for the viral capsid protein.

Amino Acid Sequence↗

PubMed2001

Cloning, transcription and chromosomal localization of the porcine whey acidic protein gene and its expression in HC11 cell line.

The whey acidic protein (WAP) is the major whey protein of rodent, rabbit and camel. Recently, it was identified in the milk of swine (Simpson et al., 1998. J. Mol. Endocrinol. 20, 27-35). In this paper, the cloning of the pig WAP cDNA and of bacterial artificial chromosome (BAC) construct containing the entire porcine WAP gene is reported. The comparison of the coding sequence of the pig WAP gene to rodent or lagomorph WAP sequence already published demonstrated that only exon sequences are partially conserved. The porcine WAP gene was localized on the subtelomeric region of the chromosome 18. The estimation of the expression of the swine WAP gene in the mammary gland from lactating animals revealed a high level of expression. In order to compare the expression level of the porcine WAP gene from the large genomic fragment which contained 70 kb downstream and 50 kb upstream the pig WAP gene or the smaller one (1 kb downstream and 2.4 kb upstream), these two genomic fragments were transfected in HC11 cell line. The BAC construct was expressed 15 times higher than the plasmid when reported to the integrated copy number. This report suggests that the HC11 cell line is a useful tool to identify the regulatory sequences of milk protein genes.

Amino Acid Sequence↗

PubMed1983

Nucleotide sequence of the Escherichia coli xanthine-guanine phosphoribosyl transferase gene.

The Escherichia coli gene coding for the enzyme xanthine-guanine phosphoribosyl transferase (gpt) has been widely used as a dominant selectable marker in a variety of mammalian cells. We have determined the complete nucleotide sequence of the 1057 base pair (bp) segment of DNA containing this gene. The coding sequence for the enzyme is 456 nucleotides long and can code for a 152 amino acid (16.9 Kd) polypeptide. A comparison of the amino acid sequence of the bacterial enzyme with that of the mammalian hypoxanthine-guanine phosphoribosyl transferase (hprt) reveals no significant homology between the two polypeptides.

Amino Acid Sequence↗

PubMed1994

Expression in Escherichia coli of a secreted invertebrate ferritin.

The coding regions of the cDNAs for cytoplasmic soma ferritin and secreted yolk ferritin from the snail Lymnaea stagnalis were inserted into the prokaryotic expression vector pEMBLex2. The vector directed the synthesis in Escherichia coli of soma ferritin up to a concentration of 15% of soluble proteins. Soma ferritin was expressed as the multimeric protein (480 kDa). Its similarity with natural soma ferritin was confirmed by PAGE, immunostaining and electron microscopy. Yolk ferritin was expressed in the form of inclusion bodies. Attempts to refold and assemble the purified yolk ferritin subunit in vitro failed. The yolk ferritin coding sequence was therefore inserted into the expression vector pMAL-p2. At a growth temperature of the bacterial cells of 23 degrees C and at an isopropyl beta-D-thiogalactopyranoside concentration of 50 microM, about 5% of the induced MalE-yolk-ferritin fusion protein was secreted into the periplasmic space and could be purified by affinity chromatography on amylose; the rest occurred as insoluble cytoplasmic inclusion bodies. Soluble MalE-yolk-ferritin fusion protein was capable of assembly into ferritin-like particles. Fully assembled yolk apoferritin shells (610 kDa) were obtained by digestion of these particles with proteinase K (yield: 180 micrograms yolk ferritin/l bacterial culture). Recombinant yolk ferritin was capable of taking up iron in vitro. Yolk ferritin (610 kDa) and soma ferritin (480 kDa) were run to the pore limit of a non-denaturing 5-20% PAGE gradient gel. Under these conditions, yolk ferritin had a higher mobility than soma ferritin (480 kDa) and therefore the yolk ferritin may have a rather compact structure. A 41-amino-acid-residue stretch of the insertion, a distinctive feature of the yolk ferritin subunit, was deleted by site-directed mutagenesis. The MalE-yolk-ferritin variant thus obtained was readily degradable by proteinase K and could not be assembled into ferritin-like particles. Therefore residues in the deleted peptide must be important for the maintenance of the native structure.

ATP-Binding Cassette Transporters↗

PubMed1993

Cloning and sequencing of a soybean nuclear gene coding for a chloroplast translation elongation factor EF-G.

A plant nuclear gene coding for a chloroplast specific translation elongation factor EF-G (cEF-G) was cloned and sequenced for the first time. We screened two partial soybean genomic libraries with a short PCR amplified pea DNA probe constructed according to the N-terminal peptide sequence of pea chloroplast EF-G. The gene is three times split, codes for a chloroplast type transit peptide and a protein very similar to bacterial translation elongation factor EF-G. The gene is expressed as evidenced by Northern hybridisations.

Amino Acid Sequence↗

PubMed1997

A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria.

The hydrogenosomal malic enzyme (ME) was purified from the anaerobic fungus Neocallimastix frontalis. Using reverse genetics, the corresponding cDNA was isolated and characterized. The deduced amino acid sequence of the ME showed high similarity to ME from metazoa, plants and protists. Putative functional domains for malate and NAD+/NADP+ binding were identified. Phylogenetic analysis of the deduced amino acid sequence of the new ME suggests that it is homologous to reference bacterial and eukaryotic ME. Most interestingly, the cDNA codes for a protein which contains a 27-amino-acid N-terminus which is not present on the purified mature protein. This presequence shares features with known mitochondrial targeting signals, including an enrichment in Ala, Leu, Ser, and Arg, and the presence of an Arg at position-2 relative to amino acid 1 of the mature protein. This is the first report of a mitochondrial-like targeting signal on a hydrogenosomal enzyme from an anaerobic fungus and provides support for the hypothesis that hydrogenosomes in Neocallimastix frontalis might be modified mitochondria.

Amino Acid Sequence↗

PubMed1983

Analysis of a bacterial hygromycin B resistance gene by transcriptional and translational fusions and by DNA sequencing.

We have characterized hygromycin B and apramycin resistance genes from an E. coli plasmid. We have localized the coding and control regions of these genes by deletion of DNA fragments from plasmids containing the genes. It was found that polypeptides with apparent molecular weights of 33,000 and 31,500 daltons are encoded by the apramycin resistance gene and polypeptides with apparent molecular weights of 42,500 and 41,500 daltons are encoded by the hygromycin B resistance gene. DNA sequence analysis identified a typical promoter sequence upstream of the genes. Deletion of this promoter eliminated both resistance phenotypes, and hygromycin B resistance could be restored by substitution of a promoter from a foreign gene. The region known to be necessary for hygromycin B resistance contained an open reading frame large enough to encode the hygromycin B resistance gene product. This open reading frame was fused with the amino terminus of beta-galactosidase. This hybrid gene conferred hygromycin resistance to E. coli, and expression of resistance was under IPTG control.

Anti-Bacterial Agents↗

PubMed2003

Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase.

BACKGROUND: The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects. RESULTS: Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the gamma-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (gamma-Proteobacteria) possess similar plasmid-encoded arsC sequences. CONCLUSION: The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT) in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

Adenosine Triphosphatases↗

PubMed1993

Regulation of rabbit alpha 1-acid glycoprotein gene expression in acute-phase liver. Identification of inducible and constitutive proteins like CCAAT-enhancer binding protein that interact with the 5'-proximal promoter elements.

To identify the cis-acting DNA sequences responsible for inducible transcription of rabbit alpha 1-acid glycoprotein gene, 5'-flanking region containing 529 bp of this gene and its various 5'-deletions were linked to the reporter gene coding for the bacterial chloramphenicol acetyltransferase (CAT) and analyzed for their ability to confer cytokine-mediated inducibility to the reporter CAT gene in liver cells. Deletion analysis has identified a 151-bp region from the sequence -186 to -35, that contains the regulatory promoter element(s) responsible for stimulation mediated by cytokines present in the conditioned-medium. Using mobility shift assays, we have identified highly inducible nuclear factors in acute liver nuclear extract that interact with this regulatory promoter region. DNase I footprint analysis has revealed two adjacent nuclear factor binding sites and competition of DNA-binding activity has indicated that the distal element of these two sites has higher affinity for nuclear factors than the proximal one. Both of these two regions have been found to be capable of directing conditioned-medium-induced transcription. Studies on the characterization of nuclear factors binding to these elements have shown that they belong to a class of transcription factors called CCAAT-enhancer binding protein (C/EBP). Our results indicate that binding of C/EBP-like factors to the inducible promoter elements of rabbit alpha 1-acid glycoprotein gene is highly specific and the induction of this gene under acute-phase conditions may involve their participation.

Animals↗

PubMed1997

Nucleotide sequence of a putative periplasmic Mn superoxide dismutase from Acinetobacter calcoaceticus ADP1.

We determined 5.8 kilobases of nucleotide sequence upstream of the rubredoxin encoding rubA gene of Acinetobacter calcoaceticus (Ac) ADP1. Sequence analysis revealed four open reading frames named cysD', cobQ, sodA and lysS, coding for proteins with high similarity to known sulfate adenylate transferases (partial), cobyric acid synthases, superoxide dismutases (Sod) and lysyl tRNA synthetases, respectively. Out of a large number of bacterial Sod sequences SodA of Ac ADP1 is the first member of the Fe/Mn Sod family apparently located in the periplasmic space.

Acinetobacter calcoaceticus↗

PubMedDate not supplied

Rearrangement of nitrogen fixation genes during heterocyst differentiation in the cyanobacterium Anabaena.

Nitrogen fixation by the cyanobacterium Anabaena is carried out in heterocysts, specialized, non-dividing cells which differentiate under conditions of ammonia or nitrate deprivation. In Anabaena, heterocyst differentiation is accompanied by rearrangement of some nitrogen fixation genes. A site-specific recombination between an 11 base-pair direct repeat sequence flanking the nifK and nifD genes removes 11 kilobases of intervening DNA, resulting in juxtaposition of the two genes and an alteration of the nifD protein-coding sequence.

Cell Differentiation↗

PubMed1982

Isolation and expression of cloned hook protein gene from Caulobacter crescentus.

Previous genetic analysis of Caulobacter crescentus showed that the periodic synthesis of hook protein, flagellin A, and flagellin B, the major flagellar subunits, is coupled in some way to chromosome replication. To examine the regulation of flagellar gene expression at the molecular level, we isolated the gene that codes for the 72,000-dalton hook protein. A specific 125I-labeled anti-hook protein IgG was used to screen a hybrid lambdaL47.1 bank of 4,500 clones and to compare peptide maps of the cloned gene product with purified hook protein. Restriction analysis of DNA from the positive lambda clones and plasmid subclones showed that the structural gene for the hook protein is contained on a 2.3-kilobase (kb) BamHI fragment. The direction of transcription was established by demonstrating the inducibility of hook protein gene in strains with the 2.3-kb fragment fused to the Escherichia coli lipoprotein gene-lactose gene promoter-operator region of pIN-II. Preliminary genomic analysis showed that the hook gene occupies a single location on the C. crescentus chromosome. These results suggest that the periodic expression of the hook protein gene in the cell cycle does not involve a major or persistent rearrangement of the 2.3-kb coding sequence during the cell cycle.

Bacteria↗

PubMed1995

Transcription termination at intrinsic terminators: the role of the RNA hairpin.

Intrinsic termination of transcription in Escherichia coli involves the formation of an RNA hairpin in the nascent RNA. This hairpin plays a central role in the release of the transcript and polymerase at intrinsic termination sites on the DNA template. We have created variants of the lambda tR2 terminator hairpin and examined the relationship between the structure and stability of this hairpin and the template positions and efficiencies of termination. The results were used to test the simple nucleic acid destabilization model of Yager and von Hippel and showed that this model must be modified to provide a distinct role for the rU-rich sequence in the nascent RNA, since a perfect palindromic sequence that is sufficiently long to form an RNA hairpin that could destabilize the entire putative 12-bp RNA-DNA hybrid does not trigger termination at the expected positions. Rather, our results show that both a stable terminator hairpin and the run of 6-8 rU residues that immediately follows are required for effective intrinsic termination and that termination occurs at specific and invariant template positions relative to these two components. Possible structural or kinetic modifications of the simple model are proposed in the light of these findings and of recent results implicating "inchworming" and possible conformational heterogeneity of transcription complexes in intrinsic termination. Thus, these findings argue that the structure and dimensions of the hairpin are important determinants of the termination-elongation decision and suggest that a complete mechanism is likely to involve specific interactions of the polymerase, the RNA terminator hairpin, and, perhaps, the dT-rich template sequence that codes for the run of rU residues at the 3' end of the nascent transcript.

Bacterial Proteins↗

PubMed2005

Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes.

Although it is well known that there is no long range colinearity in gene order in bacterial genomes, it is thought that there are several regions that are under strong structural constraints during evolution, in which gene order is extremely conserved. One such region is the str locus, containing the S10-spc-alpha operons. These operons contain genes coding for ribosomal proteins and for a number of housekeeping genes. We compared the organisation of these gene clusters in 111 sequenced prokaryotic genomes (99 bacterial and 12 archaeal genomes). We also compared the organisation to the phylogeny based on 16S ribosomal RNA gene sequences and the sequences of the ribosomal proteins L22, L16 and S14. Our data indicate that there is much variation in gene order and content in these gene clusters, both in bacterial as well as in archaeal genomes. Our data indicate that differential gene loss has occurred on multiple occasions during evolution. We also noted several discrepancies between phylogenetic trees based on 16S rRNA gene sequences and sequences of ribosomal proteins L16, L22 and S14, suggesting that horizontal gene transfer did play a significant role in the evolution of the S10-spc-alpha gene clusters.

Bacteria↗