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PubMed1989

Isolation of dynein heavy chain cDNAs from trout testis which predict an extensive carboxyl-terminal alpha-helical coiled-coil domain.

A Mg2+-dependent ATPase activity has been purified from trout sperm axonemes which has properties characteristic of a dynein ATPase. A polyclonal antiserum prepared against the dynein heavy chains has been used to isolate dynein heavy chain (DYHC) cDNAs from a trout testis lambda gt11 cDNA expression library. beta-galactosidase fusion proteins produced in lambda gt11 by these trout cDNAs cross-reacted with a heterologous anti-sea urchin dynein antiserum. Northern blot analyses demonstrated that the RNA transcripts detected have sizes (7.5 - 12 kb) consistent with those expected for the dynein heavy chains. All the DYHC cDNAs encode portions of a highly unusual DNA coding sequence comprised of 21 bp direct repeats. The predicted open reading frame of this repeat is Ile/Leu-His-Val-Ile-Gln-Tyr-Ser and is characteristic of an extensive alpha-helical coiled-coil domain. The presence of an in-frame translation termination codon indicates that this domain is located at the carboxyl-terminus of the DYHC. Southern blot analyses demonstrated a low, if not single, copy number for this gene and conservation of this domain in other vertebrates. DYHC transcripts reach their highest level in testis, but are also abundant in brain tissue.

Adenosine Triphosphatases↗

PubMed1989

Cloned human snRNP proteins B and B' differ only in their carboxy-terminal part.

Antibodies to the snRNP proteins B' and B are frequently observed in autoimmune diseases. We analyzed different types of cDNAs encoding these proteins. One type of cDNA encoded a protein whose predicted mol. wt is 24.6 kd, whereas another type encoded a protein with a predicted mol wt of 23.7 kd. When translated in vitro from cDNA transcripts, the apparent mol. wts of these proteins on SDS-polyacrylamide gel were 29.5 and 28.5 kd respectively. The main difference between these two types of cDNAs proved to be the presence of an additional sequence of 146 nucleotides in the 3' part of the open reading frame of the clone encoding the shorter protein. This insert contains a termination codon in frame, at 9 nucleotides downstream from the 5' end of the insert. The additional sequence revealed at the 3' end a consensus sequence of vertebrates for intron-exon junctions. We demonstrated the presence of mRNAs corresponding with both types of cDNA in human cells. We hypothesize that the B' and B protein are derived from one pre-mRNA by alternative splicing, and show that they differ only at the carboxy terminus, where a proline rich motive is repeated once more in B'. A comparison with amino acid sequences of other cloned snRNP proteins is included.

Amino Acid Sequence↗

PubMed1990

Cleavage-site preferences of Sindbis virus polyproteins containing the non-structural proteinase. Evidence for temporal regulation of polyprotein processing in vivo.

The non-structural proteins of Sindbis virus, nsP1, 2, 3 and 4, are produced upon cleavage of polyproteins P123 and P1234 by a proteinase residing in nsP2. We used cell free translation of SP6 transcripts to study the proteolytic activity of nsP2 and of nsP2-containing polyproteins. To generate polyprotein enzymes, a set of plasmids was made in which cleavage sites were eliminated and new initiation and termination codons introduced by in vitro mutagenesis. As a substrate, we used a polyprotein in which the nsP2 proteinase had been inactivated by a single amino acid substitution. All nsP2-containing polyproteins cleaved the nsP1/2 site in trans. However, proteinases containing nsP1 were unable to cleave the nsP2/3 site. Furthermore, only proteinases containing nsP3 could cleave the nsP3/4 site. These differences in cleavage site specificity result in a temporal regulation of processing in vivo. At 1.7 h post infection P123 and nsP4 accumulated and only small amounts of P34 were found. However, at 4 h post infection P123 was processed rapidly and P34 was produced rather than nsP4. Since nsP4 is thought to be the viral RNA polymerase, the temporal regulation of the nsP4/P34 ratio may be responsible for the temporal regulation of RNA synthesis.

Animals↗

PubMed1991

Distinct cis-acting signals enhance 3' endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisiae.

The cyc1-512 mutant of the yeast Saccharomyces cerevisiae contains a 38 bp deletion in the 3' untranslated region of the CYC1 gene, resulting in CYC1 mRNAs that are elongated, presumably labile, and reduced to 10% of the normal level. Analysis with S1 nuclease and a novel PCR procedure revealed that the low amount of cyc1-512 mRNA contained many discrete 3' termini at certain sites, ranging from the wild-type position to over 2000 nucleotides (nt) downstream. The cyc1-512 mRNA deficiency was completely or almost completely restored in eight intragenic revertants that contained six different single and multiple base-pair changes within a 300 bp region downstream from the translation terminator codon. Two of the six different reversions formed the sequence TAG...TATGTA, whereas the other four reversions created the sequences TATATA or TACATA. The positions of these revertant sequences varied, even though they caused an increased use of specific major downstream mRNA 3' endpoints, apparently identical to those seen in the cyc1-512 mRNA. However, several revertants contained minor end points not corresponding to any of the cyc1-512 mRNAs. The capacity of these three signals to form 3' ends was confirmed with sequences constructed by site-directed mutagenesis. We therefore suggest that the production of 3' termini of yeast mRNA may involve at least two functionally distinct elements working in concert. One type of element determines the sites of preferred 3' mRNA termini, as represented by the cyc1-512 termini. The second type of element, which includes TAG...TATGTA and TATATA motifs, operates at a distance to enhance the use of the downstream 3' preferred sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1983

Mitochondrial DNA of an African trypanosome.

The maxicircles of African trypanosome kDNA are the genetic equivalent of other mitochondrial DNAs, but the function of minicircles is unknown. The maxicircle of Trypanosoma brucei 164 encodes conventional mitochondrial gene products and is largely but not completely transcribed. Nucleotide sequence analysis of a region not found to be transcribed revealed numerous translation termination codons in all three reading frames of both strands and numerous inverted repeats, suggesting that this segment does not have polypeptide-coding function. This segment may encode a t-RNA and has a sequence resembling a consensus sequence found in mitochondrial introns, thus implying that transcript processing occurs in trypanosome mitochondria. While several cloned minicircles had distinct restriction maps reflecting T brucei minicircle heterogeneity, one segment of the minicircle contained a sequence that was conserved by minicircles from other trypanosome strains and species. Of nine mutants unable to grow as the respiring procyclic forms, seven were devoid of kDNA. The other two mutants retained normal amounts of all maxicircle restriction fragments and normal amounts of those minicircle sequences tested. Minicircle alterations probably occur in these mutants, since the kDNA does not stain with Giemsa and bands at an altered density in cesium chloride/ethidium bromide density gradients.

Animals↗

PubMed2006

A homozygous frameshift mutation in the ESCO2 gene: evidence of intertissue and interindividual variation in Nmd efficiency.

Roberts syndrome (RS) is a rare disorder characterized by tetraphocomelia and several other clinical features. Cells from RS patients exhibit characteristic premature separation of heterochromatic region of many chromosomes and abnormalities in cell cycle. Mutations in the ESCO2 gene have recently been identified in 20 RS families. We performed mutational analysis of the ESCO2 gene in two fetuses diagnosed with RS and their normal parents. In both fetuses, we identified homozygosity for the c. 745_746delGT mutation, while the non-consanguineous parents were both heterozygous for the same mutation. Considering the position of the mutation identified, we carried out qualitative and quantitative real-time ESCO2 cDNA analysis on RNA isolated from CVS-stromal cells in one fetus, amniocytes in the second fetus, and lymphocytes from the heterozygous parents. The results of this analysis showed that despite the presence of a premature termination codon (PTC) 112 nucleotides upstream of the next exon3-exon4 junction, the mutant ESCO2 mRNA was present in both fetuses, albeit at low levels, indicating a partial resistance to nonsense mediated decay (NMD). Interestingly, when cells derived from the two fetuses were treated with an inhibitor of translation, they revealed the presence of tissue and individual variability in NMD efficiency, despite the identical mutational status. The existence of such a variation in the NMD efficiency could explain the broad intrafamilial and interfamilial variability in the clinical presentation of RS patients, and in other genetic diseases where nonsense mutations are responsible for most of the mutation load. Moreover, considering that a mutated full length mRNA was produced in both fetuses, we used Western blot analysis to demonstrate the absence of the ESCO2-truncated protein in cells derived from both fetuses and in a lymphoblastoid cell line derived from the parents.

Abnormalities, Multiple↗

PubMed1995

Precore and core mutations in HBV from individuals in India with chronic infection.

Ten hepatitis B surface antigen seropositive carriers (5 asymptomatic and 5 with chronic liver disease) were tested for HBeAg/anti-HBe and for HBV-DNA using the polymerase chain reaction. Five were DNA-positive, 2 with HBeAg and 3 with anti-HBe. Nucleotide sequences were determined for these 5 cases. Hepatitis B virus DNA from one cirrhotic carrier with anti-HBe had a mutation in the precore region (nucleotide position 1862) which may affect signal peptide cleavage and HBeAg synthesis. In the other 2 anti-HBe- and DNA-positive cases, a cirrhotic carrier and an asymptomatic case, there was a mutation at nucleotide position 1896 leading to a termination codon in the precore region. In all 5 patients, except for one or two missense mutations, there was no significant variation in the core region.

Amino Acid Sequence↗

PubMed1995

Genetic basis of lethal junctional epidermolysis bullosa in an affected fetus: implications for prenatal diagnosis in one family.

Fetal skin biopsy at 20 weeks' gestation in a woman at risk for a child with the lethal skin-blistering disorder junctional epidermolysis bullosa (Herlitz) confirmed an affected fetus. Genomic DNA from the aborted fetus was examined for mutations in laminin 5, a macromolecule involved in adhesion at the dermal-epidermal junction, and a candidate protein in this condition. Polymerase chain reaction (PCR) amplification of exon 10 and parts of the flanking introns of the gene encoding the beta 3 chain of laminin 5 (LAMB3) and subsequent analysis by agarose gel electrophoresis showed a more slowly migrating band in the affected fetus compared with the normal control. Nucleotide sequencing of the abnormal PCR product revealed a homozygous 77 bp duplication within the exon, resulting in a premature termination codon 250 bp downstream from the 3' end of the duplication. Maternal DNA was heterozygous for the mutant and wild-type alleles. These findings illustrate the genetic basis of the skin disease in this case and also offer the prospects of a simple, rapid, and reliable first-trimester DNA-based prenatal, or even preimplantation, diagnostic test for future pregnancies in this family.

Adult↗

PubMed1993

Design of synthetic gene libraries encoding random sequence proteins with desired ensemble characteristics.

Libraries of random sequence polypeptides are useful as sources of unevolved proteins, novel ligands, and potential lead compounds for the development of vaccines and therapeutics. The expression of small random peptides has been achieved previously using DNA synthesized with equimolar mixtures of nucleotides. For many potential uses of random polypeptide libraries, concerns such as avoiding termination codons and matching target amino acid compositions make more complex designs necessary. In this study, three mixtures of nucleotides, corresponding to the three positions in the codon, were designed such that semirandom DNA synthesized by repeated cycles of the three mixtures created an open reading frame encoding random sequence polypeptides with desired ensemble characteristics. Two methods were used to design the nucleotide mixtures: the manual use of a spreadsheet and a refining grid search algorithm. Using design targets of less than or equal to 1% stop codons and an amino acid composition based on the average ratios observed in natural, globular proteins, the search methods yielded similar nucleotide ratios, Semirandom DNA, synthesized with a designed, three-residue repeat pattern, can encode libraries of very high diversity and represents an important tool for the construction of random polypeptide libraries.

Amino Acid Sequence↗

PubMed1985

Primary structure of the Saccharomyces cerevisiae GAL7 gene.

We present the nucleotide sequence of a 1599-base pair (bp) DNA fragment containing the entire GAL7 gene that encodes galactose-1-phosphate uridyltransferase of Saccharomyces cerevisiae. The deduced peptide was composed of 364 amino acid residues. The expected molecular weight was 42,005 daltons, which agreed with the observed value for the purified enzyme. The 3'-end of the GAL7 transcript mapped at a position 82 bp downstream from the UAA termination codon by the S1 nuclease protection experiment. We constructed a GAL7'-lac'Z fusion on various types of yeast plasmid vectors. The fused gene on any type of vector was induced by galactose and repressed by glucose as for the GAL7 gene on the chromosome. The response of GAL7'-lac'Z fusion to gal4 delta and gal80 delta regulatory mutations was also similar to the response of the chromosomal GAL7 gene. By using various deletions in the 5'-flanking region of the gene fusion, we delimited the sequence essential for galactose controlled expression with a 180 bp-fragment of DNA lying 92 bp upstream of the transcription initiation site.

Amino Acid Sequence↗

PubMed1991

The YDp plasmids: a uniform set of vectors bearing versatile gene disruption cassettes for Saccharomyces cerevisiae.

The YDp plasmids (Yeast Disruption plasmids) are pUC9 vectors bearing a set of yeast gene disruption cassettes, all uniform in structure and differing only in the selectable marker used (HIS3, LEU2, LYS2, TRP1 or URA3). The markers, surrounded by translational termination codons, are embedded in the slightly modified sequence of the pUC9 multiple cloning sites.

Base Sequence↗

PubMed1995

Cloning, DNA sequencing, and amino acid sequencing of catechol 1,2-dioxygenases (pyrocatechase) from Pseudomonas putida mt-2 and Pseudomonas arvilla C-1.

Catechol 1,2-dioxygenase catalyzes the oxygenative ring cleavage of catechol to form cis,cis-muconic acid and is encoded by a catA gene. We have cloned a catA gene from Pseudomonas putida mt-2 using a PCR product of amino acid sequence-based primers as a probe. The amino acid sequence deduced from the 930 nucleotides was in complete agreement with the chemically determined sequence of the protein. Crude extracts of Escherichia coli cells carrying the catA gene downstream from the lac promoter showed the enzyme activity. By using the same probe, we also cloned and sequenced the catA beta gene for catechol 1,2-dioxygenase isozyme beta beta from Pseudomonas arvilla C-1, which has three isozymes, alpha alpha, alpha beta, and beta beta (C. Nakai, H. Horiike, S. Kuramitsu, H. Kagamiyama, and M. Nozaki, 1990, J. Biol. Chem. 265, 660-665). There was very high homology between isozyme beta beta of the C-1 strain and the enzyme of the mt-2 strain in both the amino acid (98%) and the DNA sequences (97%). A preference for the use of codons terminating in C and G was found in the coding region of both the enzymes, which contributed to the high G + C content (65-66%) of the genes. A comparison of the DNA sequences of various catA genes from other sources revealed their common ancestry, whereas a comparison of the amino acid sequences of the enzymes revealed clear reflection of substrate specificity. Tyrosyl and histidyl residues for proposed ligands of ferric ion are conserved in all catechol 1,2-dioxygenases.

Amino Acid Sequence↗

PubMed1996

Molecular analysis of the Drosophila catalase gene.

The main objective of this study was to isolate and characterize the catalase gene and accompanying cis-regulatory regions in Drosophila melanogaster. Genomic clones were obtained on the basis of cross-hybridization to catalase cDNA and a 7-kb SalI-KpnI fragment encompassing the catalase gene was introduced into Drosophila by P element-mediated transformation. A single transgene, when placed in a catalase null background, was sufficient to restore resistance to H2O2 as well as reduce susceptibility to early death. DNA sequence of the catalase gene domain was obtained. This included 1365 bp of sequence upstream of the transcription initiation site and 1423 bp downstream of the termination codon. The Drosophila catalase gene is composed of 3 exons, encoding 19, 307, and 180 amino acids, which are separated by 3520- and 96-bp introns. Sequence analysis of the promoter domain is presented, revealing multiple sequence similarities between catalase and Cu,Zn superoxide dismutase promoter domains. Developmental RNA get analysis shows that peaks of catalase mRNA accumulation correspond roughly with major peaks of ecdysone titer during third instar and pupal stages. Candidate ecdysone response element sequences are noted downstream of the catalase polyadenylation site.

Amino Acid Sequence↗

PubMed1997

Fungal P450nor: expression in Escherichia coli and site-directed mutageneses at the putative distal region.

P450nor, nitric oxide reductase from Fusarium oxysporum, was expressed in the soluble fraction of Escherichia coli cells by modifying the N-terminal codons and utilizing the pCW vector. The modified P450nor purified to electrophoretic homogeneity had spectral and enzymatic properties identical to those of native P450nor obtained from the fungi. Residues 239 to 247 of the modified P450nor were replaced with Lys by site-directed mutagenesis. Thr-243 to His- and Arg-mutants were also created. Among 11 mutants, only the Thr-243 to Lys-mutant exhibited an absorption spectrum characteristic of a nitrogenous ligand-bound form of P450 at pH 8.0 in the ferric state, but the spectrum was altered to that of the wild-type P450nor as the pH was lowered. Other mutants had spectra typical of the low- and high-spin mixed form of P450 in the ferric state. In the ferrous state, all mutants showed the same spectrum as the wild-type P450nor. Nitric oxide reductase activity was considerably decreased by the replacement of Thr-243 with Lys, His, or Arg or Ala-239 with Lys. These findings indicate that Thr-243 is located more closely to the heme iron than other residues in the putative distal helix of P450nor and plays an important role in the catalytic activity, but a specific difference in the structure of the heme pocket from other P450s is suggested.

Amino Acid Sequence↗

PubMed1994

Nonsense mutations in human transcobalamin II deficiency.

Reverse transcription-polymerase chain reaction has been used to amplify, clone and sequence transcobalamin II (TC II) cDNA from fibroblasts of three unrelated TC II deficient patients who had undetectable TC II protein and mRNA in their fibroblasts (Li et al., Biochem. J, 301, 585-590, 1994). One child of a consanguineous marriage contained a single nucleotide deletion at position 258 in both alleles, while the child from unrelated parents revealed a nonsense mutation at position 1206 in one allele and a single nucleotide deletion at position 483 in the other allele. Both the single nucleotide deletion mutations caused a frameshift and introduced a premature termination codon (indirect nonsense mutations). No mutation was detected in TC II cDNA from the third patient. Based on these results we suggest that TC II deficiency due to lack of TC II protein/mRNA in these patients is due to heterogeneous types of nonsense mutations.

Alleles↗

PubMed1994

Mutation analysis of the role for the carboxy-terminus encoding region in NGF-induced stabilization of GAP-43 mRNA.

NGF-induced stabilization of rat GAP-43 mRNA has been shown to be mediated by the 292 nt segment including both 3' untranslated region and a 115 nt segment encoding the carboxy-terminus region. Further analysis shows that the 115 nt segment, which is additionally inserted just downstream from the open reading frame, abolished most of the stabilizing effect of NGF. On the contrary, an in-frame insertion of the 115 nt segment just upstream from the termination codon does not affect the stabilization. Frameshift mutation of the segment encoding the carboxy-terminus region also abolishes the NGF effect. These findings suggest an essential role for the direct translation of the mRNA segment encoding the carboxy-terminus region in the stability regulation mediated by the 292 nt segment. In addition, presented results suggest a role for the cis interaction between the sub-segments in the 292 nt segment, which are the part of the 3'untranslated region and the segment for the carboxy-terminus.

Amino Acid Sequence↗

PubMed1997

Presence of mRNAs encoding the soluble D-factor/LIF receptor in human choriocarcinoma cells and production of the soluble receptor.

Four different kinds of cDNAs encoding the receptor for the differentiation stimulating factor (D-factor)/leukemia inhibitory factor (LIF) were isolated from a human liver cDNA library. Three kinds of the cDNAs had different intronic sequences, which introduced a termination codon before the transmembrane domain. However, the site of insertion in human cDNAs is different from those in mouse cDNAs. Recombinant proteins produced by COS-7 cells after transfection of these cDNAs bound D-factor/LIF. mRNAs corresponding to these cDNAs are expressed by the human liver, placenta, and choriocarcinoma cell line NJG. In conditioned medium of choriocarcinoma cells, a native soluble receptor for the D-factor/LIF with a dissociation constant of 7.8 nM and a MW of 160 kDa was found.

Alternative Splicing↗

PubMed1998

Compound heterozygosity for an out-of-frame deletion and a splice site mutation in the LAMB3 gene causes nonlethal junctional epidermolysis bullosa.

Laminin-5 is the major adhesion ligand of epithelial cells. Mutations in the genes encoding laminin-5 cause junctional epidermolysis bullosa (JEB), a clinically and genetically heterogeneous group of recessively inherited blistering disease of skin and mucous membranes. In this report, we describe a patient with a non-lethal variant of JEB who is a compound heterozygous for mutations affecting the LAMB3 gene. The paternally inherited mutation is a deletion of a single base (T) leading to a frameshift and premature termination codon. It results in mRNA decay. The maternally inherited mutation is a G-->A transition at the last base of exon 7 (628G-->A) which converts a codon for glutamic acid in a codon for lysine (E210K). The mutation 628G-->A alters the correct splicing of LAMB3 pre-mRNA giving rise to two aberrant mRNA, in addition to the RNA transcript carrying the G-->A substitution. This result is compatible with the reduced expression of mutated laminin 5 molecules with altered biological activity, and the mild JEB phenotype observed in the patient.

Base Sequence↗