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PubMed1991

Splotch (Sp2H), a mutation affecting development of the mouse neural tube, shows a deletion within the paired homeodomain of Pax-3.

The molecular basis of the mouse mutation splotch (Sp), which is associated with spina bifida and exencephaly, was analyzed at three of its alleles, Sp, Sp2H, and Spr. We mapped the paired box gene Pax-3 within the Inha to Akp3 interval, near or at the Sp locus on chromosome 1, and found Pax-3 to be deleted in heterozygous Spr/+ mice. Analysis of genomic DNA and cDNA clones constructed from Sp2H/Sp2H embryos identified a deletion of 32 nucleotides in the Pax-3 mRNA transcript and gene. This deletion maps within the paired homeodomain of PAX-3 and is predicted to create a truncated protein as a result of a newly created termination codon at the deletion breakpoint. Our study provides evidence for a causal link between deletion of the paired homeodomain of Pax-3 and the Sp2H mutation, and infers that Pax-3 plays a key role in normal neural development.

Amino Acid Sequence↗

PubMed1993

Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer.

Recent studies have shown that a locus responsible for hereditary nonpolyposis colorectal cancer (HNPCC) is on chromosome 2p and that tumors developing in these patients contain alterations in microsatellite sequences (RER+ phenotype). We have used chromosome microdissection to obtain highly polymorphic markers from chromosome 2p16. These and other markers were ordered in a panel of somatic cell hybrids and used to define a 0.8 Mb interval containing the HNPCC locus. Candidate genes were then mapped, and one was found to lie within the 0.8 Mb interval. We identified this candidate by virtue of its homology to mutS mismatch repair genes. cDNA clones were obtained and the sequence used to detect germline mutations, including those producing termination codons, in HNPCC kindreds. Somatic as well as germline mutations of the gene were identified in RER+ tumor cells. This mutS homolog is therefore likely to be responsible for HNPCC.

Amino Acid Sequence↗

PubMed1988

Two pseudogenes among three rat immunoglobulin lambda chain genes.

In order to examine the number and organization of the immunoglobulin lambda light chain genes of the rat, we have used mouse lambda chain cDNA probes to isolate hybridizing fragments from a partial EcoRI rat liver DNA library. We have determined the partial nucleotide sequence of two such clones. One clone, containing a 5.8 kb EcoRI insert which hybridizes to both mouse C lambda 1 and C lambda 2 probes, includes an apparently expressible C lambda 2-like gene as well as a C lambda 1-like pseudogene (psi C lambda 1.1), arranged similarly to the mouse C lambda gene complexes. Sequence analysis of a second cloned EcoRI fragment (1.15 kb in length) revealed part of a second C lambda 1-like pseudogene (psi C lambda 1.2), the coding regions of both pseudogenes being interrupted by multiple frame-shifting size differences. In the case of psi C lambda 1.2, the degree of sequence identity with mouse C lambda 1 drops abruptly immediately following the termination codon, suggesting that translocation events have played a role in its generation. These two rat pseudogenes, and the mouse C lambda 4 pseudogene, clearly have been rendered unexpressible by separate evolutionary events. Comparisons between C lambda coding and non-coding regions of rats and mice indicate that some of the unusual patterns of divergence we have observed in recently diverged Ck genes may exist in C lambda genes as well.

Animals↗

PubMed1992

Linkage of two pseudogenes from V kappa 1 and V kappa 9 murine immunoglobulin families.

As an initial step towards the molecular analysis of the murine V kappa locus, a cosmid library from BALB/cJ mouse liver DNA was screened with probes representing 10 V kappa families. Of eight cosmids that were isolated from the initial screen, five contained a single restriction fragment that hybridized to the probes. Two cosmids contained two fragments that hybridized to the same probe, V kappa 4, indicating that some V kappa 4 gene segments are linked. One cosmid had two genes that belonged to different families, V kappa 1 and V kappa 9. The two gene segments were located within 12 kb of each other and lay in the same transcriptional orientation. Linkage of gene segments from the V kappa 1 and V kappa 9 families is consistent with a genetic map of the locus, and provides physical evidence for the first time that two genes from different families are closely linked in the murine kappa locus. Sequence analysis revealed that both genes are pseudogenes: the V kappa psi 1.7 gene segment has eight mutations, including termination codons, insertions, and deletions, and the V kappa psi 9B.8 gene segment has two mutations of an insertion and altered RNA splice site. Both genes have the potential to rearrange based on the sequence of their heptamer-nonamer motifs. The identification of pseudogenes raises the question of how many nonfunctional genes are present in the murine germline repertoire.

Amino Acid Sequence↗

PubMed1994

A bifunctional murine::human chimeric antibody with one antigen-binding arm replaced by bacterial beta-lactamase.

We here report the genetic engineering of a murine::human chimeric antibody--directed against the tumor marker human placental alkaline phosphatase--in which one antigen-binding arm (Fab) has been replaced by Escherichia coli beta-lactamase (Bla). A mutated Bla gene in which the termination codon had been replaced by GAG, was fused in-phase to the cDNA sequence encoding the hinge region, CH2 and CH3 of the human IgG3 heavy chain. The resulting BlaHG3f fusion gene was placed under control of the Simian Virus 40 late promoter, and transiently expressed in COS-1 cells together with the genes encoding the murine light and murine::human chimeric heavy chains. Approximately 200 ng/ml of correctly assembled bifunctional antibody-Bla immunoconjugates were detected in the culture supernatant. This observation indicates that Bla (with its own leader peptide) can efficiently direct secretion into the culture medium of adventitious sequences fused at its C-terminus. Furthermore, the assembly in the Fc region was not affected by steric hindrance due to a Bla moiety and an Fab arm in close proximity. The antibody-Bla immunoconjugate could be of therapeutic value for the activation of cephalosporin-based anti-cancer prodrugs at the tumor site. Moreover, the expression strategy adopted here is particularly suitable for a quick and convenient analysis of newly designed gene products in which the Bla moiety has been replaced by other enzymes or by antigen-binding fragments in order to engineer bispecific antibodies.

Alkaline Phosphatase↗

PubMed1985

Molecular characterization of a mutant hybridoma secreting truncated IgM.

We have identified the mutation in an IgM hybridoma mutant line which produces truncated mu protein. DNA sequencing has revealed that two base pairs are deleted in the Cmu3 domain, resulting in an early termination of protein synthesis by forming an in-frame termination codon (UGA). The mutant mu chain is incorporated into monomeric IgM which is secreted efficiently.

Base Sequence↗

PubMed1993

Direct cloning and expression of PCR amplified DNA and RNA sequences: application to the hepadnaviruses nucleocapsid proteins.

Gene amplification may benefit from the construction of primers that augments the speed at which cloning and protein expression proceeds. Such primers include EcoRI or HindIII linkers as well as an in phase initiation or termination codon. PCR was carried out directly from viral particles of human hepatitis B virus (HBV) and woodchuck hepatitis virus (WHV) without DNA purification and from RNA extracted from WHV infected liver. Amplified products were directly cloned in the pKK223-3 expression vector under the control of the tac promoter. The characterization of the recombinant clones expressing the nucleocapsid protein (C protein) was done by direct incubation of the filter with 125I-labelled anti-HBc and confirmed by radioimmunoassay and Western-blot analysis. This procedure allows easy selection of recombinant clones expressing a given protein and could be applied to many other genes.

Animals↗

PubMed1989

A tandem pair of Leishmania donovani cation transporting ATPase genes encode isoforms that are differentially expressed.

The second gene (ATPase 1b) of a tandem pair of cation transporting ATPases from Leishmania donovani was cloned and sequenced. The sequence of this gene was very similar to its upstream neighbor (ATPase 1a). Both genes contained a 2922 base open reading frame capable of encoding a protein of 974 amino acids. The genes differed at 34 nucleotide base positions, predicting 20 amino acid differences between the two peptides. These changes were clustered at the carboxy terminus with 15 changes occurring in the COOH-terminal 37 amino acids. However, these changes did not alter the highly charged nature of the carboxy terminus observed in ATPase 1a. The sequence was also conserved for 73 bases upstream of ATPase 1a and 1b but downstream conservation was limited to 15 bases beyond the termination codon. RNA from ATPase 1a was 5.2 kb and was present in both developmental forms of Leishmania. By contrast the ATPase 1b gene expressed a 5.75 kb transcript which was much more abundant in the amastigote form of Leishmania than in the promastigote form.

Adenosine Triphosphatases↗

PubMed1991

Carboxy-terminal sequence conservation among variant-specific surface proteins of Giardia lamblia.

Antigenic variation in the parasitic protozoan Giardia lamblia was studied by characterizing the expression and genomic organization of a variant-specific surface protein (VSP) gene. Transcripts from this gene, vsp1267, were abundant in the cloned variant WB/1267, but undetectable in the parental clone from which WB/1267 was derived or in variant progeny of WB/1267. Two identical copies of vsp1267 exist in the WB/1267 genome, separated by 3 kb and arranged as convergent transcription units. Primer extension sequencing and S1 nuclease protection analysis suggested that the 5' untranslated region (UTR) of VSP1267 mRNA consists of a single nucleotide (nt). Primer extension sequencing mapped the site of VSP1267 transcript polyadenylation 25 nt beyond the termination codon. vsp1267 contained no introns and predicted a cysteine-rich polypeptide with features common to other VSPs. Comparison of vsp1267 with another VSP gene sequence revealed striking conservation, both at the nucleotide and amino acid levels, and the 3' ends of the genes. An oligonucleotide derived from this region detected size-variant VSP transcripts in 4 of 5 G. lamblia clones analyzed, suggesting the general utility of this probe in studying VSP genes and their expression.

Amino Acid Sequence↗

PubMed1993

A Trypanosoma brucei gene family encoding protein kinases with catalytic domains structurally related to Nek1 and NIMA.

Using polymerase chain reaction technology we cloned a Trypanosoma brucei gene fragment that has a deduced amino acid sequence with a high degree of homology to protein kinase catalytic domains. This clone detects two genes by genomic Southern analysis. These genes, nrkA and nrkB, share a 97% nt sequence homology over their 1.3-kb coding regions. NrkA encodes a 48-kDa protein which possess all 11 protein kinase homology regions. The 279-aa N-terminal catalytic domain has highest homology with Nek1, a bifunctional kinase, and NIMA, a protein serine/threonine kinase. Both alleles at the nrkB locus in T. brucei strain IsTAR 1 encode a truncated protein kinase catalytic domain due the presence of a premature termination codon. However, the TREU667 strain is heterozygous at the nrkB locus, encoding one truncated and one full-length molecule. NrkA and NrkB possess multiple phosphorylation site motifs. Both nrk transcripts are constitutively expressed during parasite development.

Alleles↗

PubMed1996

Targeted disruption of expression site-associated gene-1 in bloodstream-form Trypanosoma brucei.

Each variant surface glycoprotein (Vsg) expression site (ES) in bloodstream-form Trypanosoma brucei is a polycistronic transcription unit containing several distinct expression site-associated genes (esag), in addition to a single vsg gene. esag1 genes from different ESs encode a highly polymorphic family of membrane-associated glycoproteins, whose function is unknown. In the hope of producing a phenotype that could indicate a function, we disrupted the esag1 genes in two ESs by targeted insertion of a hygromycin phosphotransferase gene. Our failure to produce an obvious phenotype prompted us to search for other esag1 transcripts. RNA from the mutant trypanosomes hybridized with an esag1-specific oligonucleotide. Cloning and sequencing of mRNA from both mutant and wild-type cells showed that several esag1 family members were expressed, each at a much lower level than the esag1 transcript from the active ES in wild-type trypanosomes. Long-range DNA mapping showed that these additional esag1 genes, some of which contained premature translation-termination codons, most probably originate from chromosomal-internal genes and pseudogenes. We have therefore been unable to determine whether esag1 is an essential gene, or what function it fulfils, or whether any competent Esag1 protein is expressed in the mutant trypanosomes.

Amino Acid Sequence↗

PubMed1983

The origin of multiple polypeptides of molecular weight below 110 000 encoded by tobacco mosaic virus RNA in the messenger-dependent rabbit reticulocyte lysate.

Multiple polypeptides encoded by tobacco mosaic virus (TMV) RNA in the messenger-dependent rabbit reticulocyte lysate are not attributable to contaminating 3'-coterminal RNA fragments, multiple leaky termination codons or endonuclease activity opening-up legitimate or spurious internal initiation sites. Quantitative analysis of polypeptides encoded over a range of added RNA concentrations from 0.09 microgram X ml-1 to 180 micrograms X ml-1 compared with those synthesized in response to size-fractionated RNAs from a crude virus preparation, or with RNA extracted from the alkali-stable fraction of TMV suggest that apart from four legitimate virus-coded products of apparent Mr approx. 165 000, 110 000, 30 000 and 17 500 all other polypeptides arise from the overlapping 5'-proximal cistrons either by (i) site-selective endonucleolytic cleavage, (ii) sense codon misreading, or (iii) specific regions of secondary structure on TMV RNA which impede ribosome translocation.

Animals↗

PubMed1986

Immunological identification of rat tissue kallikrein cDNA and characterization of the kallikrein gene family.

A tissue kallikrein cDNA was identified by direct immunological screening with affinity-purified anti-rat tissue kallikrein antibody from a rat submandibular cDNA library constructed with the expression vector pUC8. Sequence analysis of the kallikrein cDNA revealed an encoded protein 97% homologous to the partial amino acid sequence of rat submandibular kallikrein. This cDNA was used to hybrid-select kallikrein-specific RNA from submandibular gland. Translation of the hybrid-selected RNA in a cell-free assay system resulted in the production of a 37 kDa peptide representing the preproenzyme. In addition, hybrid-selection of RNA under less stringent conditions showed cross-hybridization with other submandibular gland mRNA species. In correlation with these results, analysis of rat genomic DNA showed extensive hybridization, suggesting a family of closely related kallikrein-like genes. Consequently, a Charon 4A rat genomic library was screened for kallikrein genes by hybridization with rat tissue kallikrein cDNA. Thirty-four clones were isolated and found to be highly homologous by hybridization and restriction enzymes analyses. Fourteen unique clones were identified by restriction enzyme site polymorphisms within DNA segments which hybridized to the kallikrein cDNA probe and it was estimated that at least 17 different kallikrein-like genes are present in the rat. Sequence and structural analysis of one of the genomic clones revealed a gene structure similar to that of other serine proteinases. Comparison of the partially sequenced exon regions of the gene with the sequence of rat tissue kallikrein cDNA reveals 89% identity when aligned for the greatest homology. However, the genomic sequence predicts termination codons in all three translational reading frames, implying that this gene is nonfunctional, i.e., a pseudogene. Comparison of the rat genomic sequence to a kallikrein-like gene from the mouse reveals extensive preservation of exons, less identity within introns and no significant homology between extragenic regions.

Animals↗

PubMed1986

A novel suppressor tRNA from the dimorphic fungus Candida albicans.

Unfractionated tRNAs from a number of prokaryotes and eukaryotes were examined for their ability to promote termination codon readthrough in a cell-free system isolated from Saccharomyces cerevisiae. tRNA from the dimorphic fungus Candida albicans was found to have significant UGA and UAG readthrough activity and this activity was present in tRNA extracted from both the yeast and the hyphal phase of the fungus. Unusually the efficiency of readthrough activity in vitro was not affected by the [psi] determinant. C. albicans tRNA was fractionated by one-dimensional and two-dimensional gel electrophoresis and both readthrough activities appeared to be associated with a single species of tRNA.

Candida albicans↗

PubMed1990

cis-acting sequences involved in the translational control of GCN4 expression.

Four short upstream open reading frames (uORFs) in the mRNA leader are required for the translational control of GCN4 expression in response to amino acid availability. Data are reviewed demonstrating that the fourth (3' proximal) uORF is sufficient to establish the repressed levels of GCN4 expression, while the first uORF functions as a positive regulatory element under starvation conditions to stimulate GCN4 translation. Furthermore, positive and negative trans-acting regulatory factors, the activities of which appear to be modulated according to amino acid availability, exert their effects on GCN4 expression through the uORFs. Direct comparison of the uORFs indicates that there are important nucleotide sequence differences between uORF1 and 4, and that these are located primarily around the termination codons of these elements. Recent findings suggest that the sequences that mediate repression of GCN4 expression are complex, but can be overcome under starvation conditions by ribosomes that have previously translated uORF1.

Alleles↗

PubMed1991

Molecular cloning of porcine alpha 1-microglobulin/HI-30 reveals developmental and tissue-specific expression of two variant messenger ribonucleic acids.

A 1008 basepair (bp) cDNA clone encoding 335 amino acids followed by an inframe TGA translation termination codon and a 295-nucleotide 3' untranslated (UT) region has been isolated from a pig liver cDNA library. Based on the deduced amino acid and nucleotide sequence homology to a human cDNA (Kaumeyer, J.F., Polazzi, J.O. and Kotick, M.P. (1986) Nucleic Acids Res. 14, 7839-7850), the 5' amino terminus was found to code for alpha 1-microglobulin (alpha 1-M), a 183 amino acid protein belonging to the lipocalin protein superfamily (Pervaiz, S. and Brew, K. (1985) Science 228, 335-337). The 3' half encoded HI-30 which constitutes the Kunitz-type proteinase inhibitory (L-chain) domain of porcine inter-alpha-trypsin inhibitor (I alpha TI). In Northern blot hybridization, this cDNA identified two equally abundant mRNA species of approx. 1.3 kb and 1.6 kb in length. However, a 125 bp cDNA probe derived from the 3' UT region of the cDNA hybridized only to the 1.6 kb mRNA. The differences observed in the 3' UT region of these mRNAs suggest the utilization of alternative polyadenylation signals or presence of unprocessed nuclear RNA. Densitometric scanning of Northern blots indicated that alpha 1-M/HI-30 mRNA levels were higher (5-8-fold) in fetal and neonatal liver compared to that of primiparous pigs. In contrast, the RNA levels did not change significantly during pregnancy. Dot blot analysis of RNA indicated liver to be the major site of alpha 1-M/HI-30 mRNA expression with lower levels observed in the stomach. The results suggest that modulation of alpha 1-M/HI-30 gene expression could play a role during porcine growth. Increased I alpha TI L-chain mRNA levels may be particularly important in fetal and neonatal development when regulation of the inflammatory response and protection of macromolecules from proteolytic degradation is vital to survival and sustained growth.

Alpha-Globulins↗

PubMed1994

Mosquito ribosomal protein rpL31 resembles rat rpL34: cDNA and deduced amino acid sequence.

An Aedes albopictus ribosomal protein rpL31 cDNA was sequenced, and found to encode a protein with homology to rat rpL34. The 544 bp mosquito cDNA contained an ATG start site, three in-frame termination codons, and an AATAAA polyadenylation signal. Mosquito rpL31 had a mass of 15,137 Da, a pI of 12.39 and contained 14.5% Arg and 14.5% Lys. PCR analyses with genomic DNA suggested the presence of a large intron near the 5'-end of the gene.

Aedes↗

PubMed1986

The endogenous mouse mammary tumour virus locus Mtv-8 contains a defective envelope gene.

The Mtv-8 associated provirus, GR40, is not expressed in vivo. However, upon transfection into rat XC cells, the two MMTV specific mRNAs of 35S and 24S are transcribed. Further, the level of these transcripts is augmented when the transfected cells are grown in the presence of dexamethasone (Ponta et al., 1983). No virus can be detected in the medium of the transfected cells. Intracellular protein analysis of these transfected cells shows that although apparently authentic gag proteins are synthesized, a novel protein of 68 kDa is the only env related protein detectable. The sequence of the env gene of GR40 was determined and the predicted amino acid sequence of the env protein obtained. A premature termination codon is present 68 amino acids before the COOH-terminus of the known MMTV env precursor Pr73env. This would result in an env protein of about 68 kDa, in agreement with the size of the env protein found in GR40 transfected cells. The lack of the carboxy terminus may be responsible for the non-processing of the aberrant env precursor protein, p68.

Amino Acid Sequence↗