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PubMed1988

Structural and functional analysis of mitochondrial plasmids in Claviceps purpurea.

Several strains of Claviceps purpurea, a phytopathogenic Ascomycete, contain mitochondrial (mt) plasmids in high molar excess relative to mtDNA. Comparative analysis of plasmids of four strains of different geographic origin revealed that all the plasmids are structurally related (size; linearity; restriction map; probably 5'-linked terminal protein; terminal inverted repeats, TIRs); two of them are even identical, indicating a possible mobility of these genetic entities. In strain K it was shown that plasmid titres are comparably high in axenic cultures and in parasitic structures (sclerotia). Detailed analysis of plasmid pClK1 proved the existence of a perfect TIR of 327 bp; the plasmid's structure and details of its nucleotide sequence indicate a replication modus comparable to that of adenoviruses. pClK1 is almost completely transcribed resulting in two major transcripts of 3.5 and 3.15 kb, respectively. In plasmid-free strains (cured by ethidium bromide treatment) these mRNAs are not detectable; nevertheless they show no significant difference in phenotype. As judged from their structural properties they could be derived from viral ancestors. In this context the plasmids' close relationship to mt plasmids of higher plants may be of special interest.

Adenoviridae↗
PubMed1989

Structural analysis of proviruses in additional hamster tumour cell lines transformed by provirus II rescued from XC cells and definition of a new cell line harbouring amplified proviruses.

Additional 18 Syrian hamster tumour cell lines induced independently with the virus rescued from XC cells (provirus type II) have been analysed by restriction mapping. Taking into account the already published results of an analysis of other six tumour cell lines, altogether 24 tumour cell lines were characterized. In 62.5% of these lines a complete proviral unit has been integrated; 20.8% of the lines harbour altered proviral structures where the 3' end of the gag gene and the entire pol gene had been deleted; 8.3% of the lines carry both such a deleted provirus and a complete provirus. Apart from the already published cryptic provirus found in H-19 cells, no such provirus has been found in another cell line. Therefore the appearance of the cryptic provirus represents an infrequent event (4.16%). Similarly, the significant amplification of proviruses accompanied with a rearrangement in the env gene was found only in one tumour cell line. H-42, in the genome of which five proviral units are accommodated. The probable arrangement of amplified proviruses and the mechanism of their genesis are discussed.

Animals↗
PubMed1990

Structural characterization of the human estrogen synthetase (aromatase) gene.

The estrogen synthetase (aromatase, cytochrome P-450AROM) gene has been isolated from human genomic libraries and characterized. The restriction map of 43 positive clones obtained indicated that this enzyme is present as a single copy gene. The aromatase gene is unexpectedly large compared with other forms of the cytochrome P-450 superfamily, spanning at least 70 kilobases. The gene consists of 10 exons and its 5'-untranslated region is divided into 2 exons by an intron of more than 35 kilobases long. This organization of the first exon in the aromatase gene is unique in the cytochrome P-450 superfamily. All the exon-intron junctional sequences conform to the canonical GT/AG rule. The sequences of a TATA box and a CAAT box are present 27 and 83 base pairs upstream from the transcriptional initiation site. Within 3 kilobases upstream from the initiation site, there are no typical consensus sequences of responsive elements for glucocorticoid and c-AMP, which regulate aromatase expression.

Aromatase↗
PubMed1989

Variable and constant regions in African swine fever virus DNA.

An analysis of the SalI restriction pattern of African swine fever virus DNA showed that the SalI recognition sites did not change after more than 100 virus passages in porcine macrophages. The virus strain BA71V, obtained from the virus isolate BA71 by adaptation to grow in VERO cells, differed from the nonadapted virus in two deletions with a length of 2.5 and 7 kb located close to the DNA ends. A restriction analysis of several virus clones obtained from a naturally infected pig revealed length heterogeneity in both variable regions. A comparison of SalI restriction maps from 23 African swine fever virus field isolates (8 African, 11 European, and 4 American) has shown that the virus genome consists of a central region with a constant length of about 125 kb and two variable regions located close to the DNA ends with a length of 38-47 kb for the left DNA end, and 13-16 kb for the right DNA end. The total length of ASF virus DNA varied between 178 (BA71) and 189 (MOZ64) kb. The 23 African swine fever virus isolates were classified into five groups, according to the arrangement of the SalI sites in the central region. Four groups contained only African isolates, whereas all the European and American isolates belonged to the same group. This distribution of isolates suggests that all non-African virus field isolates have a common origin.

Africa↗
PubMed1989

Construction and nucleotide sequence of a cDNA encoding the full-length preprotein for human branched chain acyltransferase.

A cDNA (1.6 kilobases) for branched chain acyltransferase (E2b) isolated from a human liver library encoded only the amino-terminal half of the protein (Hummel, K. B., Litwer, S., Bradford, A. P., Aitken, A., Danner, D. J., and Yeaman, S. J. (1988) J. Biol. Chem. 263, 6165-6168). Here we report the isolation of other cDNAs which encode the carboxyl-terminal half of E2b and the construction of a cDNA which encodes the entire pre-E2b. cDNA from the original clone encoding the leader sequence, lipoate binding domain, and E3 binding domain was ligated to the cDNA from a clone which by restriction maps contained an additional 3' sequence. Both cDNAs used in the construct made a fusion protein in their original phage isolate recognized by antibodies to E2b. The nucleotide sequence of the constructed cDNA was determined, and the 1431 base pairs in the open reading frame encoded a protein of 477 amino acids. In vitro transcription and translation of this cDNA produced a 57-kDa protein recognized by E2b-specific antibodies. Mouse liver mitochondria imported and processed the 57-kDa protein to a 52-kDa antigenic protein which co-migrated with E2b isolated from tissue. Comparing the protein structure of this human pre-E2b protein with that for other acyltransferase proteins showed a similarity in structure throughout all the proteins suggesting evolutionary conservation. Branched chain acyltransferase from Pseudomonas putida showed the most similarity to human E2b.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
PubMed1994

Putative "MDR enhancer" is located on human chromosome 20 and not linked to the MDR1 gene on chromosome 7.

The physiologic expression of the human multidrug resistance MDR1 gene product P-glycoprotein is controlled in a tissue- and cell-specific manner, but the regulatory mechanisms have not been characterized in great detail. Studies by Kohno et al. [(1990) J Biol Chem 265:19690-19696] suggested that a tissue-specific enhancer element located approximately 10 kb upstream from the major MDR1 transcription start site may act to increase the levels of transcription in cultured adrenal and kidney cells. Using this putative "MDR enhancer" as a probe, we isolated a 14 kb DNA fragment from a genomic DNA library prepared from human fetal liver. The restriction map and partial nucleotide sequence of this DNA fragment were consistent with the previously described data obtained for a similar piece of genomic DNA derived from human placenta by Kohno et al. (ibid.). Pulsed-field gel electrophoresis of large genomic DNA fragments, however, showed that the DNA sequences, including the putative "MDR enhancer," were not linked to the MDR1 gene. Fluorescence in situ hybridization analysis revealed that this enhancer-like element is located on chromosome 20 at band q13.1 and is, therefore, distinct from the MDR locus on chromosome 7, band q21.1. Thus, this putative regulatory element does not modulate the tissue specificity of expression of the MDR1 gene in vivo, but may play a role in the regulation of expression of another, so far unknown gene.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1989

The yes proto-oncogene is present in amphibians and contributes to the maternal RNA pool in the oocyte.

Low stringency screening of a cDNA library from the frog Xenopus laevis with a viral yes oncogene probe resulted in the isolation of clones with restriction maps which were distinct from previously identified X. laevis src cDNA clones. The polypeptide produced by in vitro translation of RNA synthesized from one of the clones was slightly larger in size than X. laevis pp60src, but gave protease cleavage patterns which were nearly identical to those yielded by pp60src. Determination of the DNA sequence of this clone revealed that it is derived from a X. laevis yes gene homologue. Transcripts from the yes gene were found in the ovary and consisted of a major 3.4 kb species and additional minor species. These findings indicate that the duplication event separating the src and yes genes occurred prior to the appearance of amphibians and that the yes gene product is likely to play an important role in oogenesis or early development.

Amino Acid Sequence↗
PubMed1989

Molecularly cloned simian immunodeficiency virus SIVagm3 is highly divergent from other SIVagm isolates and is biologically active in vitro and in vivo.

Simian immunodeficiency viruses have been isolated from African green monkeys originating from Ethiopia. A molecular clone, termed SIVagm3, was found to be highly divergent from SIVagmTYO-1 in terms of its restriction map and partial nucleotide sequence. A premature stop codon present in the transmembrane protein of SIVagm TYO-1 was absent in SIVagm3. SIVagm3 was biologically active in vitro and in vivo and displayed characteristics reminiscent of the wild-type virus. Biological activity was demonstrated by seroconversion of juvenile African green monkeys and Macaca nemestrina after inoculation. In contrast to antibody reactivity mainly directed against env proteins in naturally infected African green monkeys. African green monkeys and M. nemestrina infected with the cloned virus showed antibody reactivity directed against all major proteins as demonstrated by immunoblot analysis. The availability of a biologically fully competent molecular clone of SIVagm allows us now to address various pertinent questions in an animal model system which should help to understand features of human immunodeficiency virus infection in human beings.

Amino Acid Sequence↗
PubMed1996

Genomic organization of human MXI1, a putative tumor suppressor gene.

MXI1, a member of the MYC family of transcription factors, is thought to negatively regulate MYC function and may therefore be a potential tumor suppressor gene. Using detailed restriction mapping and partial DNA sequencing analysis, we have determined the genomic organization of the human MXI1 gene to facilitate a search for mutations that affect MXI1 function. The gene spans a region of approximately 60 kb on chromosome 10q24-q25 and comprises six exons. The correspondence of these exons to previously identified Mxi1 functional domains suggests that alternatively spliced transcripts may regulate Mxi1 functional activity. The presence of a cryptic ATG start codon in exon 2 suggests that a functional protein missing the SIN3-interacting domain (exon 1) may be generated by alternative splicing. Finally, we have identified two polymorphic regions within the MXI1 locus: a polymorphic CA repeat in the third intron and an AAAAC polymorphism in the noncoding region of exon 6. These findings will facilitate the analysis of tumors for the presence of inactivating mutations in MXI1 coding and regulatory sequences.

Alternative Splicing↗
PubMed1989

The Bacillus subtilis flagellin gene (hag) is transcribed by the sigma 28 form of RNA polymerase.

The Bacillus subtilis gene hag, which codes for the flagellin structural protein, was identified by DNA sequence analysis in a collection of DNA fragments bearing in vitro promoters for the sigma 28 form of RNA polymerase. The hag gene and adjacent regions of the B. subtilis chromosome were restriction mapped, and the nucleotide sequence was determined. The hag gene was transcribed at all stages of growth from a single promoter that had sequences in the promoter recognition region characteristic of the consensus sequence for the sigma 28 holoenzyme. Transcription of hag was eliminated by insertion mutations that blocked synthesis of the sigma 28 protein. These findings provide strong support for the previous proposal that the sigma 28 form of RNA polymerase controls transcription of a regulon specifying flagellar, chemotaxis, and motility functions in B. subtilis (J. D. Helmann and M. J. Chamberlin, Proc. Natl. Acad. Sci. USA 84:6422-6424, 1987). The steady-state levels of hag mRNA increased during exponential growth and peaked as the B. subtilis cells entered the stationary phase. The transcript levels then decreased to zero within 4 h after the onset of sporulation. Hence, sigma 28 RNA polymerase function is temporally regulated.

Amino Acid Sequence↗
PubMed1991

Breakpoint clustering in t(4;11)(q21;q23) acute leukemia.

Chromosome 11 band q23 is commonly involved in nonrandom chromosomal translocations in hematopoietic malignancies, especially in infant acute leukemias. By using pulsed-field gel electrophoresis (PFGE) with restriction endonuclease digests of DNA from both a leukemia cell line (RS4;11) bearing the t(4;11)(q21;q23) and from human/hamster hybrid cells, we have been able to construct a detailed restriction map of the chromosome 11q23 region and have localized the t(4;11) chromosome 11 breakpoint to a region located approximately 200 to 230 kb telomeric to the CD3 gamma region and approximately 580 kb centromeric to the PBGD gene. PFGE analyses of DNA from clinical leukemia specimens and cell lines indicated a tight clustering of breakpoints in all eight t(4;11) acute leukemias studied. These data strongly suggest that discrete genetic loci are interrupted on both chromosomes 4 and 11 in a manner likely to be critically involved in the pathogenesis of t(4;11) acute leukemias. To our knowledge, these results represent the first evidence of breakpoint clustering in t(4;11) acute leukemias. In contrast to t(4;11), other 11q23 abnormalities studied to date have frequently shown evidence for alternative breakpoint sites in 11q23.

Acute Disease↗
PubMed1990

Active hepatitis B virus replication in the presence of anti-HBe is associated with viral variants containing an inactive pre-C region.

Although rise of anti-HBe immunity in the course of hepatitis B virus (HBV) infection is generally followed by clearance of the infectious virions, ongoing chronic liver disease with circulating virions has been repeatedly observed in a significant number of anti-HBe patients, especially in Mediterranean countries. To investigate the possible role of HBV variants, we cloned HBV DNA from the serum of three such anti-HBe cases. Comparative restriction mapping of HBV clones suggested circulation of different HBV genomes in the three cases. DNA sequencing revealed an inactive pre-C region in all 11 HBV clones derived from the three cases, either as one or two point mutations in the 3' terminus generating an in-frame TAG stop codon, or a 1 nucleotide insertion in the 5' terminus resulting in frameshift mutation. Furthermore, for one clone the complete 3182 nucleotide sequence was determined and no significant mutation was found in the remainder of the genome. We conclude that chronic hepatitis cases positive for anti-HBe are associated with HBV variants containing an inactive pre-C region and hence cannot synthesize pre-C region-derived HBeAg. This finding may provide a molecular explanation for the continued viral replication despite presence of anti-HBe immunity.

Base Sequence↗
PubMed1996

Sequence and functional analysis of an upstream regulatory region of human HOXA7 gene.

The Hox genes have been known to be involved in pattern formation during vertebrate development through differential expression along the anteroposterior body axis. Human homologue of position-specific regulatory region of murine Hoxa-7 was cloned from human genomic library. The restriction map of the 18-kb insert was determined, of which a 3.9-kb region was sequenced. Homology plot between the murine and the corresponding human sequence showed high sequence conservation over 70% in several regions. The homologous region has been reduced to about 1.1 kb (HCR: human control region), which contained several putative factor binding sites. The function of HCR was analyzed in transgenic mice and turned out to be a position-specific regulatory element of human, setting the precise anterior boundary of expression in transgenic embryos; at day 12.5 post-coitum a distinct anterior limit of expression was noted at the level of C5 in neural tube and spinal ganglia in transgenic embryos. These results indicate that the regulatory sequences as well as the molecular mechanism for Hox gene expression are highly conserved among vertebrates.

Animals↗
PubMed1989

Isolation of an endoglucanase gene from Bacteroides ruminicola subsp. brevis.

A gene coding for endo-1, 4-beta-glucanase activity has been isolated from Bacteroides ruminicola subsp. brevis by cloning in Escherichia coli. After restriction mapping of a 6.4 kb insert, a 2.2 kb DNA fragment was sub-cloned in pUC19 to produce the enzymically active clone pJW3. Recloning of the gene fragment in the reverse orientation in pUC18 (clone pJW4) indicated that a gene promoter was present in the cloned fragment and was able to function in E. coli. The clone pJW4 displayed increased activity which was attributed to expression from the lac promoter of pUC18. The enzyme encoded by pJW4 was optimally active at pH 5.5-6.0, and in the temperature range 37-42 degrees C. The preferred substrate was carboxymethylcellulose, but the enzyme displayed 50-60% of maximal activity on both acid-swollen cellulose and soluble xylan. No significant activity was detected on ball-milled filter paper or particulate xylan. Deletion experiments confirmed that both cellulase and xylanase activities were altered to a similar extent by deletion of DNA from the 3' end of the gene, suggesting that both are a function of the same polypeptide product.

Bacteroides↗
PubMed1994

Polymorphism for ribosomal RNA gene arrangement in the mitochondrial genome of fall rye (Secale cereale L.).

A restriction-fragment-length polymorphism (RFLP) in mitochondrial DNA (mtDNA) was detected between varieties of fall rye (Secale cereale L.) by Southern hybridization with rrn18, the gene encoding the mitochondrial 18S ribosomal RNA. Restriction mapping showed that the RFLP is based on differing numbers of genomic contexts (one vs three) for a recombining-repeat element (the "18S/5S repeat"). From examination of other Secale species, we conclude that the one-context state arose relatively recently, putatively by deletion of two of an ancestral set of three distinct genomic loci containing the mitochondrial 18S/5S repeat. This is consistent with our earlier conclusion that the 18S/5S repeat has probably existed in at least two genomic copies throughout much of the history of the grass family (at least 40 million years). Interestingly, the intervarietal difference in the number of distinct rrn18 loci is not accompanied by a major difference in the number of rrn18 copies per unit mass of mtDNA. This suggests the existence of a mechanism that can compensate rather precisely for differences in mitochondrial gene dosage, perhaps by over-replication or stabilization of specific subgenomic molecules.

Base Sequence↗
PubMed1993

Molecular characterisation of beta-tubulin genes present in benzimidazole-resistant populations of Haemonchus contortus.

A beta-tubulin isotype 1 gene, gru-1, from a benzimidazole (BZ)-resistant population of the nematode parasite, Haemonchus contortus, was cloned and sequenced. The predicted gene organisation showed 10 exons and 9 introns, one of which was H. contortus specific. Using probes and restriction sites selected from this sequence, restriction maps were constructed from and around beta-tubulin genes of 3 BZ-susceptible and 7 BZ-resistant populations. There was a reduction in beta-tubulin isotype 1 genes to usually one, in BZ-resistant populations. So, our previously reported reduction of beta-tubulin probe-reactive RFLP fragments in resistant populations correlated with the reduction of beta-tubulin isotype 1 genes. The beta-tubulin isotype 1 gene present on the apparently selected fragment and was not always the same, and the geographical origin of the resistant populations indicated independent development rather than geographical spread of the resistant populations. The beta-tubulin genes on the apparently selected fragments were transcribed and processed to mRNA using the nematode-specific trans-spliced leader (SL1). Comparison of the derived amino acid sequence of gru-1, with known sequences from a susceptible population, identified 3 mutations that could be involved in BZ resistance.

Amino Acid Sequence↗
PubMed1993

The internal transcribed spacers of ribosomal DNA in five members of the Anopheles gambiae species complex.

The primary and secondary structure of the internal transcribed spacers of ribosomal DNA (ITS1 and ITS2) and their utility for phylogenetic analysis of closely related species were examined using the Anopheles gambiae complex as a model. Restriction mapping revealed an unusual architectural feature in the ITS1 of several members of an An. gambiae cryptic species complex. Multiple spacer lengths are prevalent in An. merus and An. melas and are due to variable numbers of a repeated 250 bp sequence. Secondary structure analysis indicated that the repeat forms a helix and loop that may be involved in rDNA processing. Intra- and interspecific polymorphism within the species complex were further examined by DNA sequencing of forty-eight ITS2 clones obtained by polymerase chain reaction from individuals of the five species. Interspecies variation in the approximately 426 bp ITS2 sequence ranged between 0.4% and 1.6%; intraspecies variation ranged from 0.07% in An. arabiensis to 0.43% in An. gambiae. Intraindividual variation ranged from 0% in four individuals to a high of 0.4% in one An. quadriannulatus specimen. None of the variants were shared between species. The low level of variation supports the hypothesis that species of the complex evolved recently.

Animals↗
PubMed1995

The black fly Simulium vittatum trypsin gene: characterization of the 5'-upstream region and induction by the blood meal.

The events leading to blood digestion in hematophagous insects are not well understood at the molecular level. Here we report on the characterization of a trypsin gene from the black fly Simulium vittatum. Southern blot analysis indicated that the S. vittatum genome contains at least two trypsin genes. Primer extension experiments identified two closely spaced transcription initiation sites, 3 bp apart. A genomic clone containing the trypsin gene was restriction mapped and the nucleotide sequence of the 5'-upstream region was determined. Several sequence elements were identified, including a consensus TATA box 35 nucleotides upstream from the transcription initiation site, a consensus arthropod initiator site at position -7, and two conserved sequence elements, 5'GGATTAA (position -77) and 5'TGTTTCCT (position -148). The latter two elements are present at comparable distances from the transcription initiation sites in black fly and mosquito trypsin genes. Significant amounts of trypsin mRNA were detected in guts of sugar-fed flies. Upon blood feeding, trypsin mRNA levels gradually increased to reach twice the initial abundance at 8 hr after blood ingestion. In contrast to other hematophagous insects, the induced mRNA level persists for a prolonged period of time (at least 48 hr) after blood ingestion. The results of this study provide information that may be useful for the expression of transgenes in insects of medical importance.

Animals↗