Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
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1. We have used restriction enzyme analysis of petite mtDNAs to construct a detailed physical map of the 21S region on the mtDNA of the Saccharomyces cerevisiae strain JS1-3D. The map covers a segment of about 20,000 bp, on which the recognition sites of the enzymes HapII, HindII, HindIII, Sa1I, XhoI and HhaI have been localized (22 sites in total). This map has been checked in various ways against the independently constructed overall physical map of the mtDNA of strain JS1-3D. In addition, we have constructed a physical map with a resolution of about 200 bp of a HapII fragment of 1850 bp long, which carries the loci omega, RIB-1 and probably RIB-2. 2. The 21S rRNA hybridizes with the five adjacent HindII + III fragments TD9, DT19, TD15, DT14 and TT1, which lie in that order on the physical map of the 21S region. Of these, the two non-adjacent fragments TD9 and DT14 show a much stronger hybridization with 21S rRNA than DT19, TD15, and TT1. 3. The fragment DD5 (= DT19 + TD15) and part of DT14 belong to a sequence of about 1000 bp, which is absent from Saccharomyces carlsbergensis mtDNA. Although DD5 and DT14 show (very weak, respectively stronger) hybridization with 21S rRNA, the 1000 bp insert probably does not code for the 21S rRNA: the 21S rRNA of S. carlsbergensis comigrates with the 21S rRNA of JS1-3D on polyacrylamide gels under denaturing conditions. 4. Fragment DT14 hybridizes with the HindII + III fragment TD9, which shows the strongest hybridization with 21S rRNA. The presence of these sequence homologies has hampered the precise mapping of the 21S rRNA cistron. Our results are compatible, however, with the hypothesis that the sequences, coding for 21S rRNA, are located on HindII + III fragments that are not adjacent on JS1-3D mtDNA, namely TD9, DT14 and TT1.
Mol Gen Genet 1979 Jan 11
PMID:Fine structure of the 21S ribosomal RNA region on yeast mitochondria DNA. I. Construction of the physical map and localization of the cistron for the 21S mitochondrial ribosomal RNA. 37 86

A detailed molecular dissection of the yeast mitochondrial genome can be made with restriction endonucleases that generate site-specific cuts in DNA. The ordering of restriction fragments provides the basis of the physical mapping of mitochondrial transcripts and antibiotic resistance (antR) loci, and is a means of analyzing the molecular organization of mtDNA of petite and mit- deletion mutants. We have previously mapped the sites in the mtDNA of yeast strain MH41-7B recognized by the endonucleases Eco RI, Hpa I, Hind III, Bam HI, Sal I, Pst I, and Hha I, providing a total of 41 cleavage sites. We have now mapped the sites recognized by the endonucleases Xba I, Hinc II, Bgl II, Pvu II, Xho I, and Sst I, which make 6, 13, 5, 6, 2, and 2 cuts, respectively. Fragment maps for each of these endonuclease sites were derived by analysis of the products of double-enzyme digests and by hybridization of 3H-cRNA probes transcribed from low-kinetic-complexity petite mtDNAs to restriction fragments generated by various combinations of enzymes.
Mol Gen Genet 1979 Feb 16
PMID:Physical mapping of the Xba I, Hinc II, Bgl II, Xho I, Sst I, and Pvu II restriction endonuclease cleavage fragments of mitochondrial DNA of S. cerevisiae. 37 13

The European water frog Rana esculenta (RL), a natural hybrid between R. ridibunda (RR) and R. lessonae (LL), reproduces by hybridogenesis: haploid gametes usually contain an intact chromosome set of R. ridibunda (R); the lessonae nuclear genome (L) is lost from the germ line. Hybridity is restored in the next generation, via fertilization by syntopic R. lessonae. Matings between two hybrids (RL x RL) usually give inviable R. ridibunda (RR) progeny. The adult R. ridibunda subpopulation of Trubeschloo, a gravel pit in northern Switzerland, consists only of females. Fragment patterns for mitochondrial DNA (mtDNA) of these R. ridibunda were identical with those of syntopic R. esculenta and of local populations of R. lessonae; they differed from the patterns in eastern European populations of R. lessonae and of R. ridibunda mtDNAs (3.7% and 9.3% estimated sequence divergence, respectively). In contrast, mtDNAs of two R. ridibunda from an introduced Swiss population with both sexes, although different (2.7% divergence) from each other, were typical R. ridibunda rather than R. lessonae mtDNAs. These data, together with unisexuality, demonstrate conclusively that the all-female R. ridibunda population at Trubeschloo originated from matings between two R. esculenta. The formation of independently reproducing R. ridibunda populations via such hybrid x hybrid matings is precluded because progeny of these matings are unisexual. Recombination in the regenerated fertile R. ridibunda females, followed by matings with R. lessonae, nevertheless provides a mechanism for meiotic reshuffling of genetic material in ridibunda haplotypes that is not typically available in hemiclonal lineages.
Mol Biol Evol 1992 Jul
PMID:Mitochondrial DNA reveals formation of nonhybrid frogs by natural matings between hemiclonal hybrids. 135 42

A gene (ndvB) in Rhizobium meliloti that is essential for nodule development in Medicago sativa (alfalfa), specifies synthesis of a large membrane protein. This protein appears to be an intermediate in beta-1,2-glucan synthesis by the microsymbiont. Southern hybridization analysis showed strong homology between an ndvB (chvB) probe and genomic DNA of R. fredii but not from Bradyrhizobium japonicum. A cosmid clone containing the putative ndvB locus was isolated from a Rhizobium fredii gene library. The cosmid clone which complemented R. meliloti ndvB mutants for synthesis of beta-1,2-glucans and effective nodulation of alfalfa was mapped and subcloned. Fragment-specific Tn5 mutagenesis followed by homologous recombination into the R. fredii genome indicated that the region was essential for beta-1,2-glucan synthesis and for formation of an effective symbiosis with Glycine max (soybean).
Mol Microbiol 1992 Aug
PMID:Isolation and characterization of an ndvB locus from Rhizobium fredii. 140 55

Variable-number-tandem-repeats (VNTRs) are highly polymorphic and provide informative genetic markers for distinguishing between individuals. We have used PCR amplification of VNTR locus pMCT118 to identify mislabelled specimens submitted for HIV PCR testing. The method is rapid, can be applied to large numbers of samples and eliminates the need for radioactive probes. DNA samples (10 ng) are amplified for 25 cycles using fluorescence-labelled oligonucleotide primers (blue dye). An aliquot of the PCR product is then combined with an internal lane size standard (labelled with a red dye), electrophoresed through a 2% agarose gel on an automated fluorescence DNA fragment analyser and the size and quantity of the fragments determined automatically relative to the internal standard. Fifteen alleles, ranging in size from 398 tp 709 bp were readily identified in a random sampling of DNA from 63 unrelated HIV-infected patients. Fragment size was reproducible and corresponded to alleles containing from 16 to 35 repeats of a 16 bp unit. VNTR genotyping will prove useful for resolving discordant results due to specimen mix-up and ensuring that the correct samples have been analyzed.
Mol Cell Probes 1992 Aug
PMID:Rapid DNA fingerprinting to control for specimen errors in HIV testing by the polymerase chain reaction. 152 2

Active diphtheria toxin consists of two disulphide-linked fragments, termed A and B. Fragment B, which contains an internal disulphide bridge, facilitates translocation of the enzymatically active fragment A to the cytosol of eukaryotic cells. In this process cation-selective channels are formed. An in vitro translated full-length mutant lacking the internal disulphide bridge (A-58**) was functionally indistinguishable from its disulphide-containing counterpart (A-58) with respect to trypsin sensitivity, receptor binding, A-fragment translocation, and channel formation. In contrast, the B fragment of A-58** (B-36**) was slightly less trypsin resistant than the S-S-containing B fragment, B-36, and was approximately 300-fold less efficient than B-36 in permeabilizing cells. When first dialysed and then reconstituted with A fragment, B fragment without disulphide bridge yielded a less-active toxin than did wild-type B fragment. We conclude that the disulphide bridge in fragment B is not necessary for toxicity, as earlier believed, and that channel formation may play a role in membrane translocation.
Mol Microbiol 1991 Mar
PMID:Elimination of the disulphide bridge in fragment B of diphtheria toxin: effect on membrane insertion, channel formation, and ATP binding. 164 74

In order to study the antigenic structure of histone H1(0) the purified protein from mouse liver was subjected to different chemical and enzymatic treatments (CNBr, acetic acid, trypsin, chymotrypsin). The resulting peptides were fractionated in SDS-containing or acid-urea polyacrylamide gels, transferred by electroblotting onto nitrocellulose paper and probed with specific rabbit anti-H1(0) antiserum. The C-terminal fragments 99-193 (obtained following acetic acid hydrolysis) and 107-193 (obtained by chymotrypsin digestion) also exhibited strong immunoreactivity. Fragment 1-30 (CNBr cleavage) contained antigenic determinants while the shorter fragments 1-22 and 1-28 (acetic acid hydrolysis) failed to show any detectable reactivity. It was concluded that, in contrast to histone H5 whose reactivity is mainly concentrated to the globular domain of the molecule, the antigenic determinants in histone H1(0) are more or less evenly distributed along the polypeptide chain with the possible exception of the short unstructured N-nose.
Mol Cell Biochem 1991 Oct 16
PMID:Antigenic structure of histone H1(0). 172 85

Exon 2 nucleotide sequence of the DRB1 gene encoding the HLA-DRw13b allele defined by DNA-RFLP (Restriction Fragment Length Polymorphism) typing, has been obtained by using five heterozygous individuals genomic DNA and a non isotopic automated "dideoxi" methodology. Its comparison with other known homologous DRB1 sequences suggests that two different mechanisms which generate HLA allele variability may have occurred in this particular exon 2: a gene conversion between DRw11 or DRw13 as acceptors and DR4-Dw15 or DRw8.1 as donors and in addition, a non-conservative point mutation at base 221. The relationship between this HLA sequence characteristics and certain diseases susceptibility is discussed.
Mol Immunol 1990 Mar
PMID:Exon 2 DNA sequence of the HLA-DRw13b allele obtained from genomes of five different individuals. 234 92

We previously showed the importance of the 3-deoxy-D-manno-2-octulosonic acid (KDO) residue in endotoxins (lipopolysaccharides, LPS) for the induction of the synthesis and release of interleukin-1 (IL-1) by human monocytes. We further investigated the effect of some structural variations within the KDO molecule on IL-1 production induced by LPS. Deamination of Bordetella pertussis LPS, followed by mild anhydrous acidic methanolysis released a hexasaccharide (fragment B'), which had a terminal methyl ketoside KDO residue with a methyl-esterified carboxyl group. This fragment was unable to induce IL-1 production by human monocytes. Fragment B' could be converted into an active hexasaccharide by de-esterification (fragment B-OMe), but not by reduction of the methyl ester group. The KDO residues in the LPS of some bacterial species have been shown to be phosphorylated and we observed that these LPS were weak IL-1 inducers. Phosphorylated KDO present in Vibrio cholerae and B. pertussis LPS respond poorly in the thiobarbiturate assay (specific for KDO). However, if these LPS were dephosphorylated with aqueous hydrofluoric acid (HF) their KDO response in this assay was increased 5.4- to 2.6-fold, respectively. In parallel, the HF-treated LPS were more potent IL-1 inducers than untreated endotoxins. These data confirm that the KDO residue(s) present in all endotoxins play(s) a major role in the signal(s) leading to IL-1 production by human monocytes, and show that IL-1 induction by LPS (1) requires a free carboxyl group in the KDO and (2) is correlated with the degree of substitution of the KDO.
Mol Immunol 1989 May
PMID:Interleukin-1 induction by lipopolysaccharides: structural requirements of the 3-deoxy-D-manno-2-octulosonic acid (KDO). 254 3

Nuclei of different cell lines contain protein factors interacting with octamer ATTTGCAT. Fragment k53 of kappa-gene promoter region was used as DNA-probe. The factors from lymphoid cells yield a DNA/protein complex with mobility B0. The proteins are referred to as HF-B0. The nonspecific ubiquitous factor present in many non-lymphoid cells (for instance, HeLa cells) interacts with the probe to produce a complex whose mobility is much lower. The protein NF-B0 was isolated from the nuclear extract of myeloma MOPC21 cells. It was purified by chromatography on ion exchangers, hydroxylapatite, heparin-Sepharose and affinity sorbent containing a synthetic octamer sequence. At all the steps of purification, protein fractions were chosen for their ability to interact selectively with the octamer yielding a complex with the mobility B0. As a result, NF-B0 protein (60 +/- 2)kDa was purified 6.10(4) times to the electrophoretically homogeneous state. Purified factor NF-B0 selectively interacts with the octamer.
Mol Biol (Mosk)
PMID:[Protein factors, interacting with the octamer sequence of immunoglobulin genes]. 277 Jul 40


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