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Biomedical subjects

J E Ikeda

Publications and source records attributed to J E Ikeda.

14 recordsLinked to original sources
PubMed1992

Cauliflower mosaic virus reverse transcriptase. Activation by proteolytic processing and functional alteration by terminal deletion.

We have previously expressed the cauliflower mosaic virus (CaMV) reverse transcriptase (RTase) gene, the ORFV gene, in yeast in an active form (RTase-Y). An activity gel analysis revealed that the molecular size of RTase-Y as well as an RTase associated with the CaMV particles (RTase-V) is 60 kDa. This size is about 18 kDa smaller than that of the inactive form previously expressed in Escherichia coli (RTase-E) (78 kDa), which corresponds to the coding capacity estimated for the ORFV gene. To investigate the possible involvement of proteolytic processing in the de novo synthesis of CaMV RTase, we constructed a series of deletions from either terminus or both termini of the ORFV coding sequence and expressed them in E. coli. Among the various truncated RTases, those (denoted delta N) that lack N-terminal peptide fragments 143-185 amino acids long were active on the synthetic RNA template-primer, poly(rC)-oligo(dG). Those RTases (denoted delta C) lacking C-terminal peptide fragments 50-102 amino acids long and those lacking both termini (denoted delta NC) were also active on this template. However, only the delta N RTases showed enzyme properties indistinguishable from the RTase-Y in that they transcribed natural RNA into DNA and required either Mg2+ or Mn2+ for their activity. The length of the deletion corresponded approximately to the difference of the molecular weights between RTase-Y and RTase-E. These results suggest that CaMV RTase is translated in an inactive precursor form and then converted to an active form by proteolytic processing during de novo synthesis. We have also demonstrated that C-terminal deletions cause a loss of activity on a natural RNA template accompanied by an alteration in metal ion requirement. The inability to incorporate dTTP accounts for the loss of activity on the natural RNA template. However, the affinities for dTTP and the corresponding template, poly(rA)-oligo(dT), were found to be unaltered.

Binding Sites↗
PubMed1991

Laser microdissection and single unique primer PCR allow generation of regional chromosome DNA clones from a single human chromosome.

We have developed an argon laser chromosome microdissection technique in conjunction with a polymerase chain reaction (PCR) approach to directly amplify microdissected chromosomes. The single 22-mer primer used in PCR, although unique in sequence (5'-TAGATCTGA-TATCTGAATTCCC-3'), randomly primed and amplified any target DNA. These methods were applied to the distal half of the short arm of human chromosome 4 containing the Huntington disease (HD) locus. Forty-four percent of representative clones from this library identify single-copy DNA sequences. This calculation suggests that the resulting chromosome-specific DNA library contains approximately 600 nonoverlapping sequences with an average size 350 bp at an average spacing of 30 kbp along chromosome 4. This microdissection and PCR cloning procedure is a simple and general approach for constructing a chromosome region-specific DNA library from a single metaphase spread.

Base Sequence↗
PubMed1991

Laser microdissection of the fragile X region: identification of cosmid clones and of conserved sequences in this region.

Laser microdissection has been used to dissect material from the X-chromosome region involved in fragile-X-linked mental retardation. After dissection, single chromosome slices corresponding to this fragile site were subjected to DNA amplification using either a vector ligation method (to provide known anchor sequences) or primer oligonucleotides corresponding to the ubiquitous Alu sequences. Amplified material was then cloned or, alternately, used to screen a gridded cosmid library. Eight cosmid clones identified in this way were regionally mapped using a panel of hybrid cell lines and shown to originate from a narrow interval centered on the fragile X site. Two clones are included in the approximately 6-cM interval defined by probes RNI (DXS369, 5 cM proximal) and VK21 (DXS 296, 1-2 cM distal) and which includes the fragile site, and at least one clone contains sequences conserved across species suggestive of a gene. This method combines the focused approach of microdissection and the convenience of obtaining cosmid (rather than small-insert) clones; it may be useful for studies of other defined chromosomal regions.

Animals↗
PubMed1990

Studies on DNA markers (D4S10 and D4S43/S127) genetically linked to Huntington's disease in Japanese families.

This is the first full report on the genetic linkage between Japanese Huntington's disease and the DNA markers D4S10 and D4S43/S127. With use of the HindIII, BglI, and EcoRI polymorphisms detected at D4S10, and the combination of all these polymorphisms to give composite haplotypes, nine Japanese Huntington's disease families were found to be informative. Three recombinants for D4S10 were detected in these families, giving a maximum lod score of 1.662 at a theta of 0.10. Similarly, when we used the MspI and PvuII polymorphisms detected by D4S43/S127, five families gave informative results. No recombinant was detected in these families, giving a maximum lod score of 3.348 at a theta of 0.00. These results clearly support the view that the Japanese Huntington's disease gene may be identical with the Western gene, in spite of the lower prevalence rate in Japan.

Adolescent↗
PubMed1990

Linear plasmid DNAs of the plant pathogenic fungus Rhizoctonia solani with unique terminal structures.

Three linear DNA plasmids were found in isolate RI-64 of anastomosis group 4 (AG-4) of Rhizoctonia solani. These plasmids, designated pRS64-1, -2, and -3, possessed the same size of 2.7 kb. Restriction mapping and Southern hybridization analysis of pRS64-1, -2, and -3 revealed the presence of homologous regions at both termini. The plasmid DNAs were resistant to both 3'-exonuclease and 5'-exonuclease even after treatment with proteinase K or alkali. The length of both terminal fragments that were generated by restriction endonuclease digestion was doubled under the denaturation condition, indicating that the linear plasmid DNAs have hairpin loops at both termini. Southern blotting analysis of total DNA showed the presence of two types of dimeric forms of pRS64 DNA. One is a head-to-head dimer and the other is a tail-to-tail dimer. The role of these unique DNA structures in replication of the plasmids is discussed.

Base Sequence↗
PubMed1990

Exclusion mapping of the hereditary dentatorubropallidoluysian atrophy gene from the Huntington's disease locus.

Hereditary dentatorubropallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder. Clinical and genetic findings in hereditary DRPLA are very similar to those of Huntington's disease (HD). However, it can be differentiated from HD by the pathological findings of dentatorubral and pallidoluysian atrophies and by a lack of prominent atrophy of the striatum at necropsy. The hereditary DRPLA gene has not been localised and the possibility that the two disease loci are allelic has been suggested. We have searched for linkage between the locus for hereditary DRPLA and D4S10 using the G8 probe, which is a genetic marker linked to HD. In four families, there were negative scores at all recombination fractions and the lod score was -2.215 at recombination fraction theta = 0.15. These data indicate that the locus for hereditary DRPLA is not closely linked to D4S10 and that hereditary DRPLA is a distinct disease from HD.

Blotting, Southern↗
PubMed1979

Role of polymeric forms of the bacteriophage phi X174 coded gene A protein in phi XRFI DNA cleavage.

Gene A of the phi X174 genome codes for two proteins, A and A* (Linney, E.A., and Hayashi, M.N. (1973) Nature New Biol. 245, 6-8) of molecular weights 60,000 and 35,000, respectively. The phi X A* protein is formed from a natural internal initiator site within the A gene cistron while the phi X A protein is the product of the entire A gene. These two proteins have been purified to homogeneity as judged by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Previous studies have shown that the phi X A protein is an endonuclease which specifically introduces a discontinuity in the A cistron of the viral strand of supertwisted phi XRFI DNA. In addition to this activity, the phi X A protein also causes relaxation of supertwisted phi XRFI DNA and formation of a phi XRFH DNA . phi X A protein complex which has a discontinuity in the A cistron of the viral strand. This isolatable complex supports DNA synthesis when supplemented with extracts of uninfected Escherichia coli which lack phi X A protein and phi XRFI DNA. The phi XRFII DNA . phi X A protein complex can be attacked by exonuclease III but is not susceptible to attack by E. coli DNA polymerase I, indicating that the 5'-end of the complex is blocked. Attempts to seal the RFII structure generated from the phi XRFII DNA . phi X A protein complex with T4 DNA ligase in the presence or absence of DNA polymerase were unsuccessful. The phi X A protein does not act catalytically in the cleavage of phi XRFI DNA. Under conditions leading to the quantitative cleavage of phi XRFI DNA, the molar ratio of phi XRFI DNA to added phi X A protein was approximately 1:10. At this molar ratio, cross-linking experiments with dimethyl suberimidate yielded 10 distinct protein bands which were multiples of the monomeric phi X A protein. In the absence of DNA or in the presence of inactive DNA (phi XRFII DNA) no distinct protein bands above a trimer were detected. We found it possible in vitro to form a phi XRFII DNA . phi X A protein complex with wild-type phi XRFI DNA (phi X A gene+) and with phi XRFI DNA isolated from E. coli (su+) infected with phage phi X H90 (an am mutant in the phi X A gene). Thus, in vitro, in contrast to in vivo studies, phi X A protein is not a cis acting protein. The purified phi X A* protein does not substitute for the phi X A protein in in vitro replication of phi XRFI DNA nor does it interfere with the action of the phi X A protein which binds only to supertwisted phi XRFI DNA. In contrast, the phi X A* protein binds to all duplex DNA preparations tested. This property prevents nucleases of E. coli from hydrolyzing duplex DNAs to small molecular weight products.

Bacteriophage phi X 174↗
PubMed1979

The effect of aphidicolin on adenovirus DNA synthesis.

Aphidicolin inhibits adenovirus DNA replication in HeLa cells and in a cell-free, infected, nuclear extract in which viral DNA is elongated. The compound inhibits alpha DNA polymerase, extensively purified from HeLa cells, but has little or no effect on the beta or gamma DNA polymerases similarly purified. Aphidicolin does not affect thymidine uptake by cells nor does synthesis as it also inhibits DNA replication in uninfected cells. The inhibition by aphidicolin is reversible if the drug is removed within 18 hrs after addition to HeLa or Chinese Hamster Ovary cells but the cells are irreversibly affected if the drug remains for 48 hours.

Adenoviruses, Human↗
PubMed1977

Selective inhibition of phiX RFII compared with fd RFII DNA synthesis in vitro. II. Resolution of discrimination reaction into multiple steps.

In the presence of RNA polymerase, RNase H, discriminatory factors alpha and beta, Escherichia coli binding protein, DNA elongation factor I, DNA elongation factor II preparation, DNA polymerase III, and ATP, UTP, GTP, CTP, dATP, dTTP, dGTP, and dCTP, fd viral DNA can be quantitatively converted to RFII containing a unique gap in the linear minus strand. This gap, mapped with the aid of restriction endonucleases HinII and HpaII, is located within Fragment Hpa-H of the fd genome. The discrimination reaction has been resolved into two steps: Step A, fd viral DNA, E. coli binding protein, and discriminatory factors alpha and beta form a protein DNA complex; Step B, the complex isolated by agarose gel filtration selectively forms fd RFII when supplemented with RNase H, RNA polymerase, and the DNA elongation proteins. The omission of any of the proteins described above during the first reaction resulted in either no discrimination or a decrease in discrimination when the missing protein was added during the second step. Results are presented which indicate that E. coli binding protein, discriminatory factors alpha and beta, and RNase H must be present during the time RNA synthesis occurs in order to selectively form RFII from fd DNA and not phiX RFII. The amount of fd and phiX174 RNA-DNA hybrid formed in vitro is directly related to the DNA synthesis observed. Thus, under discriminatory conditions, only fd viral DNA leads to fd RNA-DNA complexes and no phiX RNA-DNA hybrid is formed. Under nondiscriminatory conditions, both DNAs yield RNA-DNA hybrids and DNA synthesis. In the absence of discriminatory factor alpha, no RNA-DNA hybrid is formed with either DNA, and in turn, no DNA synthesis is detected with either DNA template.

Bacterial Proteins↗
PubMed1977

Role of DNA gyrase in phiX replicative-form replication in vitro.

Preparations containing DNA gyrase activity Gellert, M., Mizuchi, K., O'Dea, M.H. & Nash, H.A. (1976) Proc. Natl. Acad. Sci. USA 73, 3872-3876] have been extensively purified from Escherichia coli. Such fractions, in the presence of ATP and Mg2+, catalyze supertwisting of relaxed circular double-stranded DNA replicative forms of a number of DNAs that results in the formation of superhelical replicative forms. Relaxed phiX174 replicative form (phiX RFIV) is not attacked by the A protein endonuclease coded for by the phiX DNA genome. After exposure to preparations of DNA gyrase, the relaxed phiX174 replicative form is converted to phiX RFI which can then be attacked by the phiX gene A protein and participate in replication of duplex phiX DNA.

Adenosine Triphosphate↗
PubMed1976

Isolation and characterization of the protein coded by gene A of bacteriophage phiX174 DNA.

Replication of phiX174 circular replicative form (RFI) DNA by extracts of Escherichia coli infected with bacteriophage phiX174 (amber in gene A) requires the phiX174 gene A product. This requirement has been used as an assay for the isolation of this protein. The gene A product (purified 4000-fold) caused relaxation of superhelical phiX174 RFI and formation of discontinuities in the viral strand of phiX174 RFI uniquely situated in the A region of the genome, and yielded a complex after interacting with phiX174 RFI that is active in replication of phiX RFI.

Coliphages↗
PubMed1976

RNA polymerase in vegetative cells of Bacillus subtilis. I. Purification and properties of RNA polymerase L1 and L2.

Two forms of RNA polymerase [EC 2.7.7.6], RPase L1 and RPase L2, isolated from a highly synchronized vegetative culture of Bacillus subtilis Marburg strain are described. RPase L1 is the major component (identical and the vegetative RNA polymerase already reported) and RPase L2 is a minor, new component corresponding to 3--5% of the total activity. The enzymes differed in their requirements for divalent ions, though the differences depended on the template DNA employed. PRase L1 is able to transcribe phage M2 DNA in the presence of Mg2+ ions and both B. subtilis DNA and phage M2 DNA in the presence of Mn2+ ions. On the other hand, RPase L2 activity can be detected only in the presence of 3 mM Mn2+ ions with all the templates. It is of interest that the transcription of phage M2 DNA by both enzymes stringently requires KC1. It may be due to this ion dependence that RPase L2 has not been detected previously. RPase L2 consists of 1beta', 1beta gamma, 1sigma, and 2alpha subunits. The molecular weight of the beta gamma subunit (about 110,000) is close to the value reported for the beta subunit of RNA polymerase prepared from sporulating cells. However, RPase L2 as a whole molecule is different from the RNA polymerase of sporulating cells or spores in the following two respects: RPase L2 contains sigma subunit as a component essential for selective transcription, and it is resistant to 1 mug of rifampicin per ml. Elimination of the sigma subunit from RPase L2 greatly stimulates RNA synthesis by the enzyme. Conversely, the addition of sigma subunit to the core-enzyme is inhibitory.

Bacillus subtilis↗
PubMed1976

RNA polymerase in vegetative cells of Bacillus subtilis. II. New polypeptide factors, FI and FII, stimulating in vitro RNA synthesis directed by phage M2 DNA.

Two polypeptides named FI and FII were isolated from vegetative cells of Bacillus subtilis Marburg. The molecular weights of FI and FII were 15,000 and 30,000 daltons, respectively. They were able to stimulate the transcription of phage M2 DNA in the presence of Mg2+ ions by RPase L1 and RPase L2 [RNA polymerase; EC 2.7.7.6]. Although both core- and holo-RPase L2 hardly exhibited transcription activity under these conditions, the factors could stimulate both activities up to the level of RPase L1 activity. The stimulation was much less marked when B. subtilis DNA was used as a template. These stimulatory functions were found to lie not in the chain elongation but in the initiation step of transcription, following the preinitiation step. To obtain stimulation by the factors, preincubation with RNA polymerase was necessary. FI stimulated RPase L1 or RPase L2 only when preincubated in the stimultaneous presence of FII, forming a complex, RPase L1(or L2)-FI-FII. On the other hand, FII alone could stimulate transcription, forming a complex. RPase L1 (or L2)-FII. In these complexes, the ratio of FI, FII, and RPase L1(or L2) was 1 : 1: 1. Although the core-RPase L2 activity was inhibited by sigma subunits, it was not inhibited by was rather stimulated when the enzyme was present as a complex with FI and FII. Thus the complex, consisting of RPase L2 and the factors, resembled RPase L1 with respect to molecular weight, template specificity, the effect of sigma subunit, and sensitivity to rifampicin.

Bacillus subtilis↗