Biomedical subjects

H Shinagawa

Publications and source records attributed to H Shinagawa.

At least 73 records · Page 4Linked to original sources

PubMed1996

Analysis of substrate specificity of the RuvC holliday junction resolvase with synthetic Holliday junctions.

The Escherichia coli RuvC protein endonucleolytically resolves Holliday junctions, which are formed as intermediates during genetic recombination and recombination repair. Previous studies using model Holliday junctions suggested that a certain size of central core of homology and a specific sequence in the junction were required for efficient cleavage by RuvC, although not for binding. To determine the minimum length of sequence homology required for RuvC cleavage, we made a series of synthetic Holliday junctions with various lengths of homologous sequence in the core region. It was demonstrated that a monomobile junction possessing only 2 base pairs of the homology core was efficiently cleaved by RuvC. To study the sequence specificity for cleavage, we made 16 bimobile junctions, which differed only in the homologous core sequence. Among them, 6 junctions were efficiently cleaved. Cleavage occurred by introduction of nicks symmetrically at the 3'-side of thymine in all cases. However, the nucleotide bases at the 3'-side of the thymines were not always identical between the two strands nicked. These results suggest that RuvC recognizes mainly topological symmetry of the Holliday junction but not the sequence symmetry per se, that the thymine residue at the cleavage site plays an important role for RuvC-mediated resolution, and that a long homologous core sequence is not essential for cleavage.

Bacterial Proteins↗

PubMed1996

DNA binding of PhoB and its interaction with RNA polymerase.

We have identified the DNA-binding domain (DBD) of an Escherichia coli activator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the sigma 70 subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the pstS promoter. The pstS promoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed.

Amino Acid Sequence↗

PubMed1996

Whole saliva dried on filter paper or diagnosis of HIV-1 infection by detection of antibody IgG to HIV-1 with ultrasensitive enzyme immunoassay using recombinant reverse transcriptase as antigen.

Whole saliva samples collected from HIV-1 seropositive subjects by simple spitting without using any devices were dried on filter paper strips, from which filter paper discs of 3-mm diameter were punched out. The eluates of the discs were subjected to the immune complex transfer enzyme immunoassay for antibody IgG to HIV-1 using recombinant reverse transcriptase of HIV-1 as antigen and a two-site enzyme immunoassay for whole IgG. The signals for antibody IgG to HIV-1 and the amounts of whole IgG obtained with one disc per assay tube were 126-290% of those obtained with 1 microliter of whole saliva samples, provided that filter paper strips were treated with nonspecific rabbit serum prior to drying whole saliva samples and that filter paper discs were tested within a few days after drying whole saliva samples. From these results, diagnosis of HIV-1 infection was indicated to be possible with whole saliva samples dried on filter papers, since the diagnosis was previously shown to be possible with 1 microliter of whole saliva samples. The test for HIV-1 infection with whole saliva samples dried on filter papers was suggested to be useful for various purposes.

Acquired Immunodeficiency Syndrome↗

PubMed1996

Earlier diagnosis of HIV-1 infection by simultaneous detection of p24 antigen and antibody IgGs to p17 and reverse transcriptase in serum with enzyme immunoassay.

Serum samples of four HIV-1 seroconversion serum panels were subjected in a single assay tube simultaneously to ultrasensitive enzyme immunoassays (immune complex transfer enzyme immunoassays) for p24 antigen of HIV-1 and for antibody IgGs to p17 and reverse transcriptase (RT) of HIV-1. Signals became positive 7-15 days earlier than the detection of antibodies to HIV-1 by conventional methods and remained strongly positive even after levels of p24 antigen declined. Thus the simultaneous detection of p24 antigen and antibody IgGs to p17 and RT made possible both as early a diagnosis of HIV-1 infection as the appearance of p24 antigen in the circulation, shortening "the window period," and as reliable a diagnosis of the infection as that by the detection of antibodies to HIV-1 from the time of seroconversion until late stages of the infection, since the serum level of antibody IgG to RT was high not only in asymptomatic carriers but also in patients with AIDS-related complex and AIDS.

Adult↗

PubMed1996

Ultrasensitive and more specific enzyme immunoassay (immune complex transfer enzyme immunoassay) for p24 antigen of HIV-1 in serum using affinity-purified rabbit anti-p24 Fab' and monoclonal mouse anti-p24 Fab'.

Previously, an ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) for p24 antigen of HIV-1 was developed. The immune complex comprising 2,4-dinitrophenyl-biotinyl-bovine serum albumin-rabbit anti-p24 Fab' conjugate, p24 antigen, and rabbit anti-p24 Fab' -beta-D-galactosidase conjugate was trapped onto polystyrene beads coated with affinity-purified (anti-2,4-dinitrophenyl group) IgG, was eluted with epsilon N-2, 4-dintrophenyl-L-lysine, and was transferred to polystyrene beads coated with streptavidin. beta-D-Galactosidase activity bound to the streptavidin-coated polystyrene beads was assayed by fluorometry. This assay was highly sensitive. However, bound beta-D-galactosidase activity had to be assayed for a long time (20 h), and the nonspecific signal was observed in 5% serum samples from subjects with low risk of HIV infection. In the present study, the assay time for bound beta-D-galactosidase activity was shortened to 2.5 h by using 2,4-dinitrophenyl-biotinyl-bovine serum albumin-affinity-purified rabbit anti-p24 Fab' conjugate and affinity-purified rabbit anti-p24 Fab' -beta-D-galactosidase conjugate. Furthermore, the nonspecific signal was found to increase with increasing periods of time for storage of serum samples at -20 degrees C, and this increase was prevented without prolongation of the assay time for bound beta-D-galactosidase activity and without loss of the sensitivity by substituting monoclonal mouse anti-p24 Fab'-beta-D-galactosidase conjugate for affinity-purified rabbit anti-p24 Fab'beta-D-galactosidase conjugate.

Acquired Immunodeficiency Syndrome↗

PubMed1996

SOS response as an adaptive response to DNA damage in prokaryotes.

Escherichia coli possesses an elaborate adaptive mechanism called the "SOS response" to cope with various types of DNA damage. More than 20 SOS genes, most of which are known to be involved in the functions that promote the survival of DNA-damaged cells, are induced by treatments that damage DNA or inhibit DNA synthesis. All the SOS genes share similar sequences in the regulatory regions called the "SOS box", to which LexA repressor binds to repress the transcription in the absence of DNA damage. The SOS signal appears to be the single-stranded DNA produced in vicinity of DNA damage, to which RecA protein binds to be activated as a coprotease. The activated RecA promotes autocleavage of LexA protein by allosteric interaction, which activates the latent serine protease activity of LexA. The induced products of the SOS genes repair DNA lesions by various mechanisms, including recombination, excision repair and error-prone repair, and as the consequence, the SOS signal in the cell decreases and the repression of the SOS genes is restored.

Bacterial Proteins↗

PubMed1996

Shortening of the window period in diagnosis of HIV-1 infection by simultaneous detection of p24 antigen and antibody IgG to p17 and reverse transcriptase in serum with ultrasensitive enzyme immunoassay.

Following HIV infection, there is a window period of 6-8 weeks, during which HIV antibodies are not detectable and the infection cannot be diagnosed by methods for detecting HIV antibodies. However, HIV antigens are detectable in the latter part of the window period, although the level of HIV antigens declines as the level of HIV antibodies increases. We developed an ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) for the simultaneous detection of both p24 antigen of HIV-1 and antibody IgGs to p17 and reverse transcriptase of HIV-1 in a single assay tube and tested 11 HIV-1 seroconversion serum panels and serum samples randomly collected from 79 HIV-1 seropositive subjects and 100 HIV-1 seronegative subjects. The simultaneous detection was shown not only to shorten the window period significantly as compared with conventional methods for HIV-1 antibody detection but also to make possible a reliable diagnosis of HIV-1 infection from the time of seroconversion until late stages of the infection.

Antibodies, Viral↗

PubMed1996

Characterization and comparison of synthetic immobile and mobile Holliday junctions.

Eight synthetic Holliday junction (HJ) oligonucleotides containing an immobile or a mobile junction were characterized by gel electrophoresis, ultraviolet absorption and circular dichroism (CD) spectroscopy. Four 24-mer deoxyribonucleotides formed stable immobile and mobile HJs in 0.1 M NaCl at 5 muM strand concentration at room temperature. However, the immobile HJ constructed from four 18-mers was less stable, and four 12-mers did not form the HJ structure under the conditions used. A comparison of the melting profiles of the HJs with those of the duplexes corresponding to the arms of four-way junctions indicated that the thermal stability of the HJ was similar to that of the individual arm and the cooperativity of the melting behavior of the HJ was relatively higher than that of the individual arm duplex. The Tms of the mobile HJs containing 4, 6, 8, and 10 base-pair homologous cores at junctions were essentially identical with that of the immobile HJ of the same size. There is a tendency that the HJ containing a larger homologous core region becomes more resistant to thermal denaturation. The addition of divalent metal cations, Mg2+ and Ca2+, to the solutions of the HJs raised their melting temperatures. The difference found for the CD spectra of the HJs which differ only in the arrangement of the HJ depended primarily upon the DNA sequence flanking the junction. The RuvC protein binds to the immobile and mobile HJs, regardless of the presence and the size of the homologous core at the junction.

Bacterial Proteins↗

PubMed1996

A novel neutralization epitope on the 'thumb' subdomain of human immunodeficiency virus type 1 reverse transcriptase revealed by a monoclonal antibody.

We have prepared a MAb, 7C4, which inhibits the RNA-dependent DNA polymerase activity of human immunodeficiency virus type 1 (HIV- 1) reverse transcriptase (RT); this MAb has allowed identification of a previously unknown neutralizing epitope of RT. Analysis of the epitope and of the mechanism of polymerase inhibition revealed that 7C4 acts by interfering with the interaction between RT and the template-primer. 7C4 recognizes a discontinuous epitope on the two alpha-helices, alphaH and alpha(I), that make up the 'thumb' subdomain of RT. The existing crystallographic model of HIV-1 RT suggests that the 'thumb' subdomain, together with the 'fingers' and 'palm', form a nucleic-acid-binding cleft in the 66 kDa subunit of RT and that alphaH is in contact with the primer strand of the template-primer. The extent of inhibition of enzyme activity produced by 7C4 correlates with the reported primer-length-dependency of template-primer binding to RT. Inhibition by 7C4 was competitive with respect to the template-primer and mixed with respect to the substrate. Binding of 7C4 to RT was prevented by preincubation of the enzyme with high concentrations of template-primer but not with substrate. Thus, the 7C4 epitope apparently exists on part of the template-primer binding site of the alphaH and alpha(I) regions of the 'thumb' subdomain. This neutralization epitope is a logical target for the development of new types of HIV-1 RT inhibitors.

Animals↗

PubMed1996

Processing the holliday junction in homologous recombination.

The Holliday junction is a well-known intermediate of homologous recombination. Recently, the proteins involved in the correct processing of the Holliday structure into mature recombinant molecules, namely RuvA, RuvB, RuvC and RecG have been isolated and characterized. This has culminated in a model for their synergistic mechanism of action and the solving of the RuvC crystal structure.

Bacterial Proteins↗

PubMed1995

Diagnosis of HIV-1 infection with whole saliva by detection of antibody IgG to HIV-1 with ultrasensitive enzyme immunoassay using recombinant reverse transcriptase as antigen.

Whole-saliva samples were collected from 45 asymptomatic carriers, 18 patients with AIDS-related complex (ARC) or AIDS, and 76 medical students by simple spitting with no stimulation and tested by an ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) for anti-HIV-1 IgG using recombinant reverse transcriptase as antigen and beta-D-galactosidase as label. With as little as 1 microliter of whole saliva, the lowest signals among the 45 asymptomatic carriers, 8 patients with ARC, and 10 patients with AIDS were 38-, 78-, and 3-fold, respectively, higher than the highest signal among the medical students. When the volume of whole saliva for test was increased up to 100 microliters, no significant effect was observed on signals for seropositive cases and signals for the medical students increased only very slightly. Therefore, whole-saliva samples containing extremely low levels of anti-HIV-1 IgG, even 2,000-fold lower than the lowest level among the 45 asymptomatic carriers tested, were considered to be discriminated from those of seronegative individuals. Thus, the sensitivity and specificity were expected to be both 100% with whole saliva even for a larger number of samples, although the number of samples tested was limited.

Adolescent↗

PubMed1995

Autophosphorylation and activation of transcriptional activator PhoB of Escherichia coli by acetyl phosphate in vitro.

The PhoB protein, the transcriptional activator for the genes belonging to the phosphate regulon in Escherichia coli, was autophosphorylated in the presence of acetyl phosphate (acP) in vitro. The properties of phospho-PhoB, such as stability upon acid or alkali treatment and activating pstS transcription by RNA polymerase holoenzyme, were the same as those of phospho-PhoB produced from phospho-PhoR or phospho-PhoM. These results indicate that PhoB is an enzyme that catalyzes its own phosphorylation using acP, a low-molecular-weight metabolic intermediate.

Bacterial Proteins↗

PubMed1995

Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.

Escherichia coli RuvC protein is a specific endonuclease that resolves Holliday junctions during homologous recombination. Since the endonucleolytic activity of RuvC requires a divalent cation and since 3 or 4 acidic residues constitute the catalytic centers of several nucleases that require a divalent cation for the catalytic activity, we examined whether any of the acidic residues of RuvC were required for the nucleolytic activity. By site-directed mutagenesis, we constructed a series of ruvC mutant genes with similar amino acid replacements in 1 of the 13 acidic residues. Among them, the mutant genes with an alteration at Asp-7, Glu-66, Asp-138, or Asp-141 could not complement UV sensitivity of a ruvC deletion strain, and the multicopy mutant genes showed a dominant negative phenotype when introduced into a wild-type strain. The products of these mutant genes were purified and their biochemical properties were studied. All of them retained the ability to form a dimer and to bind specifically to a synthetic Holliday junction. However, they showed no, or extremely reduced, endonuclease activity specific for the junction. These 4 acidic residues, which are dispersed in the primary sequence, are located in close proximity at the bottom of the putative DNA binding cleft in the three-dimensional structure. From these results, we propose that these 4 acidic residues constitute the catalytic center for the Holliday junction resolvase and that some of them play a role in coordinating a divalent metal ion in the active center.

Aspartic Acid↗

PubMed1995

Mutational analysis of the role of the first helix of region 4.2 of the sigma 70 subunit of Escherichia coli RNA polymerase in transcriptional activation by activator protein PhoB.

Transcription of the genes belonging to the phosphate (pho) regulon in Escherichia coli requires the specific activator protein PhoB, in addition to RNA polymerase containing the major sigma factor, sigma 70, which is encoded by rpoD. We previously isolated two mutant sigma 70s (D570G and E575K) that were specifically defective in transcribing the pho genes. The mutated sites were located near and within the first helix of the helix-turn-helix (HTH) motif or region 4.2 of sigma 70. To study further the role of the first helix of the HTH motif of sigma 70 in transcriptional activation by PhoB, we made a series of rpoD mutations that alter the motif and purified the mutant sigma 70 proteins. RNA polymerases containing the mutant sigma 70s Y571A, T572L, V576T, K578E and F580V showed reduced in vitro transcription from the pstS promoter, a representative pho promoter, in the presence of PhoB, whereas RNA polymerase containing another mutant sigma 70 (E574K) showed enhanced transcription from the promoter. Transcription from the activator-independent tac promoter and the pBR-P4 promoter, which is independent of PhoB and requires cAMP-CRP (cAMP receptor protein) for transcription, was affected at most only marginally by these sigma 70 mutations. These results provide further evidence that the first helix plays an important role in the specific interaction between RNA polymerase and PhoB protein bound to the pho promoters in transcriptional activation.

Amino Acid Sequence↗

PubMed1995

Molecular mechanisms of Holliday junction processing in Escherichia coli.

Recent genetic and biochemical studies revealed the mechanisms of late stage of homologous recombination in E. coli. A central intermediate of recombination called "Holliday structure", in which two homologous duplex DNA molecules are linked by a single-stranded crossover, is formed by the functions of RecA and several other proteins. The products of the ruvA and ruvB genes, which constitute an SOS regulated operon, form a functional complex that promotes migration of Holliday junctions by catalyzing strand exchange reaction, thus enlarging the heteroduplex region. RuvA is a DNA-binding protein specific for these junctions, and RuvB is a motor molecule for branch migration providing energy by hydrolyzing ATP. The product of the ruvC gene, which is not regulated by the SOS system, resolves Holiday junctions by introducing nicks at or near the crossover junction in strands with the same polarity at the same sites. The recombination reaction is completed by sealing the nicks with DNA ligase, resulting in spliced or patched recombinants. The product of the recG gene provides an alternative route for resolving Holliday junctions. RecG has been proposed to promote branch migration in the opposite direction to that promoted by RecA protein. The atomic structure of RuvC protein revealed by crystallographic study, when combined with mutational analysis of RuvC, provides mechanistic insights into the interactions of RuvC with Holliday junction.

Bacterial Proteins↗

PubMed1995

Overproduction, purification, and diagnostic use of the recombinant HIV-1 Gag proteins, the precursor protein p55 and the processed products p17, p24, and p15.

HIV-1 Gag protein precursor p55, and its processed products, p17, p24, and p15 were overproduced in Escherichia coli and purified to near homogeneity. To study the antigenic properties and the potentiality as the diagnostic and prognostic reagents, varying amounts of the purified Gag proteins were dotted onto the polyvinylidene difluoride membrane and reacted with 40 sera of HIV-1-infected individuals (35 AC, 1 ARC, and 4 AIDS patients) and 10 sera of normal healthy donors. p55 reacted with 40 (100%) sera of HIV-1 carriers, while p17, p24, and p15 reacted with 37 (92.5%), 35 (87.5%) and 34 (85%) of the 40 sera of HIV-1 carriers, respectively. On the whole, the reaction of p55 was especially strong and that of p15 was the weakest. p55 showed the strongest reaction among the four Gag proteins with all specimens, and it showed a positive reaction with a carrier serum with which none of the processed Gag proteins showed a positive reaction. Therefore, p55 is the most useful antigen among the four Gag proteins for detection of the Gag antibodies and may even be one of the most useful antigens for the diagnosis of HIV-1 infection.

Chromatography, Gel↗

PubMed1995

Three antigenic regions in p17 of human immunodeficiency virus type 1 (HIV-1) revealed by mouse monoclonal antibodies and human antibodies in HIV-1 carrier sera.

We investigated the murine antibody response to recombinant p17 (rp17) of human immunodeficiency virus type 1 (HIV-1) and the human antibody response directed to p17 in HIV-1 infection. Three large peptides covering residues 12-29, 53-87 and 87-115 of p17 were synthesized. The cysteine residues 57 and 87 of peptide 53-87 were reoxidized to form a disulfide bridge. Eighteen out of 19 murine monoclonal anti-rp17 antibodies had relatively high affinities (KA = 1.9 x 10(5)-1.4 x 10(8) M-1) with one of the 3 p17 peptides in the liquid phase. Each monoclonal antibody reacted only with one particular peptide and had no reactivity with the other 2 p17 peptides. All the monoclonal antibodies reacted with rp17 in the liquid phase with a reasonable degree of affinity (KA = 2.0 x 10(5)-1.8 x 10(7) M-1). Four HIV-1 carrier sera, which were positive in ELISA using rp17 as the antigen, reacted positively in an ELISA using 3 p17 peptides which were used to titrate murine monoclonal antibodies. Murine monoclonal antibodies having specificity for the 3 p17 peptides stained live HIV-1-infected cells by means of indirect membrane immunofluorescence, irrespective of their specificity. This suggests that the various portions of p17 (at least 3 regions of p17) were exposed on the surface of live infected cells, probably as short polypeptide chains.

Amino Acid Sequence↗

PubMed1995

Mode of promoter recognition by the Escherichia coli RNA polymerase holoenzyme containing the sigma S subunit: identification of the recognition sequence of the fic promoter.

Transcription of a number of genes during stationary phase in Escherichia coli requires the alternative sigma factor sigma S, encoded by the rpoS gene. No consensus sequence for the promoters recognized by the RNA polymerase holoenzyme containing the sigma S subunit (E sigma S) is known. To identify the E sigma S recognition sequence, we analysed the promoter region of the fic gene, whose expression depends on E sigma S both in vivo and in vitro. By random mutagenesis, we isolated a large number of the fic promoter mutants that had defective promoter activities in an rpoS+ strain. All such mutants contained alterations within the -10 region, TATACT, whereas no mutant was isolated with alterations in the -35 region. Based on further analyses including scanning mutagenesis and DNase I footprinting assays of the fic promoter region, and in vitro transcription assays, we conclude that the -10 hexamer is essential to transcription initiation from the fic promoter by E sigma S.

Bacterial Proteins↗