Biomedical subjects

M Inouye

Publications and source records attributed to M Inouye.

At least 307 records · Page 17Linked to original sources

PubMed1990

Enhancement of RNA polymerase binding to promoters by a transcriptional activator, OmpR, in Escherichia coli: its positive and negative effects on transcription.

The OmpR binding sequence (OBS) in the upstream region of the ompF promoter of Escherichia coli was fused to 27 synthetic promoters. Transcription from a number of weak promoters, regardless of their sequences, was dramatically activated in the presence of OmpR, a transcriptional activator. In vivo DNA footprinting revealed that OmpR enhanced the binding of RNA polymerase to the promoters. This enhancement was essential for transcription of weak promoters, while OmpR binding to the OBS fused to a strong promoter was inhibitory for transcription. These results indicate that OmpR stabilizes the formation of an RNA polymerase-promoter complex, possibly a closed promoter complex, and that a transcription activator can serve not only as a positive but also as a negative regulator for gene expression.

Bacterial Outer Membrane Proteins↗

PubMed1990

Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: a potential transposable element encoding both reverse transcriptase and Dam methylase functions.

The region (retron-Ec67) required for the biosynthesis of a branched-RNA-linked multicopy single-stranded DNA (msDNA-Ec67) from a clinical isolate of Escherichia coli was mapped at a position equivalent to 19 min on the K-12 chromosome. The element containing the retron consisted of a unique 34-kilobase sequence that was flanked by direct repeats of a 26-base-pair sequence found in the K-12 chromosomal DNA. This suggests that the 34-kilobase element was probably integrated into the E. coli genome by a mechanism related to transposition or phage integration. In the 34-kilobase sequence an open reading frame of 285 residues was found, which displays 44% sequence identity with the E. coli Dam methylase. Interestingly, there are three GATC sequences, the site of Dam methylation, in the promoter region of the gene for reverse transcriptase.

Amino Acid Sequence↗

PubMed1990

Two independent retrons with highly diverse reverse transcriptases in Myxococcus xanthus.

A reverse transcriptase (RT) was recently found in Myxococcus xanthus, a Gram-negative soil bacterium. This RT has been shown to be associated with a chromosomal region designated a retron responsible for the synthesis of a peculiar extrachromosomal DNA called msDNA (multicopy single-stranded DNA). We demonstrate that M. xanthus contains two independent, unlinked retrons, one for the synthesis of msDNA-Mx162 and the other for msDNA-Mx65. The structural analysis of the retron for msDNA-Mx65 revealed that the coding regions for msdRNA (msr) and msDNA (msd), and an open reading frame (ORF) downstream of msr are arranged in the same manner as found for the Mx162 retron. The ORF encodes a polypeptide of 427 amino acid residues. The amino-terminal domain (residues 1-138) shows no striking similarity to these proteins presently available in the data bases including the msDNA-Mx162 ORF, while the sequence from residues 139-394 can be aligned with various known RT sequences and has 47% identity with the RT domain of the msDNA-Mx162 ORF. On the basis of these findings, possible origins of two highly diverse retrons on the M. xanthus chromosome are discussed.

Amino Acid Sequence↗

PubMed1990

Pro-subtilisin E: purification and characterization of its autoprocessing to active subtilisin E in vitro.

The formation of active subtilisin E from pro-subtilisin E requires the removal of the N-terminal pro-sequence of 77 residues. Pro-subtilisin E produced in Escherichia coli using a pINIII-ompA vector was first extracted with 6 M guanidine-HCl and 5 M urea and purified to homogeneity in the presence of 5 M urea. Upon drop dialysis against 0.2 M sodium phosphate buffer (pH 6.2), the purified pro-subtilisin in 5 M urea was processed to active subtilisin of which the N-terminal sequence and migration in SDS-polyacrylamide gel electrophoresis were identical to those of authentic active subtilisin E. This process was found to be very sensitive to the ionic strengths and anions used. Under the optimum conditions (dialysis against 0.5 M (NH4)2SO4 and 1 mM CaCl2 in 10 mM Tris-HCl buffer (pH 7.0) at 4 degrees C for 1 h), approximately 20% of pro-subtilisin E was converted to active subtilisin E. The activation process was not inhibited by Streptomyces subtilisin inhibitor, and pro-subtilisin E in which the active site was mutated (Asp32 to Asn) was unable to be processed under the optimum conditions. These results confirmed the previous hypothesis that the processing of pro-subtilisin occurs by an intramolecular, autoprocessing mechanism.

Ammonium Sulfate↗

PubMed1990

Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli.

Multicopy single-stranded DNA (msDNA), a branched DNA-RNA molecule, has been shown in Escherichia coli B and clinical strain Cl-1 to be synthesized by reverse transcriptase. We report that 13% of the strains of the ECOR collection, a sample of 72 E. coli isolates representing the breadth of genetic variation of the species, produce msDNA. Three of the four major subspecific groups include msDNA-producing strains. Screening of 25 isolates that are genetically related to msDNA-producing clinical strains uncovered 22 additional msDNA-producing strains. A phylogenetic tree based on allelic variation detected electrophoretically at 20 enzyme-encoding loci revealed two major clusters and several deep branches composed of strains that synthesize msDNA. Although E. coli K-12 does not harbor msDNA, other closely related strains of the K-12 family do. The results support the hypothesis that msDNA-synthesizing systems, including reverse transcriptase genes, were acquired recently and independently in different lineages of E. coli.

Animals↗

PubMed1990

Enhancement of protein translocation across the membrane by specific mutations in the hydrophobic region of the signal peptide.

The hydrophobic region of the signal peptide of the OmpA protein of the Escherichia coli outer membrane was extensively altered in its hydrophobicity and predicted secondary structure by site-specific mutagenesis. The mutated signal peptides were fused to nuclease A from Staphylococcus aureus, and the function of the signal peptide was examined by measuring the rate of processing of the signal peptide. Six of the 12 mutated signal peptides in the nuclease hybrid were processed faster than the wild-type. In particular, the processing of the mutated signal peptide in which the alanine residue at position 9 was substituted with a valine residue was enhanced almost twofold over the processing of the wild-type signal peptide. In addition, the production of nuclease A fused with this mutated signal peptide also increased twofold. However, these effects were not observed when the mutated signal peptide was fused to TEM beta-lactamase. Analysis of the present mutations suggests that both overall hydrophobicity and distinct structural requirements in the hydrophobic region have important roles in signal peptide function.

Amino Acid Sequence↗

PubMed1990

In vivo phosphorylation of OmpR, the transcription activator of the ompF and ompC genes in Escherichia coli.

An in vivo approach was taken to assess whether the phosphorylated state of the transcription activator OmpR was affected by changes in the osmolarity of the growth medium or by mutations in envZ, the gene encoding the inner membrane histidine kinase that phosphorylates OmpR. We present results that support the view that increased phosphorylation of OmpR is correlated with enhanced expression of ompC. The in vivo phosphorylation approach was also used to show that OmpR can be phosphorylated in an envZ null strain. This result indicates that phosphorylation cross talk can occur in vivo between OmpR and a kinase(s) that is functionally homologous to envZ.

Bacterial Outer Membrane Proteins↗

PubMed1990

micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change.

The repressor RNA, micF RNA, is regulated by temperature, osmolarity, and other stress conditions during growth of Escherichia coli. Northern (RNA) blot analyses showed that levels of micF RNA differ widely in various ompB mutant strains when cells are grown at 24 degrees C in LB broth. For example, relative to the parental strain MC4100, the ompR101 mutant strain (which contains no functional OmpR) had about a 10-fold reduction in micF RNA, whereas the envZ11 strain showed about a 5-fold increase. At 37 degrees C, however, micF RNA levels in the ompR101 and envZ11 strains and other ompB mutants differed by less than two-fold compared with the level in strain MC4100, thus indicating that a factor(s) independent of the ompB locus regulates micF RNA expression with temperature increase and that there is an additional control mechanism(s) which maintains the levels of micF RNA in these mutants close to that of the wild type during growth at high temperatures. In a plasmid strain containing the micF gene but without the upstream OmpR-binding site, steady-state levels of micF RNA increased with temperature increase but did not change with osmolarity increase. This showed that osmolal regulation but not temperature regulation of micF depends on these upstream sequences and suggested that while osmolal regulation of the micF gene depends on OmpR, thermal regulation does not.

Bacterial Outer Membrane Proteins↗

PubMed1990

Sex difference in acute renal dysfunction induced by methylmercury in mice.

To investigate the sex-related difference of susceptibility of renal function to methylmercury (MeHg) toxicity, various doses of MeHg chloride (MMC, 20-200 mumol/kg) were orally administered to C57BL/6N mice of both sexes. On days 1, 3, 5, and 7 after MMC administration, the extent of damage to renal function and the renal Hg levels were examined. After dosing, female mice survived much longer than males. With the increase in the dose level to 200 mumol/kg, the changes of the renal Hg levels 24 h after administration showed biphasic features with a plateau of around 85 micrograms/g. The renal Hg in male mice increased more rapidly to the plateau than in females. The doses by which the renal Hg level reached the plateau were 80 and 120 mumol/kg for males and females, respectively. The time-dependent decrease of the renal Hg became much slower with dose levels exceeding 80 and 160 mumol/kg for males and females, respectively. Inhibition of phenolsulfonphthalein excretion and increase of plasma creatinine after the MMC administration were more marked in males than in females. Inorganic Hg levels in the kidney of MeHg-intoxicated mice were much lower than that of HgCl2-intoxicated mice, indicating that the involvement of inorganic Hg, a product of biotransformation of MeHg, in the renal failure caused by MMC treatment would be negligible. Although pathological changes in the renal proximal tubules of HgCl2-intoxicated mice were marked, those of the MeHg-intoxicated group were slight.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1990

Antisense RNA.

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Animals↗

PubMed1989

Characterization of OmpR binding sequences in the upstream region of the ompF promoter essential for transcriptional activation.

In Escherichia coli the expression of the outer membrane porin gene ompF requires the transcriptional activator protein OmpR. Previous DNase I footprinting experiments with purified OmpR localized the OmpR binding site from positions -105 to -60 (relative to the transcriptional start site) in the ompF promoter, and three tandem 10-base pair sequences elements (Fa, Fb, and Fc) within this region were proposed to be important for OmpR recognition. In order to elucidate the roles of the F boxes for transcriptional activation of ompF, various F box deletions and point mutations were constructed and analyzed for their effects on ompF-lacZ expression and OmpR binding. Removal of 102 nucleotides, which included a portion of the OmpR binding region (the Fa box), evidenced the largest decrease in transcriptional activation and significantly reduced OmpR binding. Additional deletion of four more base pairs in this target site (representing half of the Fb box) further reduced ompF expression. OmpR interactions with DNA sequences representing the OmpR binding region were analyzed by DNA mobility shift experiments. A 43-base pair ompF oligonucleotide containing the Fa, Fb, and Fc regions was sufficient for OmpR-dependent DNA binding using either purified OmpR or cell supernatants. The central C residue in each F box was changed to a T and unique patterns of protein-DNA complexes were observed that were different from that of the wild type binding site. The most dramatic effect on OmpR binding was observed when the C to T transversion occurred in the Fb box, and this mutation also reduced the level of ompF-lacZ expression. Our results indicate that the F boxes play important roles in the activation of ompF expression, and we suggest that OmpR may interact cooperatively with these boxes.

Bacterial Outer Membrane Proteins↗

PubMed1989

The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli.

The role of chromosomally derived micF RNA as a repressor of outer membrane protein OmpF of Escherichia coli was examined for various growth conditions. Levels of micF RNA as determined by Northern analyses are found to increase in response to cell growth at high temperature, in high osmolarity or in the presence of ethanol. After a switch to higher growth temperature, the levels of ompF mRNA and of newly synthesized OmpF decrease with time in E. coli strain, MC4100 but these decreases are not observed in isogenic micF deletion strain, SM3001. In addition, while levels of ompF mRNA are substantially reduced in both strains in response to high osmolarity or ethanol at 24 degrees C, the reduced levels in the parental strain are still 4-5-fold lower compared with the micF deletion strain. These findings indicate that chromosomally derived micF RNA plays a major role in the thermal regulation of OmpF and represses OmpF synthesis in response to several environmental signals by decreasing the levels of ompF mRNA. Analyses of the effect of a multicopy micF plasmid on the levels of OmpF and ompF mRNA after an increase in temperature indicated that multicopies of micF RNA markedly inhibited OmpF synthesis but did not accentuate ompF mRNA decrease. These data suggest that multicopy micF inhibits OmpF synthesis primarily through translational inactivation of ompF mRNA and that a limiting factor in addition to micF RNA is necessary to destabilize ompF mRNA.

Bacterial Outer Membrane Proteins↗

PubMed1989

Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate.

The Tar chemoreceptor of Escherichia coli is a membrane-bound sensory protein that facilitates bacterial chemotaxis in response to aspartate. The EnvZ molecule has a membrane topology similar to Tar and is a putative osmosensor that is required for osmoregulation of the genes for the major outer membrane porin proteins, OmpF and OmpC. The cytoplasmic signaling domain of Tar was replaced with the carboxyl portion of EnvZ, and the resulting chimeric receptor activated transcription of the ompC gene in response to aspartate. The activation of ompC by the chimeric receptor was absolutely dependent on OmpR, a transcriptional activator for ompF and ompC.

Aspartic Acid↗

PubMed1989

Myxococcus xanthus msDNA.Mx162 exists as a complex with proteins.

Myxococcus xanthus, a myxobacterium, contains a peculiar branched RNA-linked DNA called msDNA. Reverse transcriptase has been shown to be required for the production of msDNA. Existence of proteins that bind to one of the two msDNAs in M. xanthus, msDNA.Mx162, was examined by gel retardation assays. Total cell-free extract yielded two distinct retarded bands. Both bands were sensitive to treatment with proteinase K, indicating that there is a protein(s) that is able to bind to msDNA. Further, the formation of the bands was inhibited by the addition of nonradioactive msDNA but not by a large excess of poly(dA) in the presence of a 5000-fold excess of poly(dI.dC).poly(dI.dC). In vivo footprinting using dimethyl sulfate revealed that the deoxynucleotide stretch from 60 to 161 is protected. When a M. xanthus cell lysate was centrifuged in a 16-30% glycerol gradient, msDNA was found to sediment in two peaks: a major peak corresponding in size to 14 S, and a minor one at 5 S. These results indicate that msDNA.Mx162 exists as a complex with specific proteins in the cell.

Base Sequence↗

PubMed1989

Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting.

Expression of the ompF and ompC genes of Escherichia coli requires the OmpR protein for transcriptional activation. In vivo binding of the OmpR protein to the ompF and ompC promoter regions was observed using an in vivo dimethyl sulfate DNA footprinting technique. Two different sequence motifs were found to be protected by OmpR in both the ompF and ompC promoter regions. This technique was further used to localize the DNA-binding domain of OmpR to be within the C-terminal 117 amino acid residues. Binding of the C-terminal portion OmpR to the ompF and ompC promoter regions, however, did not result in activation of transcription. Our results, together with sequence homologies between OmpR and other regulatory proteins, suggests that OmpR has separable domain structures: the C-terminal portion for binding-specific DNA sequences and the N-terminal portion for interacting with RNA polymerase and/or other transcription factors.

Bacterial Outer Membrane Proteins↗

PubMed1989

Pro-sequence of subtilisin can guide the refolding of denatured subtilisin in an intermolecular process.

Subtilisin E, an alkaline serine protease consisting of a single polypeptide chain of 275 amino acids is produced from a pre-pro-protein. The pre-sequence functions as the signal peptide for protein secretion across the membrane. Deletion of the pro-sequence yields mature but inactive subtilisin: the 77-amino acid pro-sequence must precede the mature subtilisin to guide the latter into an active conformation. Pro-subtilisin denatured in 6 M guanidine-HCl can be self-processed to the active enzyme intramolecularly, with concomitant cleavage of the pro-sequence, when dialysed against renaturing buffer. We have constructed an active-centre mutant of pro-subtilisin (Asp 32----Asn) which is not processed to active enzyme, unlike the wild-type pro-subtilisin, because intramolecular processing is prevented. Here we report an intermolecular pathway for the refolding of the inactive mature protein to an active enzyme in vitro with the aid of exogenously added pro-sequence. We establish conditions under which the mature inactive form, as well as acid-denatured subtilisins Carlsberg and BPN', can be renatured by the mutant pro-subtilisin.

Enzyme Activation↗

PubMed1989

Structural requirements of the RNA precursor for the biosynthesis of the branched RNA-linked multicopy single-stranded DNA of Myxococcus xanthus.

A precursor RNA molecule (pre-msdRNA) of approximately 375 bases is considered to form a stable secondary structure which serves as a primer as well as a template to synthesize the branched RNA-linked multicopy single-stranded DNA (msDNA) of Myxococcus xanthus. When 3-base mismatches were introduced into the stem structure immediately upstream of the branched rG residue to which msDNA is linked by a 2',5'-phosphodiester linkage, the production of msDNA was almost completely blocked. However, if additional 3-base substitutions were made on the other strand to resume the complementary base pairing, msDNA production was restored, being consistent with the proposed model of msDNA synthesis. We also found that the branched rG residue of pre-msdRNA could not be replaced with either rC or rA, while the 5' end (dC) of msDNA which is linked to the branched rG could be substituted with a dG residue. Together with several other mutations, the structural requirements of pre-msdRNA are discussed with respect to the mechanism of msDNA biosynthesis.

DNA, Bacterial↗

PubMed1989

Factors affecting the efficiency of protein synthesis in Escherichia coli. Production of a polypeptide of more than 6000 amino acid residues.

Factors affecting the efficiency of protein synthesis were analyzed in Escherichia coli. For this purpose the lacZ gene was fused to produce polypeptides from a dimer (molecular weight 229,957) to a hexamer (molecular weight 684,924) of beta-galactosidase. From pulse-chase experiments it was found that only 45% of the ribosomes which reached to the end of the first monomer were able to complete the second monomer unit. Similarly, for every addition of a monomer unit to synthesize the multimers from the trimer to the hexamer approximately half of the ribosomes failed to complete the synthesis of the added unit. Furthermore, the stability of the polypeptides decreased as their sizes increased. As a result, the overall efficiency of the production of the beta-galactosidase polymers dropped by a factor of approximately 3 on a weight basis for each addition of a monomer unit.

Amino Acids↗