Biomedical subjects

M Inouye

Publications and source records attributed to M Inouye.

At least 397 records · Page 22Linked to original sources

PubMed1985

Characterization of the lep operon of Escherichia coli. Identification of the promoter and the gene upstream of the signal peptidase I gene.

The DNA sequence flanking the gene (lep) encoding signal peptidase I of Escherichia coli has been determined. The upstream flanking sequence contains a gene (lepA) that encodes a polypeptide of 598 amino acid residues and terminates 18 base pairs from the initiation codon of the lep gene. The position of the lep promoter was determined by both gene fusion with the lacZ gene as well as by S1 nuclease mapping of the lep mRNA to be 73 base pairs upstream from the initiation codon of the lepA gene. The lepA gene was cloned into a high expression vector (pIN-III), and its gene product was identified to be a protein of apparent molecular weight of 76,000. This gene product was preferentially localized in the cytoplasmic membrane and periplasmic fractions upon subcellular fractionation. The DNA sequence immediately downstream of the lep gene contains features consistent with a rho factor-independent transcriptional termination site, indicating that the lep operon encodes only two proteins (lepA and lep).

Amino Acid Sequence↗

PubMed1985

Up-promoter mutations in the lpp gene of Escherichia coli.

The promoter of the gene for the major outer membrane lipoprotein, the most abundant protein in Escherichia coli, is considered to be one of the strongest promoters in E. coli. The nucleotide sequences of the -10 and the -35 regions of the lpp promoter were altered in a step-wise manner to conform to their respective consensus sequences by synthetic oligonucleotide-directed site-specific mutagenesis. The mutated promoters were then fused to the lacZ gene to measure promoter activity. The beta-galactosidase activity increased approximately 1.9 and 2.4 fold when the -10 region (AATACT) was altered to TATACT(P1) and TATAAT (consensus sequence; P2), respectively. Similarly, it increased approximately 1.2 and 4.2 fold, when the -35 region (TTCTCA) was altered to TTCACA(R1) and TTGACA (consensus sequence; R2), respectively. When the mutations at the -10 and -35 regions were combined, the overall improvement of the promoter activity for R2-P1 was 4.0 fold over that of the wild-type promoter, while it was only 2.5 fold for R2-P2. These results indicate that substantial improvement of the promoter activity can be achieved by changing either of the two key regions to their respective consensus sequences. However, the complete conformity to consensus sequences at both regions does not necessarily result in the highest activity. With use of the improved lpp promoter in an expression cloning vehicle pIN-III-ompA, staphylococcal nuclease A was produced at a level of approximately 47% of the total cellular protein.

Bacterial Outer Membrane Proteins↗

PubMed1985

The ompA signal peptide directed secretion of Staphylococcal nuclease A by Escherichia coli.

The hybrid pre-enzyme formed by fusion of the signal peptide of the OmpA protein, a major outer membrane protein of Escherichia coli, to Staphylococcal nuclease A, a protein secreted by Staphylococcus aureus, is translocated across the cytoplasmic membrane of E. coli with concomitant cleavage of the signal peptide. A DNA fragment containing the coding sequence for the ompA signal peptide was initially ligated to a DNA fragment containing the coding sequence for nuclease A, with a linker sequence of 33 nucleotides separating the coding sequences. When this fused gene was induced, an enzymatically active nuclease was secreted into the periplasmic space; sequential Edman degradation of this protein revealed that the ompA signal peptide was removed at its normal cleavage site resulting in a modified version of the nuclease having 11 extra amino acid residues attached to the amino terminus of nuclease A. The 33 nucleotides between the coding sequences for the ompA signal peptide and the structural gene for nuclease A were subsequently deleted by synthetic oligonucleotide-directed site-specific mutagenesis. The nuclease produced by this hybrid gene was secreted into the periplasmic space and by sequential Edman degradation was identical to nuclease A. Thus, the ompA signal peptide is able to direct the secretion of fused staphylococcal nuclease A, and signal peptide processing occurs at the normal cleavage site. When the hybrid gene is expressed under the control of the lpp promoter, nuclease A is produced to the extent of 10% of the total cellular protein.

Amino Acid Sequence↗

PubMed1985

Mutations upstream of the ribosome-binding site affect translational efficiency.

The DNA coding for the major outer membrane lipoprotein of Escherichia coli has been fused to the coding region of the beta-galactosidase gene to measure the effect of various mutations on the efficiency of translation initiation. The various mutants were made by either inserting or deleting a small number of nucleotides into or from a region just upstream of the ribosome-binding site. These small mutations dramatically affect translation initiation as measured by the production of beta-galactosidase. We postulate that these mutations affect translation initiation by altering the secondary structure of the messenger RNA. In one case, we predict that a stem and loop just upstream of the Shine-Dalgarno sequence sterically hinders the binding of the ribosome to the mRNA.

Base Sequence↗

PubMed1985

Alteration of putative amino acid levels and morphological findings in neural tissues of methylmercury-intoxicated mice.

Methylmercury chloride was administered PO to male Kud: ddY mice at a dose of 5 mg/kg/day for 20 days. The contents of taurine, aspartate, glutamate, glycine, and gamma-aminobutyric acid were determined in tissue and crude synaptosomal (P2) fraction of cerebellum, cerebral cortex, and spinal cord of methylmercury-treated mice with or without ataxia. In the cerebellum of ataxic mice, increased levels of taurine and glycine were found in the tissue and P2 fraction, and increased levels of glutamate were found in the P2 fraction. In the cerebral cortex, the levels of gamma-aminobutylic acid decreased in the tissue and in the P2 fraction of ataxic mice, but increased levels were found in the tissue of non-ataxic mice. A decreased aspartate level in the cerebral cortex of ataxic mice and an increased taurine level in the cerebral cortex of non-ataxic mice were also found. In the spinal cord of ataxic mice, taurine increased in the tissue and in the P2 fraction. Glutamate level decreased in the spinal cord of ataxic mice, but increased in the P2 fraction of non-ataxic mice. Increased glycine levels in the P2 fraction of the spinal cord were also found in non-ataxic mice. Histologically, some degenerative changes were demonstrated in the cerebral and cerebellar cortices of ataxic mice. Such changes were also present to a mild degree in non-ataxic mice. In conclusion, methylmercury treatment altered the levels of putative neurotransmitter amino acids in neural tissue of mice. These alterations might be caused by specific neural cell dysfunction and could be related to the appearance of ataxia.

Amino Acids↗

PubMed1985

Functional complementation between the two homologous genes, ops and tps, during differentiation of Myxococcus xanthus.

Protein S is a development-specific protein of Myxococcus xanthus encoded by the tps gene. It has been shown that there are two extensively homologous genes (ops and tps) tandemly repeated in the same direction with a 1.4 kb spacer fragment between them (Inouye et al. 1983). Seven deletion mutants were constructed by removing the ops gene, the tps gene, segments of the spacer sequence or combinations of these regions. The deleted regions were replaced with DNA fragments carrying the Tn5 gene for kanamycin resistance. The effects of deleting different regions on morphological changes and on patterns of protein synthesis during fruiting body formation were examined. The process of fruiting body formation was severely delayed when both the ops and the tps genes were deleted. However, this delay could be suppressed by either the ops gene or the tps gene, individually, although in the latter case, a slight delay was still observed. These results indicate that the ops gene is expressed during fruiting body formation and plays a role in the normal program of M. xanthus differentiation. Furthermore, the role of the ops gene can be complemented by the tps gene. The deletion of the ops and/or tps genes had no effect on glycerol-spore formation.

Bacterial Proteins↗

PubMed1985

Binding of penicillin to thiol-penicillin-binding protein 3 of Escherichia coli: identification of its active site.

In order to determine the active site of penicillin-binding protein 3 of Escherichia coli (PBP3), the serine residue at position 307 was replaced with alanine, threonine or cysteine by oligonucleotide-directed site-specific mutagenesis. Since a unique BanII site exists at the position corresponding to serine-307, BanII digestion of the plasmid DNA after mutagenesis resulted in significant enrichment of the mutant plasmids. For mutagenesis, the gene coding for PBP3 (ftsI) was inserted into the expression cloning vector pIN-IIB. The hybrid protein produced was able to bind penicillin while mutant PBP3 in which serine-307 was replaced with either alanine or threonine did not lead to any detectable binding. However, contrary to the report of Broome-Smith et al. (1985) thiol-penicillin-binding protein 3, in which serine-307 was replaced with cysteine, was still able to bind penicillin. Replacement of serine-445 with an alanine residue had no effect on penicillin binding to PBP3.

Acyltransferases↗

PubMed1985

Facilitative effects of maternal environmental enrichment on maze learning in rat offspring.

Pregnant rats were differentially reared in enriched (EC), impoverished (IC), and standard colony conditions (SC) through the pregnancy. Half of the male offspring were reared by their biological mothers and the remaining half were reared by foster-mothers. After weaning male offspring were tested in the Hebb-Williams maze apparatus. The effect of environment was significant for the total error scores; the EC group had less errors than the IC group. In a second experiment all male offspring (EC, SC and IC) were reared by foster-mothers. The effect of environment was significant for initial, repetitive, and total error scores. Further analysis revealed that the EC-SC and EC-IC differences were significant, whereas the IC-SC difference was not. Thus, the results obtained were the first to reveal that maternal environmental enrichment during pregnancy can exert a facilitatory influence on the postnatal maze learning abilities of the offspring.

Animals↗

PubMed1985

Dual functions of the signal peptide in protein transfer across the membrane.

Most secretory proteins in both prokaryotic and eukaryotic cells are synthesized from a precursor with an amino-terminal extension of 20 to 25 amino acid residues called a signal peptide. These signal peptides are removed during translocation of the secretory proteins across the membrane. When two precursor structures are fused, the internalized second signal peptide was found to exert two different roles, depending upon either the distance between the two signal peptides, or whether the first signal peptide functions cotranslationally or posttranslationally. One role is to function as the usual signal peptide to translocate the protein downstream of the internal signal peptide. The other role is to function as a stop-transfer signal to create a transmembrane protein with the second signal peptide anchoring the protein in the membrane.

Bacterial Outer Membrane Proteins↗

PubMed1985

Significance of similarities in patterns: an application to beta interferon-related DNA on human chromosome 2.

The nucleotide sequence of a 14-kilobase (kb) region of the human beta interferon (IFN-beta)-related DNA locus on chromosome 2 (genomic DNA clone lambda B3) was determined and compared to that of the IFN-beta 1 gene by using the Sellers TT algorithm. This algorithm aligns segments of one sequence with similar segments in a second sequence. A strategy was developed for assessing the significance of similarities between DNA sequences based on a scheme that recognizes patterns or runs of identities within an alignment. The pattern score (II) thus obtained is an entropy-like measure. Numerically it is a reflection of the length of the second longest run of identity in an alignment plus a correction factor due to the other shorter identity runs in the alignment. When the IFN-beta 1 gene is compared to a random nucleotide sequence, the distribution of II scores in such comparisons fits a Gaussian function. This strategy has been used to identify seven segments along one strand of lambda B3 DNA that are related to segments in IFN-beta 1; these seven alignments have II scores greater than or equal to 3 standard deviations above the mean score obtained in comparisons between IFN-beta 1 and random nucleotide sequences. One of these alignments (section 7) has a II score 8.02 standard deviations above this mean score. The likelihood of finding an alignment statement as good as that in section 7 in a random sequence the length of the human genome is approximately 10(-7). Furthermore, the lambda B3 DNA sequence in section 7 selects the human IFN-beta 1 gene as the most significant alignment in computer searches of mammalian nucleotide sequence data bases.

Base Sequence↗

PubMed1985

GTP-binding membrane protein of Escherichia coli with sequence homology to initiation factor 2 and elongation factors Tu and G.

The amino acid sequence of LepA protein, which has been shown to be cotranscribed with signal peptidase I in Escherichia coli, was compared with greater than 2000 known protein sequences. It was revealed that, of the 598 amino acid residues contained in LepA, an amino-terminal domain of 112 residues is homologous to a domain of similar size found in initiation factor 2, elongation factor Tu, and elongation factor G (IF2, EF-Tu, and EF-G), factors required for translation in E. coli. In this domain, 46 and 34 residues align perfectly with the corresponding regions of EF-G and EF-Tu, respectively. If functionally conserved residues within this domain (19 for EF-G and 17 for EF-Tu) are included, the overall resemblance is 58% and 46%, respectively, for EF-G and EF-Tu. A similar domain exists internally in IF2, where there is 42% overall resemblance with the domain of LepA. Immediately adjacent to this region is a small sequence of limited similarity that exists not only in EF-G, EF-Tu, and IF2 but also in the protooncogene c-Ha-ras-1 (from human bladder) and other GTP-binding proteins. Given these homologies, GTP-photoaffinity labeling and subcellular fractionation experiments were undertaken, and it was found that LepA is indeed a membrane-bound GTP-binding protein.

Amino Acid Sequence↗

PubMed1985

Physical mapping of a 330 X 10(3)-base-pair region of the Myxococcus xanthus chromosome that is preferentially labeled during spore germination.

Myxococcus xanthus was pulse-labeled with [3H]thymidine immediately after germination of dimethyl sulfoxide-induced spores. The restriction enzyme digests of the total chromosomal DNA from the pulse-labeled cells were analyzed by one-dimensional as well as two-dimensional agarose gel electrophoresis. Four PstI fragments preferentially labeled at a very early stage of germination were cloned into the unique PstI site of pBR322. By using these clones as probes, a restriction enzyme map was established covering approximately 6% of the total M. xanthus genome (330 X 10(3) base pairs). The distribution of the specific activities of the restriction fragments pulse-labeled after germination suggests a bidirectional mode of DNA replication from a fixed origin.

Chromosome Mapping↗

PubMed1985

Two homologous genes coding for spore-specific proteins are expressed at different times during development of Myxococcus xanthus.

The ops and tps genes of Myxococcus xanthus have ca. 90% DNA and amino acid sequence homology and are in the same orientation separated by a spacer region of only 1.4 kilobases. The products of the two genes were found to cross-react immunologically, and both were capable of Ca2+-dependent self-assembly on the surface of myxospores. However, the ops and tps genes were expressed very differently during the developmental cycle of M. xanthus. The tps gene is induced early during fruiting body formation on a solid surface, and its product, protein S, is made in large quantities (up to 15% of total protein synthesis). When the cells turn into myxospores, protein S is assembled on the outer surface of the spore. We have now also found it in much smaller quantities inside the spores. The ops gene, on the other hand, appears to be induced later in development, after the cells have sporulated, since the ops gene product was found only inside the spores. When an ops gene under the control of a tps gene promoter was inserted into a wild-type strain, the ops gene product was synthesized at the same time as protein S and assembled onto the spore surface.

Bacterial Proteins↗

PubMed1985

Uncoupling of osmoregulation of the Escherichia coli K-12 ompF gene from ompB-dependent transcription.

The expression of the genes for the Escherichia coli K-12 outer membrane proteins, ompF and ompC, is subject to osmoregulation and responds to changes in the osmolarity of the growth medium. The transcription of these genes is dependent on the products of the regulatory locus ompB (comprising the genes ompR and envZ). The native promoter of ompF was replaced with an inducible lpp promoter to eliminate this transcriptional dependence of ompF expression on ompB. As a result, it was possible for the OmpF protein to be produced in an ompB mutant strain that does not normally express ompF. Surprisingly, the expression of ompF under the lpp promoter was still osmoregulated not only in the ompB+ strain but also in two ompB strains tested. These results indicate the involvement of a factor(s) besides the ompR and envZ gene products in the osmoregulation of OmpF production. This factor may interact with a sequence downstream of the ompF promoter. In addition, we show that the expression of ompF under the lpp promoter has no direct effect on ompC expression.

Bacterial Outer Membrane Proteins↗

PubMed1985

Novel one-step cloning vector with a transposable element: application to the Myxococcus xanthus genome.

A new strategy was developed for rapid cloning of genes with a transposon mutation library. We constructed a transposon designated TnV that was derived from Tn5 and consists of the gene coding for neomycin phosphotransferase II as well as the replication origin of an Escherichia coli plasmid, pSC101, flanked by Tn5 inverted repeats (IS50L and IS50R). TnV can transpose to many different sites of DNA in E. coli and Myxococcus xanthus and confers kanamycin resistance (Kmr) to the cells. From the Kmr cells, one-step cloning of a gene which is mutated as a result of TnV insertion can be achieved as follows. Chromosomal DNA isolated from TnV-mutagenized cells is digested with an appropriate restriction enzyme, ligated, and transformed into E. coli cells with selection for Kmr. The plasmids isolated contain TnV in the target gene. The plasmid DNA can then be used as a probe for characterization of the gene and screening of clones from a genomic library. We used this vector to clone DNA fragments containing genes involved in the development of M. xanthus.

Cloning, Molecular↗

PubMed1985

Primary characterization of the protein products of the Escherichia coli ompB locus: structure and regulation of synthesis of the OmpR and EnvZ proteins.

The ompB operon of Escherichia coli contains the structural genes for two proteins, OmpR and EnvZ, which control the osmoregulated biosynthesis of the porin proteins OmpF and OmpC. By inserting XbaI octamer linkers into the cloned ompB locus, four distinct frameshift mutants were isolated and subsequently characterized for their OmpR and EnvZ protein products and their outer membrane porin phenotype. In a minicell expression system, the wild-type products of the ompR and envZ genes were found to be approximately 28 and 50 kilodaltons in size, respectively, whereas the mutant proteins were either truncated or extended due to the frame shift. The identity of the envZ gene product was confirmed by immunoprecipitation. M13 dideoxy sequencing of the DNA around the wild-type ompR-envZ junction revealed an error in the sequence published for this operon; the complete corrected sequence is presented. A sequence, ATGA, was found that forms the termination codon for the OmpR reading frame and a possible initiation codon for the EnvZ protein; these sequences are consistent with the sizes of the proteins observed after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The translational activity of this ATG codon was confirmed by fusing the lacZ gene in frame with the putative EnvZ coding sequence. The implications of these results are discussed with respect to the regulation of synthesis of the ompB gene products.

Amino Acid Sequence↗

PubMed1985

Distribution of multicopy single-stranded DNA among myxobacteria and related species.

Multicopy single-stranded DNA (msDNA) is a short single-stranded linear DNA originally discovered in Myxococcus xanthus and subsequently found in Stigmatella aurantiaca. It exists at an estimated 500 to 700 copies per chromosome (T. Yee, T. Furuichi, S. Inouye, and M. Inouye, Cell 38:203-209, 1984). We found msDNA in other myxobacteria, including Myxococcus coralloides, Cystobacter violaceus, Cystobacter ferrugineus (Cbfe17), Nannocystis exedens, and nine independently isolated strains of M. xanthus. The presence of msDNA in N. exedens would extend its phylogenetic distribution into another family of myxobacteria. Flexibacter elegans, a Cytophaga-like gliding bacteria which may be even more distantly related, also contained an msDNA but at a much lower copy number. msDNA was not detected in closely related strains of the myxobacteria Cystobacter fuscus and C. ferrugineus (Cbfe16 and Cbfe18) and the more distantly related eubacteria Herpetosiphon giganteus, Taxeobacter ocellatus, Lysobacter antibioticus, Lysobacter enzymogenes, Cytophaga johnsonae, Rhodopseudomonas sphaeroides, and Rhodospirillum rubrum. Thus far, msDNA has been found in certain gliding bacteria but not in others.

Cytophaga↗

PubMed1984

Roles of the 5' leader region of the ompA mRNA.

OmpA protein, a major outer membrane protein of Escherichia coli, is synthesized from a messenger RNA containing a 134-nucleotide 5' leader region. The role of this leader region in efficient ompA expression was investigated using a series of ompA-lacZ fusion plasmids. These plasmids differ in the amount of DNA encoding the ompA leader region which is fused to the lacZ structural gene. The fusion containing all but six nucleotides of the ompA leader produced the highest beta-galactosidase activity, while the fusion containing the shortest leader synthesized only 4% as much beta-galactosidase. Fusions with leaders intermediate in length produced between 6% and 24% of the activity found in the most efficient fusion. Quantitation of lacZ mRNA synthesis by DNA-RNA hybridization revealed differences in lacZ mRNA production reflecting the observed differences in beta-galactosidase activity. The primary effect of the ompA leader in maintaining high levels of mRNA is discussed in terms of the roles of mRNA secondary structure.

Bacterial Outer Membrane Proteins↗