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Biomedical subjects

A Nakata

Publications and source records attributed to A Nakata.

At least 127 records · Page 7Linked to original sources
PubMed1989

Overproduction, affinity purification and characterization of 65-kDa protein of Mycobacterium leprae in Escherichia coli.

The 65-kDa protein of Mycobacterium leprae was produced in an Escherichia coli strain carrying a plasmid harboring the recloned gene coding for the protein. The protein was purified through affinity chromatography prepared with the IgG fraction of a monoclonal antibody which was prepared against the 65-kDa protein. The purified 65-kDa protein also reacted immunologically with the monoclonal antibody IIIE9, which recognizes the epitope for M. leprae, prepared by Buchanan, et al. BALB/c mice were inoculated with M. leprae and 4 months later were skin tested with the purified 65-kDa protein. Gross changes were observed at the skin-test site. The role of the protein in protective immunity against M. leprae foot pad infection in mice was also studied.

Animals↗
PubMed1988

Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro.

Expression of the genes in the phosphate regulon, including the pstS (phoS) and phoB genes, is positively regulated by PhoB protein when phosphate is limited. We purified PhoB protein from overproducing cells and studied its interaction with the pstS gene. It binds specifically to the DNA fragment containing the promoter region of pstS. The transcription initiation site of the gene in vivo was identified by S1 nuclease mapping and primer-extension experiments. In-vitro transcription of pstS was activated by the PhoB protein, and the initiation site of transcription agreed with the in-vivo initiation site. Activation of in-vitro transcription by PhoB protein required both the normal sigma factor (sigma 70) and core RNA polymerase. PhoB protein binding sites on the promoter regions of pstS and phoB were determined by footprinting experiments with DNase I and a methylating agent. In both cases the protein binds to the pho box, the concensus sequence shared by regulatory regions of genes in the phosphate regulon. Our findings indicate that PhoB protein recognizes and binds to the pho box and activates transcription of the genes in the phosphate regulon.

Bacterial Outer Membrane Proteins↗
PubMed1988

RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis.

Induction of the Escherichia coli SOS system increases the ability of the cell to perform DNA repair and mutagenesis. Products of the recA and umuD,C genes are required for mutagenesis induced by radiation and many chemicals. Transcription of the SOS genes including recA and umuD,C is repressed by a repressor, LexA protein, and is derepressed by the proteolytic cleavage of LexA facilitated by RecA protein that had been activated by inducing signals produced in the cell by agents that damage DNA. An activated form of RecA protein, RecA, seems to have roles in SOS mutagenesis other than its known role as an antirepressor. Derepression of the genes involved in SOS mutagenesis such as recA and umuD,C in defective chromosomal lexA(Def) mutants does not increase the ability of the cell to perform mutagenesis. Activation of RecA protein is essential to this ability. RecA facilitates the proteolytic cleavage of several repressors such as lambda, P22, and 434 phage repressors and LexA, and UmuD protein contains a sequence homologous to the regions surrounding the cleavage sites of these repressors; therefore, we examined the possibility that UmuD protein is cleaved by RecA. We found evidence that the intact UmuD protein was cleaved after mutagenic treatment and that the cleavage was dependent on RecA. The results suggested that UmuD protein may be proteolytically processed by RecA, and that processed UmuD may be the active form of the protein participating in mutagenesis.

Bacterial Proteins↗
PubMed1988

Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination.

The ruv gene of Escherichia coli, which is involved in DNA repair and recombination, was cloned on a plasmid vector. The DNA of the ruv region was sequenced; it had two open reading frames in tandem that could code for 22- and 37-kilodalton proteins. The proteins encoded by these open reading frames were identified by the maxicell method. The two genes were aligned in the same orientation and regulated by the SOS system, so the two genes probably constitute an operon. The distal one complemented the ruv mutations. Transcription of the operon was studied both in vivo and in vitro. Two transcription initiation sites were identified upstream of the coding frames, and the transcription from both sites was repressed by the LexA repressor. A DNA sequence that is homologous to the SOS box and bound by LexA protein was found in the regulatory region of the operon. The amino acid sequence of Ruv protein deduced from the DNA sequence shows a high degree of homology to the consensus sequence shared by ATP-binding proteins.

Amino Acid Sequence↗
PubMed1988

Identification of the human beta-actin enhancer and its binding factor.

An enhancer of the human beta-actin gene and a factor that specifically interacts with it were detected. A mobility shift assay showed that the factor bound to the 25-base-pair sequence (between +759 and +783 downstream from the cap site) with high specificity. This finding correlated with those of DNase I protection and exonuclease III digestion assays. This binding region of the beta-actin enhancer contained a hyphenated dyad symmetry and an enhancer core-like sequence. In vitro competition experiments indicated that the factor did not bind to the simian virus 40 enhancer core region.

Acetyltransferases↗
PubMed1987

Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product.

The iap gene in Escherichia coli is responsible for the isozyme conversion of alkaline phosphatase. We analyzed the 1,664-nucleotide sequence of a chromosomal DNA segment that contained the iap gene and its flanking regions. The predicted iap product contained 345 amino acids with an estimated molecular weight of 37,919. The 24-amino-acid sequence at the amino terminus showed features characteristic of a signal peptide. Two proteins of different sizes were identified by the maxicell method, one corresponding to the Iap protein and the other corresponding to the processed product without the signal peptide. Neither the isozyme-converting activity nor labeled Iap proteins were detected in the osmotic-shock fluid of cells carrying a multicopy iap plasmid. The Iap protein seems to be associated with the membrane.

Alkaline Phosphatase↗
PubMed1986

Nucleotide sequence of the phoR gene, a regulatory gene for the phosphate regulon of Escherichia coli.

Genes in the phosphate regulon of Escherichia coli are positively regulated by the products of the phoB and phoR genes with limited phosphate, and negatively regulated by the product of the phoR gene with excess phosphate. We present here the complete nucleotide sequence of the phoR gene. Together with the DNA sequence of the upstream phoB gene that we determined previously, this region shows the following features. The flanking regions of the operon are abundant in A-T base-pairs. A possible stem-and-loop structure of the transcript followed by several U residues characteristic of rho-independent transcriptional terminators was distal to the phoR coding region. The operon is probably composed of only two cistrons. The nucleotide sequence of phoR indicates that its protein consists of 431 amino acid residues and has a molecular weight of 49,666. The amino acid sequence of the PhoR protein has significant homology with that of the EnvZ protein, which is a regulator for the omp regulon. Therefore, the sequences of the PhoB and PhoR proteins have considerable homologies with those of the OmpR and EnvZ proteins, respectively, indicating that the two operons share a common ancestor. The PhoR protein contains an extensive hydrophobic region in the amino-terminal portion. Thus the protein may be a membrane protein and function as a component of a signal transducer.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12.

phoB encodes a positive regulator for a number of the genes belonging to the phosphate regulon of Escherichia coli, including phoA, phoS, phoE and ugpAB. We have determined the nucleotide sequence of the chromosomal segment containing the promoter and the coding region of the phoB gene. The sequence data combined with the known amino-terminal amino acid sequence of a PhoB-LacZ hybrid protein suggest that the PhoB protein consists of 228 amino acid residues with a Mr of 26,302. In the regulatory region of the gene, a consensus nucleotide sequence shared by the regulatory regions of the phoA, phoS and phoE genes, which we name the "phosphate box", was found. Since these genes are positively regulated by the product of phoB, this suggests that transcription of the phoB gene is also regulated positively by its own product. Extensive homology was found in the amino acid sequences of the products of phoB, ompR and dye, all of which are positive regulatory genes for a number of genes coding for envelope proteins. This implies that these genes were originally duplications of a protogene that evolved to have divergent but related functions.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequence of the lig gene and primary structure of DNA ligase of Escherichia coli.

The DNA ligase of Escherichia coli catalyses the NAD-dependent formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in DNA. It is essential for DNA replication and repair of damaged DNA strands. We determined the nucleotide sequence of the lig gene of Escherichia coli coding for DNA ligase and flanking regions. The coding frame of the gene was confirmed by the amino acid composition and the amino- and carboxyl-terminal amino acid sequences of the purified ligase. The ligase consists of 671 amino acid residues with a molecular weight of 73,690.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequence of the phoM region of Escherichia coli: four open reading frames may constitute an operon.

The phoM gene is one of the positive regulatory genes for the phosphate regulon of Escherichia coli. We analyzed the nucleotide sequence of a 4.7-kilobase chromosomal DNA segment that encompasses the phoM gene and its flanking regions. Four open reading frames (ORFs) were identified in the order ORF1-ORF2-ORF3 (phoM)-ORF4-dye clockwise on the standard E. coli genetic map. Since these ORFs are preceded by a putative promotor sequence upstream of ORF1 and followed by a putative terminator distal to ORF4, they seem to constitute an operon. The 157-amino-acid ORF1 protein contains highly hydrophobic amino acids in the amino-terminal portion, which is a characteristic of a signal peptide. The 229-amino-acid ORF2 protein is highly homologous to the PhoB protein, a positive regulatory protein for the phosphate regulon. The ORF3 (phoM gene) protein contains two stretches of highly hydrophobic residues in the amino-terminal and central regions and, therefore, may be a membrane protein. The 450-amino-acid ORF4 protein contains long hydrophobic regions and is likely to be a membrane protein.

Amino Acid Sequence↗
PubMed1985

Regulation of the phosphate regulon of Escherichia coli K-12: regulation and role of the regulatory gene phoR.

The phoR gene product functions as a negative regulator with excess of phosphate and as a positive regulator with limited phosphate for the phosphate-starvation-inducible pho regulon of Escherichia coli. We constructed recombinant plasmids that contain a phoR'-'lacZ fusion gene to study the regulation of phoR expression. The genetic and physiological regulation of phoR expression was found to be very similar to that of phoB, a positive regulatory gene for the pho regulon, and phoA, the structural gene for alkaline phosphatase, both of which are inducible by phosphate limitation. The synthesis of the PhoR protein became non-inducible when the phoB promoter upstream of phoR, was removed from the hybrid plasmid, or when a transcriptional terminator was inserted in the phoB structural gene, irrespective of phosphate concentration in the medium. The results suggest that phoB and phoR constitute a single operon whose promoter is located proximal to phoB. The same low level of the PhoR protein in the cell can function as a positive regulator with limited phosphate and as a negative regulator with excess phosphate for the phoB-phoR operon. These results suggest that the maximal level of the operon is induced as consequences of both the increase in the quantity of the PhoR protein and of functional change of the protein as a positive regulator, which are induced by phosphate limitation.

DNA Transposable Elements↗
PubMed1985

Nucleotide sequence of the genes involved in phosphate transport and regulation of the phosphate regulon in Escherichia coli.

The pstA(=phoT), pstB and phoU genes are situated at 84 minutes on the Escherichia coli genetic map. All of them are involved in the negative regulation of the phosphate regulon, and all of them except for phoU are required for the binding-protein-mediated, highly specific phosphate transport. We have determined the DNA sequence of about 4 X 10(3) bases of chromosomal segment containing these genes. Four translational reading frames (TRFs) were detected in the region. We attempted to assign the TRFs to the mutant alleles. Plasmids were constructed so that each contained only one of the TRFs, downstream from the lac promoter, to be used for the complementation tests. By this test, TRF-2, TRF-3 and TRF-4 were identified with the pstA(=phoT), pstB and phoU genes, respectively. Alkaline phosphatase-constitutive mutations of the two strains in our collection were complemented by the plasmid with the TRF-1 region. Therefore, we propose to designate the allele phoW. The order of the genes in this region has been established to be phoS-phoW-pstA(=phoT)-pstB-phoU counterclockwise on the E. coli genetic map.

Base Sequence↗
PubMed1985

Use of a phoB'-'lacZ fusion gene to determine the N-terminal amino acid sequence of the phoB protein and to prepare antiserum against the protein.

phoB is a positive regulatory gene of the phosphate regulon of Escherichia coli. A plasmid carrying a phoB'-'lacZ fusion gene was constructed by in vitro recombination. A PhoB-LacZ hybrid protein was purified from the cells carrying the plasmid by monitoring beta-galactosidase activity. The amino-terminal amino acid sequence of the PhoB protein was determined by utilizing the hybrid protein. Antiserum against the PhoB protein was prepared by immunizing rabbits with the hybrid protein. The serum thus prepared showed specificity for both the PhoB protein and beta-galactosidase.

Amino Acid Sequence↗
PubMed1984

Alkaline phosphatase isozyme conversion by cell-free extract of Escherichia coli.

Isozyme type 1 of alkaline phosphatase in Escherichia coli K-12 was converted to types 2 and 3 after incubation of type 1 isozyme with the supernatant of a sonicated cell-free extract prepared from the cells carrying the cloned iap+ gene on a multi-copy plasmid. By comparison, the lysate prepared from cells carrying the iap+ gene only on the chromosome showed much less isozyme-converting activity. The reaction was promoted by Mg2+ at concentrations of 10 to 50 mM. Protease inhibitors, antipain and leupeptin which inhibit the isozyme conversion in vivo, also inhibited the isozyme conversion in vitro. These results suggest that cells carrying the multiple copy iap+ plasmid overproduce a kind of proteolytic enzyme which removes the amino-terminal arginine residues from isozymes 1 and 2.

Alkaline Phosphatase↗
PubMed1984

Normal precursors of periplasmic proteins accumulated in the cytoplasm are not exported post-translationally in Escherichia coli.

Hyperproduction of phosphate-binding protein, PhoS, in strains carrying a multicopy plasmic containing the phoS gene, resulted in saturation of export sites. As a consequence, pre-PhoS was accumulated both in the inner membrane and in the cytoplasm. This was evidenced both in electron-microscopy and after cell fractionation. Only the membrane-associated precursor could be matured and exported. The signal sequence of the cytoplasmic pre-PhoS was slowly degraded. It was first cleaved about in its middle and then completely removed. Electron microscope studies demonstrated that the cytoplasmic pre-PhoS cannot be exported post-translationally.

Bacterial Proteins↗
PubMed1984

Cloning and characterization of the alkaline phosphatase positive regulatory gene (phoM) of Escherichia coli.

The positive regulatory gene (phoM) for alkaline phosphatase of Escherichia coli was cloned on a mini-F plasmid pMF3 from the E. coli chromosome by a shotgun method. The hybrid plasmid pTHR32, which carries 10.8 kb chromosomal DNA, complemented both phoM and thrB mutations. The restriction map was constructed. Based upon this information, several PhoM- deletion plasmids and smaller PhoM+ plasmids were constructed in vitro. By examining the phenotypes and the physical maps of these plasmids, we could define the phoM gene locus in a 2.5 kb region on the restriction map of the cloned chromosomal DNA fragment. The PhoM+ plasmid not only enabled a phoM- -phoR- double mutant to express phoA (the structural gene for the alkaline phosphatase) but also phoB (another positive regulatory gene for phoA). These results are consistent with a model for genetic regulation of phoA expression that proposes that both the phoM and phoR gene products activate phoB expression under phosphate starved conditions, and PhoB protein, in turn, activates phoA expression. The phoM gene product was identified by the maxicell method as a protein with a molecular weight of 60,000. A hybrid plasmid that carries a phoM'-'lacZ fused gene on mini-F vector pMF3 was constructed in vitro. This plasmid enabled us to study phoM gene expression by measuring the beta-galactosidase level in the cells. The plasmid was introduced into various regulatory mutants related to the phosphate regulon, and phoM gene expression in these strains was studied under conditions of limited or excess phosphate. It was found that phoM expression was not regulated by phosphate nor by any of the pho genes. The transcriptional direction of phoM was found to be clockwise toward the thr operon on the E. coli genetic map. The fusion gene product interfered with phoB and phoA expression in the phoR mutants. Overproduction of PhoM protein increased phoB and phoA expression only in the phoR mutants. The implications of these findings are discussed.

Alkaline Phosphatase↗
PubMed1984

Regulation of the phosphate regulon in Escherichia coli K-12: regulation of the negative regulatory gene phoU and identification of the gene product.

The phoU gene is one of the negative regulatory genes of the pho regulon of Escherichia coli. The DNA fragment carrying phoU has been cloned on pBR322 (Amemura et al., J. Bacteriol. 152:692-701, 1982). Further subcloning, Tn1000 insertion inactivation, and complementation tests localized the phoU gene within a 1.1-kilobase region on the cloned DNA fragment. The gene product of phoU was identified by the maxicell method as a protein with an approximate molecular weight of 27,000. A hybrid plasmid that contains a phoU'-lac'Z fused gene was constructed in vitro. This plasmid enabled us to study phoU gene expression by measuring the beta-galactosidase level in the cells. The plasmid was introduced into various regulatory mutants related to the pho regulon, and phoU gene expression in these strains was studied under limited and excess phosphate conditions. It was found that phoU is expressed at a higher level when the cells are cultured under the excess phosphate condition. The higher phoU expression was observed in a phoB mutant and a phoR-phoM double mutant. The implications of these findings for the regulation of pho genes are discussed.

Alkaline Phosphatase↗