A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map

The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described. This region contains at least 681 potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%) are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical genes registered in databases, and the remaining 118 (17%) do not show a significant similarity to any other gene. In this region, we assigned a cluster of cit genes encoding multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes encoding integrase, excisionase and repressor in the e14 genetic element. In addition, a new valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B and -C, were found.

Suppressor mutations in alpha-subunit of RNA polymerase for a mutant of the positive regulator, OmpR, in Escherichia coli

The OmpR protein is a positive regulator specific for the Escherichia coli ompF and ompC genes. This protein functions in a phosphorylation-dependent manner through a presumed interaction with RNA polymerase. We previously isolated OmpR mutants which were suggested to be defective in transcription activation, but not in DNA binding (the so-called positive control (PC) mutant). In this study we isolated mutants of the alpha-subunit of RNA polymerase which can suppress one of the putative PC mutants of OmpR. A crucial amino acid substitution was identified as [V264G] in the alpha-subunit, which is located in the helix H1 of the C-terminal domain, which has been claimed, based on mutational and structural analyses, to be involved in the interaction with other positive regulators including the well-characterized cAMP receptor protein.

Construction and characterization of a deletion mutant of gpd2 that encodes an isozyme of NADH-dependent glycerol-3-phosphate dehydrogenase in fission yeast

Schizosaccharomyces pombe has two genes each encoding an isozyme of NADH-dependent glycerol-3-phosphate dehydrogenases (gpd1+ and gpd2+). To gain an insight into the function of these genes, here we constructed a gpd2 deletion mutant, in addition to the previously constructed gpd1 deletion mutant. We showed that the gpd1+ and gpd2+ gene-products are both functional in terms of the de novo glycerol synthesis. Furthermore, the gpd1(+)-mediated glycerol production is primarily responsible for the osmoregulation, but the gpd2+ gene is not. Interestingly, however, the gpd2 deletion mutant had histidine- or lysine-auxotrophy for growth on a minimal medium.

Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model

BACKGROUND

The inhibition of beta-galactosidase expression in glucose-lactose diauxie is a typical example of the glucose effect in Escherichia coli. It is generally believed that glucose exerts its effect at least partly by reducing the intracellular cAMP level. However, there is no direct evidence that the inhibitory effect of glucose on the expression of the lac operon is mediated by a reduction of the cAMP level in the glucose-lactose system.

RESULTS

To examine the roles of cAMP and the cAMP receptor protein (CRP) in the glucose effect, the intracellular levels of these factors were determined during diauxic growth in a glucose-lactose medium. We found that the levels of cAMP and CRP in a lactose-grown phase were not higher than those in a glucose-grown phase, although the cAMP levels increased transiently during the lag phase. The addition of exogenous cAMP eliminated diauxic growth but did not eliminate glucose repression. Glucose repression and diauxie were observed in cells which lack cAMP but produce a cAMP-independent CRP. In addition, inactivation of the lac repressor by the disruption of the lacI gene or the addition of IPTG, eliminated glucose repression.

CONCLUSION

We conclude that the repression of beta-galactosidase expression by glucose is not due to the reduction of the cAMP-CRP level but due to an inducer exclusion mechanism which is mediated by the phosphoenolpyruvate-dependent sugar phosphotransferase system.

A cyanobacterial gene that interferes with the phosphotransfer signal transduction involved in the osmoregulatory expression of ompC and ompF in Escherichia coli

Synechococcus sp. PCC7942 is a phototrophic cyanobacterium. In this study we cloned a Synechococcus gene that has a striking effect on the production of the Escherichia coli outer membrane proteins, OmpC and OmpF, provided that this gene was introduced by a multicopy plasmid into the heterologous cells. This multicopy gene in E. coli cells was able to specifically shut off the production of both OmpC and OmpF at the level of transcription. The nucleotides were sequenced for this gene, named sis, and its gene product was purified from E. coli to near homogeneity. A computer-aided search found that the deduced amino acid sequence consisting of 138 residues is novel, with no significant similarity to any other protein in the databases. Since the transcription of ompC and ompF is regulated by the regulatory factors EnvZ and OmpR, through phosphotransfer signal transduction, we explored the inhibitory effect of Sis in various genetic backgrounds as to envZ and ompR. In particular, the inhibitory effect of Sis was observed even in an DeltaenvZ background, but was not observed in a certain background in which the ompC and ompF transcription was supported by a mutant OmpR that can function in a phosphorylation-independent manner. These results suggested that the EnvZ kinase may not be the direct target of Sis, but rather that the process(es) concerning the phosphorylation and/or dephosphorylation of the OmpR protein may be affected by Sis. However, no direct effect of Sis was seen in an in vitro OmpR-phosphorylation assay with the purified OmpR and Sis proteins. Based on these results, possible functions of Sis are discussed with special reference to the phosphotransfer signal transduction in E. coli.

Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization

The hallmark features of rho-independent transcription terminators are a G(+)C-rich dyad symmetry sequence followed by a run of T residues on a sense strand. Both of these structural elements are required for efficient transcription termination. Besides its primary function, rho-independent terminators are also known to enhance expression of an upstream gene by stabilizing RNA in a few cases. The Escherichia coli crp gene encoding cAMP receptor protein (CRP) contains a typical rho-independent terminator. To gain further insight into the roles of the G(+)C-rich dyad symmetry sequence and the poly(T) tract both in transcription termination and mRNA stabilization, we constructed a series of variant crp terminators and analyzed their abilities regarding these two functions. Disruption of the G(+)C-rich dyad symmetry sequence almost completely eliminated terminator activity while disruption of the poly(T) tract reduced terminator activity significantly but not completely. Thus, the contribution of the G(+)C-rich dyad symmetry sequence to transcription termination is larger than that of the poly(T) tract. Disruption of the G(+)C-rich dyad symmetry region reduced expression of the upstream crp gene by accelerating the rate of mRNA degradation. However, disruption of the poly(T) sequence had no effect on the stability of the crp mRNA, indicating that the poly(T) tract plays no role in mRNA stabilization. When the crp terminator was replaced by terminators derived from other genes, the fusion genes expressed the crp mRNA at the same level as did the native crp gene, suggesting that the mRNA stabilization effect is probably a general nature of rho-independent terminators.

The osmo-inducible gpd1+ gene is a target of the signaling pathway involving Wis1 MAP-kinase kinase in fission yeast

The gpd1+ gene of Schizosaccharomyces pombe encodes an isozyme of NADH-dependent glycerol-3-phosphate dehydrogenases that is involved in glycerol synthesis, whose expression is induced upon an upshift of the medium osmolarity. We provide evidence that this osmotic induction of gpd1+ in S. pombe is under the control of a MAP-signaling pathway involving the wis1+ gene-product, which is a homologue of MAP-kinase kinases. The results suggested that the gpd1+ gene is a downstream target of the osmosensing signaling that is transmitted through Wis1, thereby defects of either of these genes result in the similar phenotype, namely, osmosensitive for growth, because of the failure in accumulation of the intracellular osmoprotectant, glycerol.

Osmoregulation of fission yeast: cloning of two distinct genes encoding glycerol-3-phosphate dehydrogenase, one of which is responsible for osmotolerance for growth

Many types of microorganisms, including both prokaryotes and eukaryotes, have developed mechanisms to adapt to severe osmotic stress. In this study, we isolated multicopy suppressor genes for a Schizosaccharomyces pombe mutant, which exhibited the clear phenotype of being osmosensitive for growth (Osms) on agar plates containing high concentrations of either non-ionic or ionic osmotic solutes. Two genes were thus identified, and each was suggested to encode an NADH-dependent glycerol-3-phosphate dehydrogenase (GPD), which is required for glycerol synthesis. The nucleotide sequences, determined for these genes (named gpd1+ and gpd2+, respectively), revealed that S. pombe has two distinct GPD isozymes. They are only 60% identical to each other in their amino acid sequences. One such isozyme, GPD1, was shown to be directly involved in osmoregulation, based on the following observations. (i) Expression of gpd1+ was regulated at the mRNA level in response to osmotic upshift. (ii) It was demonstrated that wild-type cells markedly accumulated internal glycerol under high-osmolarity growth conditions. (iii) delta gpd1 mutants, however, failed to do so even in a high-osmolarity medium, and thus exhibited an Osms phenotype. On the other hand, the gpd2+ gene was constitutively expressed at a particular low level, regardless of the osmolarity of the medium.

Gene activation by the Escherichia coli positive regulator OmpR: a mutational study of the DNA-binding domain of OmpR

The Escherichia coli DNA-binding protein, OmpR, is one of the best characterized of the bacterial positive regulators that enhance the transcriptional ability of RNA polymerase. OmpR, consisting of 239 amino acids, binds to specific sequences located upstream of the cognate ompC and ompF promoters. The C-terminal half of OmpR, consisting of about 120 amino acids, exhibits an inherent DNA-binding ability. To address the issue of DNA binding by OmpR, we selected a set of OmpR mutants, each of which has a single amino acid substitution in the C-terminal half of OmpR. In particular, we characterized a number of OmpR mutants which are defective in DNA binding and thereby result in an OmpF- OmpC phenotype. Among them, a putative positive control OmpR mutant was also obtained, which appears to be defective in phosphorylation-dependent transcriptional activation, but not in DNA binding. These results are discussed with general emphasis on DNA recognition by the E. coli family of OmpR-like regulatory proteins.

Glucose lowers CRP* levels resulting in repression of the lac operon in cells lacking cAMP

CRP-cAMP-dependent operons of Escherichia coli can be expressed in cells lacking functional adenylate cyclase when they carry a second-site mutation in the crp gene (crp*). It is known that the expression of these operons is repressed by glucose, but the molecular mechanism underlying this cAMP-independent catabolite repression has been a long-standing mystery. Here we address the question of how glucose inhibits the expression of beta-galactosidase in the absence of cAMP. We have isolated several mutations in the crp gene that confer a CRP* phenotype. The expression of beta-galactosidase is reduced by glucose in cells carrying these mutations. Using Western blotting and/or SDS-PAGE analysis, we demonstrate that glucose lowers the cellular concentration of CRP* through a reduction in crp* mRNA levels. The level of CRP* protein correlates with beta-galactosidase activity. When the crp promoter is replaced with the bla promoter, the inhibitory effect of glucose on crp* expression is virtually abolished. These data strongly suggest that the lowered level of CRP* caused by glucose mediates catabolite repression in cya- crp* cells and that the autoregulatory circuit of the crp gene is involved in the down-regulation of CRP* expression by glucose.

Functional analysis and DNA polymorphism of the tandemly repeated sequences in the 5'-terminal regulatory region of the human gene for thymidylate synthase

Triple tandemly repeated sequences and the corresponding complementary sequence are known to exist in the 5'-terminal regulatory region of the human gene for thymidylate synthase (TS). To examine the function of these sequences, a set of deletion mutants was prepared and used in a transient expression assay. The results showed that at least one repeated sequence and its complementary sequence were necessary for the efficient expression of the gene. As another approach to understanding the function of this unique structure, DNA polymorphism in the same region was analyzed. In addition to the TS gene with the triple tandem repeat, the TS gene with a double tandem repeat was found in genomes of normal human subjects at an estimated frequency of 19% when genomes of 21 unrelated Japanese were analyzed. The expression activity of a reporter gene linked to the promoter region of the human TS genes with the two types of repeated sequence was examined and the result showed that the expression activity of the gene with the double repeat was lower than that of the gene with the triple repeat in the transient expression assay. Thus, it appears that the unique repeated sequences in the 5'-terminal region of the human TS gene are polymorphic and contribute to the efficiency of expression of the gene.

Role of CRP in transcription activation at Escherichia coli lac promoter: CRP is dispensable after the formation of open complex

The role of cAMP receptor protein (CRP) in transcription activation at the Escherichia coli lac promoter was investigated focusing on the steps after the formation of open complex. Although CRP binding to the lac DNA is stabilized in the ternary open complex, a high concentration of heparin dissociates CRP from the open complex without affecting the interaction between RNA polymerase and promoter, resulting in a binary complex. The release of CRP is directly shown by Western blotting and DNase I footprinting. The binary complex exhibits a slightly increased gel mobility compared to the ternary complex. The binary complex retains the characteristics of the open complex in footprinting pattern which is essentially identical with that of the open complex of the lac UV5 promoter. The binary complex is competent for transcription. These results indicate that CRP is not necessary for the maintenance of active open complex. In addition, the removal of CRP does not increase the production of abortive RNAs. We conclude that the contact between CRP and RNA polymerase is not essential for transcription activation after the formation of the open complex at the lac promoter. In other words, the role of CRP in the lac promoter is restricted to the steps up to the formation of open complex.

Nuclear magnetic resonance study of complexes between CRP and its 22- and 28-base-pair operators

The binding of the cAMP receptor protein (CRP) to the portion of the lac promoter comprising the core of the CRP recognition sequence has been investigated. The effect of the binding of CRP to the symmetrical 22- and 28-base-pair operators was investigated by 1H NMR. The binding of cAMP*CRP to the 22mer DNA did not bring about any changes in the chemical shift values of the imino proton resonances of the DNA, but did cause selective line broadening of the imino proton resonances of specific base pairs (TA 4, GC 5). These base pairs are contained in the motif 5'(TGTGA)3', which is thought to be the region crucial to interaction with the CRP. The binding of cAMP*CRP to the 28mer DNA brought about large changes in the imino proton resonances that seem to be induced by DNA bending. Therefore it seems likely that CRP requires DNA longer than a 22mer to bend it. We also used a C-terminal protease-digested CRP (CRPcy) in a DNA-binding experiment. The binding of cAMP*CRPcy to the 28mer DNA did not induce bending. These results indicate that the C-terminal region of CRP participates in DNA binding and is important for DNA bending.

Molecular genetic analysis of a female patient with pyruvate dehydrogenase deficiency: detection of a new mutation and differential expression of mutant gene product in cultured cells

A new 18 bp insertion mutation in the gene for the alpha subunit of pyruvate dehydrogenase (E1 alpha) was found in a female patient with congenital lactic acidaemia. Cultured skin fibroblasts and Epstein-Barr virus-transformed lymphoblastoid cells from this patient showed decreased and normal pyruvate dehydrogenase complex (PDHC) activity, respectively. This 18 bp insertion was a de novo mutation, because it was not present in her parents. Although this female patient was heterozygous for the normal and the mutant alleles, 97% of cultured skin fibroblasts expressed the mutant allele, while 100% of cultured lymphoblastoid cells, 94% of peripheral blood lymphocytes and 98% of IL-2-activated T-cells expressed the normal allele. These results suggest that in this patient the X chromosome containing the normal allele was predominantly inactivated in fibroblasts and the X chromosome containing the mutant allele was predominantly inactivated in lymphocytes. The diagnosis of E1 alpha deficiency is usually established by measurement of PDHC activity and the level of immunoreactive proteins. However, these methods are not sufficient to diagnose the disorder in female patients with E1 alpha deficiency due to differential inactivation of the X chromosome. Therefore, it is necessary to develop a new method to firmly establish the diagnosis of E1 alpha deficiency.

Gene activation by the Escherichia coli positive regulator, OmpR. Phosphorylation-independent mechanism of activation by an OmpR mutant

In Escherichia coli, expression of the major outer membrane proteins, OmpC and OmpF, is regulated through the functions of OmpR and EnvZ at the transcriptional level in response to the medium osmolarity. OmpR is the crucial activator that helps RNA polymerase to efficiently trigger ompC and ompF transcription. This OmpR function is modulated by phosphorylation mediated by the cognate sensory kinase, EnvZ. Phosphorylation at the N-terminal domain of OmpR results in substantial enhancement of the DNA-binding ability of the C-terminal domain, thereby allowing the activation of ompC and ompF transcription by OmpR. Here we isolated an OmpR mutant which lacks the N-terminal half, but can enhance transcription in vivo. This novel type of OmpR mutant was revealed to have a single amino acid replacement of Gly227 to Cys. The newly-introduced-Cys residue allows OmpR molecules to form a stable dimer in vitro without the help of the N-terminal half. This altered C-terminal half is able to bind efficiently and specifically to the cognate DNA in vitro. It can function as an activator for ompC transcription in vitro in a phosphorylation-independent manner. These results suggest that the putative activator domain of OmpR, together with the DNA-binding domain, is most likely located in the C-terminal half. They also suggested that the phosphorylation of OmpR may not be essential for gene activation per se.

Mechanism of gene activation by the Escherichia coli positive regulator, OmpR: a mutant defective in transcriptional activation

The OmpR protein is an activator specific for the E. coli ompC and ompF genes. This protein functions in a phosphorylation-dependent manner through a presumed interaction with RNA polymerase. In this study we isolated OmpR mutants which were suggested to be defective for transcriptional activation, but not for DNA binding. Two such mutants, that we isolated, have a single amino acid alteration at positions 131 [P131S], and 179 [P179L], respectively, of OmpR, comprising 239 amino acids. These altered amino acids in OmpR may be implicated, directly or indirectly, in the presumed RNA polymerase/OmpR interaction that is important for transcriptional activation.

A novel gene whose expression is regulated by the response-regulator, SphR, in response to phosphate limitation in Synechococcus species PCC7942

In Synechococcus species PCC7942, the production of a subset of proteins is induced when it is grown in a phosphate-limited medium. We previously suggested that a pair of cyanobacterial two-component regulatory proteins, SphS (sensory-kinase) and SphR (response-regulator), may be involved in this particular response to phosphate limitation. Here it was found that a protein with an apparent molecular mass of 33 kDa became particularly abundant when the total cellular proteins from cells grown in a phosphate-limited medium were analysed by SDS-PAGE. A deletion mutant lacking both the sphS and the sphR genes failed to produce this 33 kDa protein in response to phosphate limitation. Thus it was reasonable to assume that this protein is a member of the group of proteins involved in the Synechococcus phosphate regulatory circuit (hence, it was named SphX). The SphX protein was purified to near homogeneity, and the corresponding structural gene was cloned. The determined nucleotide sequence revealed that the sphX gene encodes a novel protein with a calculated molecular mass of 36,374 Da, which was demonstrated to be located in the cytoplasmic membrane. Structural features of the sphX promoter were then clarified by determining its transcription start site, from which transcription was triggered in response to phosphate limitation. Furthermore, the putative response-regulator, SphR, was demonstrated to bind to the upstream region of the sphX promoter by means of in vitro DNase I footprinting. From these results, we conclude that the sphX gene is a member of the Synechococcus phosphate regulatory circuit, in which the two signal-transduction components, SphS and SphR, are crucially involved as transcriptional regulators. The SphX protein may play a role in phosphate assimilation in Synechococcus.

Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene

Glucose causes catabolite repression by lowering the intracellular levels of both cAMP and cAMP receptor protein (CRP) in Escherichia coli. The molecular mechanism underlying the down-regulation of CRP by glucose has been investigated. We show that glucose lowers the level of crp mRNA without affecting its stability. Replacement of the crp promoter with the bla promoter almost completely abolishes the glucose-mediated regulation of crp expression. Only a slight reduction in the crp expression by glucose is observed in cya- or crp- strains, suggesting that a CRP-cAMP complex is needed for this regulation. We previously showed that transcription of the crp gene is regulated both negatively and positively. Positive autoregulation of crp is caused by the binding of CRP-cAMP to the CRP binding site II located upstream of the crp promoter. Here we show that disrupting the CRP binding site II essentially eliminates the down-regulation of crp expression by glucose. We conclude that the autoregulatory circuit of the crp gene plays a key role in the down-regulation of CRP by glucose.

The sphR product, a two-component system response regulator protein, regulates phosphate assimilation in Synechococcus sp. strain PCC 7942 by binding to two sites upstream from the phoA promoter

In the photosynthetic cyanobacterium Synechococcus sp. strain PCC 7942, the sphS and sphR genes were previously suggested to encode a typical pair of two-component signal transduction proteins. A deletion mutant strain lacking these genes failed to exhibit induction of alkaline phosphatase, the phoA gene product, in response to phosphate limitation in the medium. The SphR protein was overexpressed in Escherichia coli and then purified to near homogeneity. A truncated form of the SphS polypeptide (named SphS*) was also isolated. Here, we demonstrate that purified SphR is phosphorylated by phosphotransfer from SphS and binds to two distinct sites upstream from the phoA promoter. From these results, we conclude that the SphS and SphR proteins are directly involved in the regulation of phoA transcription in response to phosphate limitation in Synechococcus species.

A cyanobacterial gene encoding a protein with extensive homology to mammalian phosphoribosylpyrophosphate synthetase

Phosphoribosylpyrophosphate (PRibPP) is the primary precursor in the biosynthesis of purine and pyrimidine nucleotides. The synthesis of PRibPP is catalysed by a ubiquitous PRibPP synthetase in many organisms. We provide evidence that a cyanobacterium, Synechococcus sp., has a gene encoding a protein with striking homology to mammalian PRibPP synthetases.

A lowered concentration of cAMP receptor protein caused by glucose is an important determinant for catabolite repression in Escherichia coli

A decreased intracellular concentration of cAMP is insufficient to account for catabolite repression in Escherichia coli. We show that glucose lowers the amount of cAMP receptor protein (CRP) in cells. A correlation exists between CRP and beta-galactosidase levels in cells growing under various conditions. Exogenous cAMP completely eliminates catabolite repression in CRP-overproducing cells, while it does not fully reverse the effect of glucose on beta-galactosidase expression in wild-type cells. When the CRP concentration is reduced by manipulating the crp gene, beta-galactosidase expression decreases in proportion to the concentration of CRP. These findings indicate that the lowered concentration of CRP caused by glucose is one of the major factors for catabolite repression. We propose that glucose causes catabolite repression by lowering the intracellular levels of both CRP and cAMP.

Cloning of a sensory-kinase-encoding gene that belongs to the two-component regulatory family from the cyanobacterium Synechococcus sp. PCC7942

A screening method employing Escherichia coli was adopted to clone a sensory-kinase (SK)-encoding gene directly from a phylogenetically distant species, the phototrophic cyanobacterium Synechococcus sp. PCC7942. From the Synechococcus chromosomal DNA, we searched for DNA clones which are able to complement phenotypically not only an E. coli envZ mutant for the expression of ompC, but also an E. coli phoR/creC mutant for the expression of alkaline phosphatase. These E. coli genes are known to encode SK. A 0.75-kb DNA fragment was thus cloned under the control of the E. coli lac promoter carried on an E. coli plasmid vector. A larger DNA fragment encompassing an entire open reading frame was then cloned and its complete nucleotide (nt) sequence determined. The nt sequence corresponds to a gene that encodes a 43,280-Da protein of 387 amino acids with a high degree of homology to the bacterial SK. Thus, we succeeded in cloning a SK-encoding gene, which most likely functions in signal transduction in Synechococcus sp. PCC7942. Hence, the gene was designated sasA (Synechococcus adaptive-response SK A). The purified SasA protein was demonstrated in vitro to undergo autophosphorylation.