Structural and functional studies of the dnaB protein using limited proteolysis. Characterization of domains for DNA-dependent ATP hydrolysis and for protein association in the primosome

Two separable structural domains were identified in the Escherichia coli dnaB protein (Mr = 52,000) by partial proteolytic cleavage under nondenaturing conditions. The hydrolysis of dnaB protein by trypsin proceeded in two distinct stages in the presence of ATP or ADP. In the first stage, 14 amino acid residues at the NH2-terminal end were removed and dnaB protein was converted into a fragment with a molecular weight of 50,000 (Fragment I). Fragment I retained about 60% of the original activity in priming DNA replication and was fully active in DNA-dependent ATPase activity. In the second stage, Fragment I was further cleaved into two separable polypeptides with molecular weights of 33,000 (Fragment II) and 12,000 (Fragment III), respectively. Fragment II, as a hexamer, retained DNA-dependent ATPase activity comparable to the intact protein but was totally inactive in priming DNA replication. No known activity of dnaB protein was detected in Fragment III alone. NH2 termini of Fragments I and III and COOH termini of dnaB protein and Fragment II were identical indicating that Fragments III and II were located at the NH2 and COOH termini of Fragment I, respectively. These results indicate that dnaB protein is composed of at least two distinct domains. 1) Fragment III, the rigid domain, is essential for protein interaction, i.e. association with dnaC protein and primase in priming DNA replication in the primosome. 2) A 14-amino acid residue fragment, at the NH2-terminal end adjacent to Fragment III, probably required to stabilize the protein interaction involved in priming DNA replication. 3) Fragment II, the flexible COOH-terminal domain, contains the active sites for DNA binding, ATP binding, and protein oligomerization. Fragment II is cleaved by trypsin at many sites in the absence of ATP or ADP ligands. The rate of conversion of Fragment I into the yield of Fragments II and III was decreased approximately by 2 orders of magnitude by changing the ligand from ADP to the nonhydrolyzed ATP analog, adenosine 5'-O-(3-thiotriphosphate). These results indicate that the conformation of the COOH-terminal domain in the dnaB protein is stabilized by ATP or ADP. Such a nucleotide-induced conformational change was also demonstrated by circular dichroism spectroscopy. Moreover, the data suggest that the conformation of the dnaB protein complexed with adenosine 5'-O-(3-thiotriphosphate) is different from that complexed with ADP.(ABSTRACT TRUNCATED AT 400 WORDS)

Glycogen storage disease type 1b: microsomal glucose-6-phosphatase system in two patients with different clinical findings

The basic defect in glycogen storage disease (GSD) type 1b was investigated in two patients: one, (Y.S.), a severely affected infant and the other, (Y.M.), an adult with mild clinical symptoms. The enzymatic studies on liver needle biopsy specimens from the two patients indicated that glucose-6-phosphate (G-6-P) phosphohydrolase activity of the "intact microsomes" was partially deficient (20% of that in controls) in Y.M. and undetectable in Y.S. Activities of G-6-P phosphohydrolase in the disrupted microsomes of Y.S. and Y.M. are higher than those in the disrupted microsomes of controls (12.60 mumole/min/g liver in Y.S., 9.18 in Y.M. and 6.26 +/- 1.22, mean +/- S.D. in controls). Our study also shows that PPi phosphohydrolase activities of the "intact microsomes" from both patients (6.07 mumol/min/g liver in Y.S. and 5.36 in Y.M.) were greater than those of the controls (3.23 +/- 0.77 mumole/min/g wet weight liver). These results indicate that the G-6-P translocase was the locus of the defect in both patients with GSD type 1b. Clinical symptoms and enzymatic studies suggest that the clinical severity of this disorder depends on the level of residual activities of G-6-P translocase. Kinetic studies showed an abnormally high Km of the residual G-6-P translocase in Y.M., suggesting a structural gene mutation. The systematic assay method for glucose-6-phosphatase system, which requires only 15 mg of liver tissues, is also described.

Hyperphenylalaninemia due to dihydropteridine reductase deficiency: diagnosis by enzyme assays on dried blood spots

Enzymatic diagnosis of hyperphenylalaninemia due to a deficiency of dihydropteridine reductase (DHPR) has previously been made by assay on liver biopsy samples, cultured skin fibroblasts, cultured lymphoid cell lines, or peripheral leukocytes. These procedures have some disadvantages for the purpose of early diagnosis of the disease. A simple method of DHPR assay using erythrocytes or dried blood spots on filter papers is described. The mean DHPR activity erythrocytes of control subjects was 3.20 +/- 0.70 (SD) nmoles/min/mg of hemoglobin, those of two patients were undetectable, and those of obligate heterozygotes for DHPR deficiency were approximately 50% of the mean control value. The assay on erythrocytes required only a 5-microliters volume of whole blood for one test. The DHPR activities in dried blood spots on filter papers from 100 normal newborns were 5.77 +/- 1.16 nmoles/min per 5-mm diameter disc; those from normal older infants, children, and adults were 3.37 +/- 0.72 nmoles/min per disc; and those from two adolescent patients with DHPR deficiency were undetectable. No false-positive results were obtained. The stability of DHPR in dried blood on filter papers was enough to mail samples in an ordinary form to a specialist laboratory. The DHPR assay on erythrocytes of dried blood spots can be easily applied to all newborn infants with hyperphenylalaninemia detected using the Guthrie tests, and will facilitate the quick and confirmative detection of DHPR deficiency among them.

Pyruvate decarboxylase deficiency in a patient with Leigh's encephalomyelopathy

A 23-month-old boy with progressive muscular hypotonia and mental and motor deterioration was described. Four days after the admission he had a respiratory arrest and required the care in a respirator thereafter. Laboratory examinations showed metabolic acidosis and high levels of pyruvate, lactate and alanine in blood and cerebrospinal fluid. Oral administration of thiamine-HCl and lipoic acid was noneffective and he died 7 months after the admission. Autopsy findings were compatible with subacute necrotizing encephalomyelopathy (Leigh's disease). The activity of pyruvate decarboxylase in autopsy samples was not detectable and that in fibroblasts was 9% of that in control cell lines. The present study confirmed that pyruvate decarboxylase deficiency is one of the causes of Leigh's disease.

Glycogen storage disease type 1b due to a defect of glucose-6-phosphate translocase

Patients with glycogen storage disease (GSD) type 1b have shown normal activity of glucose-6-phosphatase (EC 3.1.3.9) as assayed in frozen liver, though their clinical and biochemical findings were similar to those of patients with GSD 1a (McKusick 23220) (Senior and Loridan, 1968). In 1978, we suggested that a basic defect of GSD 1b exists in the glucose-6-phosphate (G6P) transport system (Narisawa et al., 1978; Igarashi et al., 1979). Since then, there have been reports confirming our observation (Beaudet et al., 1980; Lange et al., 1980; Corbeel et al., 1981; Schaub et al., 1981). Recently, it was postulated that the G6Pase system contains a phosphate translocase which mediates the efflux of phosphate, in addition to a G6P translocase and a non-specific phosphohydrolase (Arion et al., 1980). Therefore, it is possible that GSD 1b is caused by a defect of phosphate translocase. In this paper, the basic defect in GSD type 1b was investigated in two patients; one with severe, the other with mild, clinical symptoms.

Complexes of Rep protein with ATP and DNA as a basis for helicase action

The rep protein of Escherichia coli, a helicase that unwinds duplex DNA at a replication fork (Kornberg, A., Scott, J. F., and Bertsch, L. L. (1978) J. Biol. Chem. 253, 3298-3304), forms binary complexes with ATP and with DNA, and ternary complexes with both. ATP (or dATP) is bound at a single site with a dissociation constant (KD) near 10(-7) M. Other ribonucleoside triphosphates and deoxyribonucleoside triphosphates compete for the same site with far lower affinities. The protein forms a binary complex with single-stranded DNA and with duplex DNA, each at distinctive sites. Binding to single-stranded DNA covers a stretch of approximately 20 nucleotides, destabilizes secondary structure, and facilitates reannealing of complementary single strands. Ternary complexes of rep protein with ATP and DNA are manifested by ATP hydrolysis and by binding of labeled components. Nonhydrolyzed ATP analogs are useful aids for isolation and studies of such complexes. Unlike rep protein's processive action as a helicase at a replication fork, its action on single-stranded DNA is distributive, with ATP hydrolysis accelerating dissociation of the protein from the complex. These and related studies serve as guides to understanding the multiple interactions of rep protein with its ATP and DNA ligands that enable it to unwind duplex DNA at a replication fork.

Rep protein as a helicase in an active, isolatable replication fork of duplex phi X174 DNA

Rep protein as a helicase combines its actions with those of gene A protein and single-stranded DNA binding protein to separate the strands of phi X174 duplex DNA and thereby can generate and advance a replication fork (Scott, J. F., Eisenberg, S., Bertsch, L. L., and Kornberg, A. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 193-197). Tritium-labeled rep protein is bound in an active gene A protein. phi X174 closed circular duplex supercoiled DNA complex in a 1:1 ratio. Catalytic separation of the strands of the duplex by rep protein, as measured by incorporation of tritium-labeled single-stranded DNA binding protein, requires ATP at a Km value of 8 microM, and hydrolyzes two molecules of ATP for every base pair melted. When coupled to replication in the synthesis of single-strand viral circles, a "looped" rolling-circle intermediate is formed that can be isolated in an active form containing gene A protein, rep protein, single-stranded DNA binding protein, and DNA polymerase III holoenzyme. Unlike the binding of rep protein to single-stranded DNA, where its ATPase activity is distributive, binding to the replicating fork is not affected by ATP, further suggesting a processive action linked to gene A protein. Limited tryptic hydrolysis of rep protein abolishes its replicative activity without affecting significantly its binding of ATP and its ATPase action on single-stranded DNA. These results augment earlier findings by describing the larger role of rep proteins as a helicase, linked in a complex ith other proteins, at the replication fork of a duplex DNA.

A sibling case of hyperphenylalaninemia due to a deficiency of dihydropteridine reductase: biochemical and pathological findings

Three siblings with hyperphenylalaninemia were described, who showed convulsions and severe mental retardation despite dietary control of blood phenylalanine. The cultured skin fibroblasts from two patients revealed a markedly low activity of dihydropteridine reductase. These patients showed low levels of serum folate and of 5-hydroxyindoleacetic acid and homovanillic acid in cerebrospinal fluid. The postmortem examination on one of these siblings exhibited the dysmyelination in the cerebrum and spongy lesions of the white matter in the cerebellum, pons, medulla oblongata and spinal cord. Many minute foci of calcification were found in the cerebrum, which were located in the perivascular space of the small blood vessels. Such calcification was observed on CT scanning of the brain in the other two living siblings as well.

Dihydropteridine reductase deficiency: diagnosis by leukocyte enzyme assay

An assay procedure for dihydropteridine reductase in peripheral leukocytes is described. The assay utilizes the tetrahydropterin-dependent reduction of ferri-cytochrome C in the presence of NADH and requires a smaller number of cells than assays described for cultured skin fibroblasts. Dihydropteridine reductase activity was not detectable in the peripheral leukocytes nor in the cultured skin fibroblasts from two adolescent patients with malignant hyperphenylalaninemia. The parents of the patients showed approximately 50% of normal dihydropteridine reductase activity in their peripheral leukocytes. Immunochemical experiments using antibodies against bovine liver dihydropteridine reductase suggest that normal leukocytes and skin fibroblasts contain dihydropteridine reductase which is immunologically similar to that of human liver. The present studies indicate that the determination of dihydropteridine reductase activity in peripheral leukocytes can be used to diagnose hyperphenylalaninemia due to a defect in dihydropteridine reductase.

Replication of duplex DNA of phage phi X174 reconstituted with purified enzymes

Replication of the covalently closed duplex replicative form (RF) of phage phi X174 DNA has been achieved by coupling two known enzyme systems: (i) synthesis of viral strand circles (SS) from RF, and (ii) conversion of SS to nearly complete RF (RF II). In this coupled system, activated RF (gene A . RF II complex) was a more efficient template and generated as many as 10 RF II molecules per RF input, at a rate commensurate with SS synthesis. The 11 proteins required for the two component systems were all needed in the coupled RF duplication system; no new factors were required. Single-stranded DNA binding protein was needed for RF duplication at only 4% the level needed in its stoichiometric participation in SS synthesis. In addition to RF II, more complex replicative forms appeared late in the reaction, and their possible origin is discussed.

Effect of adenosine deaminase replacement therapy on a child of adenosine deaminase deficiency with severe combined immunodeficiency disease

Enzyme replacement therapy was performed for a 1-year and 5-month old boy with adenosine deaminase deficiency disease, the first case in Japan. Irradiated fresh red blood cells were administered without any clinical improvement, but there was an increase in the peripheral lymphocytes from 300/mm3 to 1849/mm3, of which 88% had T cell marker. B lymphocytes did not bear any classes of surface immunoglobulins. The proliferative responses of these lymphocytes to phytohemagglutinin, concanavalin A, pokeweed mitogen and allogeneic cells were examined. More than two-fold increase in response to these mitogens was observed in lymphocytes after treatment as compared with responsiveness before treatment, but these responses still remained to a much lesser degree than that of lymphocytes from controls.

Clinicopathological study of soft tissue tumors

Clinical aspects of patients with soft tissue tumors encountered at the Department of Orthopaedic Surgery, Toho University over a 15 year period between 1961 and 1976 were analyzed. Accurate clinical records and histological findings were available in 91 patients, 80 of whom had benign tumors and 11 of whom had malignant ones. Recurrence was seen in 7 of the 80 patients with benign tumors. The prognosis was poor in those with malignant tumors as expected, especially in those with rhabdomyosarcoma.

Studies on polypeptide-chain-elongation factors from an extreme thermophile, Thermus thermophilus HB8. 1. Purification and some properties of the purified factors

Polypeptide chain elongation factors have been purified from an extreme thermophile, Thermus thermophilus HB8. By chromatography on a DEAE-Sephadex column, the factors were separated into two peaks; peak I contained a complex of EF-Tu and EF-Ts, while peak II was composed of EF-Tu.gdp and EF-G. These factors were subsequently purified to homogeneous states and crystallized. The EF-Tu . EF-Ts complex could be resolved into EF-Tu and EF-Ts by chromatography on a Sephadex G-200 column in the presence of 8 M guanidine-HCl. The complex could be reconstituted from EF-Tu and the renatured EF-Ts. No immunological cross-reaction was detected between EF-Tu, EF-Ts, and EF-G from T. thermophilus and the antibodies to their corresponding Escherichia coli factors. The molecular weight of EF-Tu . GDP determined by sedimentation equilibrium and sodium dodecylsulfate/polyacrylamide gel electrophoresis was 49000 and 51000 respectively. On the other hand, the molecular weight of EF-Ts was estimated as 27000 and 64000, respectively, by sodium dodecylsulfate/polyacrylamide gel electrophoresis and Sephadex gel filtration, suggesting that the protein existed probably as a dimer. The molecular weight of the EF-Tu . EF-Ts complex determined by sedimentation equilibrium and by gel filtration, was 142000 and 220000, respectively. Since the molar ratio of EF-Tu to EF-Ts in the EF-Tu . EF-Ts complex was one to one, it was suggested that the complex was composed of 2 mol each of EF-Tu and EF-Ts. The molecular weight of EF-G was estimated as 85000, 80000 and 78000 by equilibrium centrifugation, gel filtration, and sodium dodecylsulfate/polyacrylamide gel electrophoresis respectively.

Studies on polypeptide-chain-elongation factors from an extreme thermophile, Thermus thermophilus HB8. 2. Catalytic properties

Catalytic properties of the elongation factors from Thermus thermophilus HB8 have been studied and compared with those of the factors from Escherichia coli. 1. The formation of a ternary guanine-nucleotide . EF-Tu . EF-Ts complex was demonstrated by gel filtration of the T. thermophilus EF-Tu . EF-Ts complex on a Sephadex G-150 column equilibrated with guanine nucleotide. The occurrence of this type of complex has not yet been proved with the factors from E. coli. 2. The dissociation constants for the complexes of T. thermophilus EF-Tu . EF-Ts with GDP and GTP were 6.1 x 10(-7) M and 1.9 x 10(-6) M respectively. On the other hand, T. thermophilus EF-Tu interacted with GDP and GTP with dissociation constants of 1.1 x 10(-9) M and 5.8 x 10(-8) M respectively. This suggests that the association of EF-Ts with EF-Tu lowered the affinity of EF-Tu for GDP by a factor of about 600 and facilitated the nucleotide exchange reaction. 3. Although the T. thermophilus EF-Tu . EF-Ts complex hardly dissociates into EF-Tu and EF-Ts, a rapid exchange was observed between free EF-Ts and the EF-Tu . EF-Ts complex using 3H-labelled EF-Ts. The exchange reaction was independent on the presence or absence of guanine nucleotides. 4. Based on the above findings, an improved reaction mechanism for the regeneration of EF-Tu . GTP from EF-Tu . GDP is proposed. 5. Studies on the functional interchangeability of EF-Tu and EF-Ts between T. thermophilus and E. coli has revealed that the factors function much more efficiently in the homologous than in the heterologous combination. 6. T. thermophilus EF-Ts could bind E. coli EF-Tu to form an EF-Tu (E. coli) . EF-Ts (T. thermophilus hybrid complex. The complex was found to exist in a dimeric form indicating that the property to form a dimer is attributable to T. thermophilus EF-Ts. On the other hand, no stable complex between E. coli EF-Ts and T. thermophilus EF-Tu has been isolated. 7. The uncoupled GTPase activity of T. thermophilus EF-G was much lower than that of E. coli EF-G. T. thermophilus EF-G formed a relatively stable binary EF-G . GDP complex, which could be isolated on a nitrocellulose membrane filter. The Kd values for EF-G . GDP and EF-G . GTP were 6.7 x 10(-7) M and 1.2 x 10(-5) M respectively. The ternary T. thermophilus EF-G . GDP . ribosome complex was again very stable and could be isolated in the absence of fusidic acid. The stability of the latter complex is probably the cause of the low uncoupled GTPase activity of T. thermophilus EF-G.

Studies on polypeptide-chain-elongation factors from an extreme thermophile, Thermus thermophilus HB8. 3. Molecular properties

Molecular properties of the polypeptide chain elongation factors from Thermus thermophilus HB8 have been investigated and compared with those from Escherichia coli. 1. As expected, the factors purified from T. thermophilus were exceedingly heat-stable. Even free EF-Tu not complexed with GDP was stable after heating for 5 min at 60 degrees C. 2. GDP binding activity of T. thermophilus EF-Tu was also stable in various protein denaturants, such as 5.5 M urea, 1.5 M guanidine-HCl, and 4 M LiCl. 3. Amino acid compositions of EF-Tu and EF-G from T. thermophilus were similar to those from E. coli. On the other hand, amino acid composition of T. thermophilus EF-Ts was considerably different from that of E. coli EF-Ts. 4. In contrast to E. coli EF-Tu, T. thermophilus EF-Tu contained no free sulfhydryl group, but one disulfide bond. The disulfide bond was cleaved by sodium borohydride or sodium sulfite under native conditions. The heat stability of the reduced EF-Tu . GDP, as measured by GDP binding activity, did not differ from that of the untreated EF-Tu . GDP. 5. T. thermophilus EF-Ts contained, in addition to one disulfide bond, a sulfhydryl group which could be titrated only after complete denaturation of the protein. 6. Under native conditions one sulfhydryl group of T. thermophilus EF-G was titrated with p-chloromercuribenzoate, while the rate of reaction was very sluggish. The sulfhydryl group appears to be essential for interaction with ribosomes, whereas the ability to form a binary GDP . EF-G complex was not affected by its modification. The protein contained also one disulfide bond. 7. Circular dichroic spectra of EF-Tu from T. thermophilus and E. coli were very similar. Binding of GDP or GTP caused a similar spectral change in both. T. thermophilus and E. coli EF-Tu. On the other hand, the spectra of T. thermophilus EF-G and E. coli EF-G were significantly different, the content of ordered structure being higher in the former as compared to the latter.

Conformational transition of polypeptide chain elongation factor G as determined by electron spin resonance

The conformational transition of the polypeptide chain elongation factor G (EF-G) induced by interaction with guanine nucleotide has been investigated by means of the spin-labeling technique. Various spin-label probes were attached specifically to the sulfhydryl group of the protein that is essential for binding to ribosomes, and the effects of these ligands on the electron spin resonance (ESR) spectra were examined. It was found that the ESR spectra of EF-G labeled with nitroxide maleimide reagents were modified by the addition of various guanine nucleotides such as GDP, GTP and, to a lesser extent, by Gpp(NH)p and Gpp(CH2)p, indicating that conformational changes accompany the binding of nucleotide ligand. However, the ESR spectra of labeled EF-G-GDP and EF-G-GTP were almost identical. On the other hand, when EF-G was labeled with nitroxide iodoacetamide reagents, a clear difference in the ESR spectra of EF-G-GDP and EF-G-GTP derivatives was observed. In this case, the spectral shape of the spin-labeled EF-G in the presence of GTP or its analogs, Gpp(NH)p or Gpp(CH2)p, was quite similar to that of free, unliganded EF-G derivative. These results, together with those previously obtained using hydrophobic probes (Arai, Arai, & Kaziro (1975) J. Biochem. 78, 243-246) demonstrate the existence of an EF-G-guanine nucleotide binary complex. They also indicate that there is a substantial difference in conformation between free EF-G, EF-G-GDP, and EF-G-GTP near the active site essential for interaction with ribosomes.

Formation of a binary complex between elongation factor G and guanine nucleotides

The interaction of the polypeptide chain elongation factor G (EF-G) from E. coli with guanine nucleotides was investigated using the hydrophobic dye, 1-anilino-8-naphthalensulfonic acid. It was found that the fluorescence intensity of the hydrophobic dye elicited in the presence of EF-G was diminished markedly by addition of GTP, and to a lesser extent, by addition of GDP. Direct evidence for the formation of the binary complexes, EF-G-GTP and EF-G-GDP, was provided by gel filtrations of EF-G on Sephadex G-25 columns equilibrated with buffers containing radioactive GTP and GDP, respectively.

Mechanism of the ribosome-dependent uncoupled GTPase reaction catalyzed by polypeptide chain elongation factor G

At low NH4-+ concentrations, 50S ribosomal subunits from E. coli were fully active in the absence of 30S ribosomal subunits, in forming a complex with the polypeptide chain elongation factor G (EF-G) and guanine nucleotide (ternary complex formation), and also in supporting EF-G dependent hydrolysis of GTP (uncoupled GTPase reaction). However, both activities were markedly inhibited on increasing the concentration of the monovalent cation, and at 160 mM NH4-+, the optimal concentration for polypeptide synthesis in a cell-free system, almost no activity was observed with 50S ribosomes alone. It was found that the inhibitory effect of NH4-+ was reversed by addition of 30S subunits. Thus, at 160 mM NH4-+, only 70S ribosomes were active in supporting the above two EF-G dependent reactions, whereas at 20 mM NH4-+, 50S ribosomes were almost as active as 70S ribosomes. Kinetic studies on inhibition by NH4-+ of the formation of 50S ribosome-EF-G-guanine nucleotide complex, indicated that the inhibition was due to reduction in the number of active 50S ribosomes which were capable of interacting with EF-G and GTP at higher concentrations of NH4-+. The inhibitory effects of NH4-+ on ternary complex formation and the uncoupled GTPase reaction were markedly influenced by temperature, and were much greater at 0 degrees than at 30 degrees. A conformational change of 50S subunits through association with 30S subunits is suggested.

Oxidized and reduced nicotinamide adenine dinucleotide phosphate levels of plants hardened and unhardened against chilling injury

Pea plants (Pisum sativum L. var. Alaska) subjected to low temperature (5 degrees ) in the light acquired resistance against chilling injury.Unhardened plants maintained high NADP and low NADPH levels during illumination at 25 degrees but hardened plants had low NADP and high NADPH levels in the light. When the unhardened plants were transferred to the dark room at 25 degrees , their NADPH levels decreased immediately. On the other hand, hardened plants maintained a high NADPH level for a few hours even in the dark.