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J P Raffin

Publications and source records attributed to J P Raffin.

At least 19 recordsLinked to original sources
PubMed2001

Characterization of two DNA polymerases from the hyperthermophilic euryarchaeon Pyrococcus abyssi.

The complete genome sequence of the hyperthermophilic archaeon Pyrococcus abyssi revealed the presence of a family B DNA polymerase (Pol I) and a family D DNA polymerase (Pol II). To extend our knowledge about euryarchaeal DNA polymerases, we cloned the genes encoding these two enzymes and expressed them in Escherichia coli. The DNA polymerases (Pol I and Pol II) were purified to homogeneity and characterized. Pol I had a molecular mass of approximately 90 kDa, as estimated by SDS/PAGE. The optimum pH and Mg(2+) concentration of Pol I were 8.5-9.0 and 3 mm, respectively. Pol II is composed of two subunits that are encoded by two genes arranged in tandem on the P. abyssi genome. We cloned these genes and purified the Pol II DNA polymerase from an E. coli strain coexpressing the cloned genes. The optimum pH and Mg(2+) concentration of Pol II were 6.5 and 15-20 mm, respectively. Both P. abyssi Pol I and Pol II have associated 3'-->5' exonuclease activity although the exonuclease motifs usually found in DNA polymerases are absent in the archaeal family D DNA polymerase sequences. Sequence analysis has revealed that the small subunit of family D DNA polymerase and the Mre11 nucleases belong to the calcineurin-like phosphoesterase superfamily and that residues involved in catalysis and metal coordination in the Mre11 nuclease three-dimensional structure are strictly conserved in both families. One hypothesis is that the phosphoesterase domain of the small subunit is responsible for the 3'-->5' exonuclease activity of family D DNA polymerase. These results increase our understanding of euryarchaeal DNA polymerases and are of importance to push forward the complete understanding of the DNA replication in P. abyssi.

Amino Acid Sequence↗
PubMed2000

The PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase delta.

We have cloned the gene encoding proliferating cell nuclear antigen (PCNA) from the hyperthermophilic euryarchaeote Thermococcus fumicolans (Tfu). Tfu PCNA contains 250 amino acids with a calculated M(r) of 28,000 and is 26% identical to human PCNA. Next, Tfu PCNA was overexpressed in Escherichia coli and it showed an apparent molecular mass of 33.5 kDa. The purified Tfu PCNA was tested first with recombinant Tfu DNA polymerase I (Tfu pol) and second with calf thymus DNA polymerase delta (pol delta). When tested with the homologous Tfu pol on bacteriophage lambda DNA, large amounts of Tfu PCNA were required to obtain two- to threefold stimulation. Surprisingly, however, Tfu PCNA was much more efficient than human PCNA in stimulating calf thymus pol delta. Our data suggest that PCNA has been functionally conserved not only within eukaryotes but also from hyperthermophilic euryarchaeotes to mammals.

Amino Acid Sequence↗
PubMed2000

Coordinated changes of adenylate energy charge and ATP/ADP: use in ecotoxicological studies.

The coordinated variations of the adenylate energy charge and ATP/ADP ratio were modeled and a function that depends on the numerical value of the adenylate kinase-catalyzed reaction has been derived. The model allows sensitive detection of the effects of xenobiotics on adenylate kinase and its cellular environment and offers a robust estimation of the direct or indirect effects of pollutants on the adenylate kinase system: data obtained in laboratory studies on shrimp exposed to cadmium and in field studies on oysters either exposed to polychloro-biphenyl compounds or located in a heavily polluted area indicate that xenobiotics affect the adenylate kinase reaction directly or by changing its cellular environment. These results demonstrate that application of the model to the treatment of ecotoxicological data allows detection of energetic changes that would have been missed by simple analysis of the usual energetic parameters, and should overcome problems encountered in using energetic parameters during assessment of pollution monitoring.

Adenosine Diphosphate↗
PubMed2000

Purification and characterization of a new DNA polymerase modulator from the hyperthermophilic archaeon Thermococcus fumicolans.

During purification of the native alpha-like DNA polymerase from the hyperthermophilic euryarchaeote Thermococcus fumicolans, two activity peaks were detected after cation-exchange chromatography. One of the peaks (Ppol) was identified as the T. fumicolans DNA polymerase and the second peak (Pf) was shown to contain a factor which increased the DNA polymerase activity over 70-fold when tested with activated calf thymus DNA as substrate. The factor also stimulated nucleotide incorporation when using primed lambda DNA as substrate (approximately 8-fold), while inducing a very large decrease in the turnover rate of the enzyme. The factor, therefore, maximizes the ability of the DNA polymerase to synthesize small fragments, which is compatible with DNA repair or lagging strand DNA replication.

Animals↗
PubMed1999

Cloning and over-expression in Escherichia coli of the gene encoding NADPH group III alcohol dehydrogenase from Thermococcus hydrothermalis. Characterization and comparison of the native and the recombinant enzymes.

A NADP-dependent group III alcohol dehydrogenase (ADH) was purified from the hyperthermophilic strictly anaerobic archaeon Thermococcus hydrothermalis, which grows at an optimum temperature of 85 degrees C and an optimum pH of 6. The gene encoding this enzyme was cloned, sequenced, and over-expressed in Escherichia coli. The recombinant enzyme was purified, characterized and compared with the native form of the enzyme. The enzyme structure is pH-dependent, being a 197-kDa tetramer (subunit of 45 kDa) at pH 10.5, the pH optimum for alcohol oxidation, and a 80.5-kDa dimer at pH 7.5, the pH optimum for aldehyde reduction. The kinetic parameters of the enzyme show that the affinity of the enzyme is greater for the aldehyde substrate and NADPH cofactor, suggesting that the dimeric form of the enzyme is probably the active form in vivo. The ADH of T. hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. T. hydrothermalis ADH is the first Thermococcale ADH to be cloned and overproduced in a mesophilic heterologous expression system, and the recombinant and the native forms have identical main characteristics.

Alcohol Dehydrogenase↗
PubMed1996

Modelization of coordinated changes of adenylate energy charge and ATP/ADP ratio: application to energy metabolism in invertebrate and vertebrate skeletal muscle.

Regulation of the coordinated adenylate energy charge (AEC) and ATP/ADP ratio variations was studied with the aid of computer-made simulations. When the equilibrium state for the adenylate kinase-catalyzed reaction has been assumed, the function describing the coordinated AEC and ATP/ADP ratio variations can be simply derived from the formulas describing these 2 parameters. The model was used to analyze incidence of AMP deamination in the coordinated regulation of cellular energy metabolism.

AMP Deaminase↗
PubMed1994

Amplification of myoadenylate deaminase during evolution. A comparative study.

Myoadenylate deaminase activity was measured, by using a specific assay technique, in a wide range of animal species, including four invertebrates, one cyclostome, 13 chondrosteans, one teleost and one mammal. The results are discussed considering the known genetic events that have lead to the appearance of the higher vertebrates myoadenylate deaminase molecular form. It is proposed that, during the extensive gene duplication that occurred in the beginning of vertebrate evolution, genetic modification of the myoadenylate deaminase molecule took place in at least two different taxa: the one that evolved to rajiform elasmobranch fishes and the other to the land vertebrates.

AMP Deaminase↗
PubMed1993

Detection of phosphodiester resonances in the perfused heart from vertebrate ectotherms with nuclear magnetic resonance.

In vivo 31P NMR has been used to characterize the phosphorylated compounds present in the heart from vertebrate ectotherms. The perfused hearts from all animals experimented showed prominent resonances between the inorganic phosphate and phosphocreatine peaks. The pattern of these compounds was found to be different in the heart of the different species. As shown by 31P and proton NMR of perchloric extracts, the chemical shift of some of the compounds was characteristic of glycerophosphorylcholine, glycerophosphorylinositol, phosphorylcholine, phosphorylserine, phosphorylethanolamine and phosphoenolpyruvate. The non-identified resonances were found to be phosphodiesters, as demonstrated by alkaline phosphatase hydrolysis. The physiological significance of these high levels of phosphodiesters in the heart from vertebrate ectotherms is discussed.

Alkaline Phosphatase↗
PubMed1991

A specific AMP deaminase assay and its application to tissue homogenates.

1. A rapid method for the determination of AMP and IMP by HPLC is described. 2. Its application to the assay of AMP deaminase allows the specific determination of enzyme activities in crude extracts, eliminating any interference by other enzyme systems (5'-nucleotidase and adenosine deaminase). 3. The method was routinely used for the determination of the AMP deaminase activity in the muscles of marine animals.

AMP Deaminase↗
PubMed1991

Comparative studies on heart and skeletal muscle AMP-deaminase from rainbow trout (Salmo gairdneri).

1. AMP-deaminases from fish heart and skeletal muscle have been isolated, and their kinetic and regulatory properties compared. 2. The results obtained indicate that the enzyme variants present in fish heart and skeletal muscle, in contrast to their mammalian counterparts, show very similar chromatographic, kinetic and regulatory characteristics. 3. The above may reflect evolutionary programmed differences in AMP-deaminase gene(s) organization.

AMP Deaminase↗
PubMed1987

In vivo 31P NMR in crustacean muscles: fatigue and recovery in the tail musculature from the prawn Palaemon elegans.

31P NMR has been used to observe the in vivo phosphometabolite concentrations in the tail musculature from the prawn Palaemon elegans, at rest and after escape swimming and subsequent recovery. Muscular fatigue corresponds to a 60% breakdown of phosphoarginine, and a 45% increase of sugar phosphates. The pHi fell from 7.10 to 6.86. During recovery, the sugar phosphates and arginine phosphate are replenished after 20 minutes. The ATP concentration did not change throughout the experiment. The pHi was restored within 20 minutes.

Adenosine Triphosphate↗
PubMed1987

Regulatory properties of pigeon heart muscle AMP deaminase.

The kinetic and regulatory properties of purified pigeon heart muscle AMP deaminase were investigated. In the presence of 100 mM potassium chloride, the enzyme exhibited a slightly sigmoidal type of kinetics. Addition of ATP to the incubation medium changed the reaction rate versus substrate concentration plot into a hyperbolic one, and caused a decrease of the half-saturation constant (S0.5). ADP presence caused the change of both the S0.5 and Vmax parameters, exerting either an activating or inhibitory effect, depending upon the substrate concentration. Orthophosphate inhibited the enzyme at all substrate concentrations, increasing the value of the S0.5 parameter. In the presence of ATP, ADP and orthophosphate, added to the incubation medium at approximately physiological concentrations, pigeon heart AMP deaminase still seems to preserve its activated form. Active long chain fatty acids clearly inhibited enzyme activity even at micromolar concentrations. Interpretation of the kinetic data in terms of the allosteric theory of Monod et al. (1965, J. Mol. Biol. 12, 88-118) indicates that heart muscle AMP deaminase may operate as a functionally active dimer.

AMP Deaminase↗
PubMed1986

Activation of trout gill AMP deaminase by an endogenous proteinase--I. Effects on the regulatory properties of the enzyme.

Some regulatory properties of trout gill AMP deaminase were determined in crude extracts, before or after modification of the enzyme by the endogenous proteinase. After proteolysis, the optimal concentrations for activation by sodium and potassium were shifted from 10 to 75 mM, resulting in a large increase of enzyme activity near the physiological potassium concentration. This activation was shown to be the consequence of a much lower sensitivity of AMP deaminase to inhibition by increasing ionic strength. The modified enzyme was also less sensitive to modifications of pH and to inhibition by physiological concentrations of inorganic phosphate. When all these modifications were considered, limited proteolysis of gill AMP deaminase resulted in a 40 times increase of enzyme activity under in vivo conditions.

AMP Deaminase↗
PubMed1986

Activation of trout gill AMP deaminase by an endogenous proteinase--II. Modification of the properties of the enzyme during starvation, pollution and salinity changes.

The relative amount of modified AMP deaminase has been determined by taking advantage of the different effects of monovalent cations on the two enzymatic forms. When trout were subjected to different environmental perturbations (starvation, pollution of the water by a pesticide, transfer to sea water or reverse transfer to fresh water), modified AMP deaminase could be detected in the gill extracts. Depending on the nature of the stress and the period of experimentation, 8 to 100% of the enzyme had been modified by limited proteolysis. As a consequence of the much higher activity of the proteolyzed AMP deaminase form, a 2 to 12 times increase of the intracellular AMP deaminase activity could be expected. At the same time, limited proteolysis will modify the regulatory properties of the enzyme, since it can be estimated that 50 to 100% of the enzyme activity expressed in the cell will be an AMP deaminase form less sensitive to inhibition by inorganic phosphate and ionic strength, and to variations of the intracellular pH. Limited proteolysis will result in increased AMP deaminase activity under conditions of increased energy demand, where the concentration of inorganic phosphate is dramatically increased. The consequence should be stabilization of the adenylate energy charge.

2,4,5-Trichlorophenoxyacetic Acid↗
PubMed1986

Activation of trout gill AMP deaminase by an endogenous proteinase--III. Comparative studies on the gill AMP deaminase from different fresh water and sea water teleosts.

The effects of monovalent cations and inorganic phosphate, on gill AMP deaminase, were compared in different fresh water and sea water stenohaline and euryhaline Teleosts. Generally, sea water species displayed a lower sensitivity to these effectors than fresh water species. During salinity changes, the sensitivity of gill AMP deaminase to cations and phosphate were modified proportionally to the tolerance of a given species to variations of environmental salinity. In particular, these parameters were modified in the weak euryhaline, Salmo gairdneri, but not in the real euryhaline, Anguilla anguilla. In sea water adapted trout, the appearance of a modified AMP deaminase form, with similar properties to that found in sea water species, is suggested. When compared with the conclusions from the preceeding papers [Raffin (1986) Comp. Biochem. Physiol. 85B, 157-162; 85B, 163-171], the results suggest that modification of gill AMP deaminase by limited proteolysis should be a rather general adaptation mechanism to stress.

AMP Deaminase↗
PubMed1985

Regulation of trout gill AMP deaminase by lipid bilayers. Effects of phospholipid composition and temperature.

Trout gill AMP deaminase is inhibited by liposomes made of synthetic phosphatidylcholines containing higher saturated fatty acids. A preincubation of 1 hr, at 4 degrees C, was necessary to obtain the maximal effect. At 4 or 25 degrees C, these phospholipids modified essentially the substrate affinity of the enzyme by increasing the Michaelis constant proportionally to the length of the fatty acid chain. At 13 degrees C, the liposomes decreased the Hill coefficient also, thus inducing a negative cooperativity. Natural phosphatidylcholine and phosphatidylserine were without significant effect on gill AMP deaminase while natural sphingomyelin exhibited a similar effect to that shown in the presence of synthetic phosphatidylcholines. These results are discussed in relation to a possible effect of sphingomyelins in vivo.

AMP Deaminase↗
PubMed1984

Properties of the lysosomes from liver and gill of rainbow trout, Salmo gairdnerii R.: effect of starvation, salinity and 2,4,5-T.

Three isolation procedures were used to test the labilization of the lysosomes after adaptation of the animals to seawater, starvation or acute and chronic treatments with 2,4,5-T, an organochlorine pesticide. The lysosomes from gill and liver had different properties with respect to their resistance to osmotic and mechanical shocks, or treatments with digitonin. Starvation induced a significant labilization of the lysosomes in liver, but not in gill. Salinity changes were without effect on the stability of the gill lysosomes, but induced an increase of the specific activity of the lysosomal enzyme beta-acetylglucosaminidase. Acute treatments with 2,4,5-T increased lysosomal fragility in the gill but not in the liver, while chronic treatments with this herbicide increased lysosomal lability in the two tissues. Liver lysosomes were much more susceptible to in vitro treatments with 2,4,5-T than gill lysosomes. The results are discussed with respect to the different functions of gill and liver, their exposure to the environment, and the possible discrimination between different lysosomal populations.

2,4,5-Trichlorophenoxyacetic Acid↗