Differences in biochemical properties of two 5′-nucleotidases from deep- and shallow-sea Shewanella species under various harsh conditions

Deep-sea Shewanella violacea 5′-nucleotidase (SVNTase) activity exhibited higher NaCl tolerance than that of a shallow-sea Shewanella amazonensis homologue (SANTase), the sequence identity between them being 70.4%. Here, SVNTase exhibited higher activity than SANTase with various inorganic salts, similar to the difference in their NaCl tolerance. In contrast, SVNTase activity decreased with various organic solvents, while SANTase activity was retained with the same concentrations of the solvents. Therefore, SVNTase is more robust than SANTase with inorganic salts, but more vulnerable with organic solvents. As to protein stability, SANTase was more stable against organic solvents and heat than SVNTase, which correlated with the differences in their enzymatic activities. We also found that SANTase retained higher activity for three weeks than SVNTase did in the presence of glycerol. These findings will facilitate further application of these enzymes as appropriate biological catalysts under various harsh conditions.

Abbreviations: NTase: 5′-nucleotidase; SANTase: Shewanella amazonensis 5′-nucleotidase; SVNTase: Shewanella violacea 5′-nucleotidase; CD: circular dichroism     

Properties of a 5′-nucleotidase purified from mouse liver plasma membranes

1. Extraction of a mouse liver plasma-membrane fraction with a detergent buffer, N-dodecylsarcosinate-Tris buffer (sarcosyl-Tris buffer), solubilized 90% of the protein and 70% of the 5'-nucleotidase activity. 2. The proteins of the sarcosyl-Tris buffer extract were fractionated by a rate-zonal centrifugation in a sucrose-detergent gradient. The major protein peak sedimented ahead of phospholipids, which mainly remained in the overlay. Glycoproteins were separated ahead of the protein peak. 3. The 5'-nucleotidase activity peak was associated with 5% of the protein applied to the gradient, and contained relatively few protein bands. 4. The 5'-nucleotidase was purified further by gel filtration on Sepharose and Sephadex columns equilibrated with sarcosyl-Tris buffer, to give a single glycoprotein band on sodium dodecyl sulphate-polyacrylamide-gel electrophoresis. The purified enzyme was lipid-free. 5. Electrophoresis in polyacrylamide gels in sarcosyl-Tris buffers showed that the enzymic activity was coincident with the protein band. 6. The molecular weight suggested for the enzyme activity by gel filtration or centrifugation in sucrose gradients was 140000-150000. Sometimes, a minor enzyme peak of lower molecular weight was obtained. 7. Polyacrylamide-gel electrophoresis in sodium dodecyl sulphate indicated that as the polyacrylamide concentration was increased from 5 to 15%, the apparent molecular weight of the enzyme decreased from 130000 to 90000. 8. The evidence that 5'-nucleotidase is composed of two active and similar, if not identical, glycoprotein subunits and the role of detergent in effecting the separation of membrane proteins and glycoproteins are discussed. 9. Substrate requirements, pH optima and the nature of inhibition by an analogue of adenosine diphosphate are reported.     

Characterization of a 5′-AMP binding site in purified membranes from Dictyostelium discoideum

Although D.discoideum amoebae do not bind AMP at their surface if they are not disrupted, total cell lysates display high levels of AMP binding activity specifically associated with the plasma membrane. The binding of AMP is not competed by adenosine and only poorly by ADP and ATP. The AMP binding sites have a single affinity of 0.6 μM for AMP; the association and dissociation rate constants are respectively 8×10³ sec^?1M^?1 and 4.8 ×10^?3sec^?1. The AMP binding occurs at a site distinct from the cAMP binding site and from the catalytic site of a membrane bound enzyme.     

Conservation and change in structural and 5′ flanking sequences of esterase 6 in siblingDrosophila species

Esterase 6 (Est-6/EST6) is the major β-carboxylesterase inD. melanogaster and its siblingsD. simulans andD. mauritiana. It is expressed in several tissues but its major site of expression is the sperm ejaculatory duct of the adult male. Although EST6 activity affects reproductive fitness, there are high levels of electrophoretic and activity polymorphism, at least withinD. melanogaster andD. simulans. Here we present the nucleotide sequences of anEst-6 allele and its flanking regions from each ofD. simulans andD. mauritiana and compare them with the publishedD. melanogaster sequences. As might be expected, replacement sites are significantly less divergent than exon silent sites in all comparisons, suggesting that selection is acting to maintain EST6 structure and function among the three species. Nevertheless, the ratio of the levels of replacement to silent site divergence is still much higher forEst-6 than for seven of ten other genes (including both isozyme-coding loci) for which comparable data have been published for these species. This is consistent with the high levels of EST6 electrophoretic polymorphism withinD. melanogaster andD. simulans and implies that selective constraints against amino acid change are relatively weak for EST6. By contrast, comparisons involving promotor sequences show that the level of divergence in the first 350bp 5′ of the gene is significantly lower than those for four of the six other loci for which comparable data have been published for these species. In particular, there are two perfectly conserved stretches (−1 to −158bp and −219 to −334bp) each over 100bp long included in this 350bp region. Thus the data suggest a relatively low level of selective constraint on the amino acid sequence of EST6 but a relatively high level of constraint on sequences affecting aspects of its expression.     

New violet 3,3′-bipyridyl pigment purified from deep-sea microorganism <Emphasis Type="Italic">Shewanella violacea</Emphasis> DSS12

We have purified a new violet pigment derived from Shewanella violacea DSS12 to determine its chemical structure. The pigment colored blue in tetrahydrofuran (THF) or chloroform and showed a broad absorption spectrum from 500 to 700 nm. X-ray diffraction analysis of single crystals showed that the chemical structure of this pigment was 5,5′-didodecylamino-4,4′-dihydroxy-3,3′-diazodiphenoquinone-(2,2′), containing the same chromophore as an indigoidine known as microbial blue pigment. The violet color of this pigment was due to hypsochromic shift (blue shift) caused by the side-by-side orientation of this pigment molecule, revealed by X-ray structural analyses of a single crystal. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Stability of cytochromes c′ from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure

Extremophiles - The stability of dimeric cytochrome c′ from a thermophile, as compared with that of a homologous mesophilic counterpart, is attributed to strengthened interactions around the...     

Formation of nucleoside 5′-polyphosphates from nucleotides and trimetaphosphate

Summary When solutions of nucleoside 5-phosphates and trimetaphosphate are dried out at room temperature, nucleoside 5-polyphosphates are formed. The Mg⁺⁺ ion shows a superior catalytic function in this reaction when compared with other divalent metal ions. Starting with nucleoside 5-phosphates, Mg⁺⁺ and trimetaphosphate, the predominant products in the nucleoside 5-polyphosphate series p_nN are p₄N, p₇N and P₁₀N. Nucleoside 5-diphosphates yield p₅N and p₈N, nucleoside 5-triphosphates give p₆N and p₉N. The prebiological relevance of these reactions is discussed.Abbreviations P_n (n = 1,2,3,) linear polyphosphate containing n phosphate residues - P₃! trimetaphosphate - A adenosine - U uridine - dA 2-dexyadenosine - T thymidine - P_nN nucleoside 5-polyphosphate containing n phosphate residues, e.g. with N = A and n = 4 - p₄A adenosine 5-tetraphosphate     

Bioleaching in brackish waters—effect of chloride ions on the acidophile population and proteomes of model species

High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L⁻¹ NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.     

Deuteration and Tritiation of 2′-Deoxyribonucleosides in the 5′ and 4′ Positions

Abstract

The deuterations of 2′-deoxyguanosine in the 4′ and 5′ positions have been described elsewhere (1). The starting material is the 5′-aldehyde formed by mild oxidation with N,N-dicyclohexyl carbodiimide in dimethyl sulphoxide of the fully protected nucleoside with free 5′-alcoholic function. The 5′4euteration was achieved by reduction with deuterated sodium borohydride. Incorporation of deuterium in the 4′-position was achieved v i a an enhanced keto-enol tautomerim by heating the aldehyde in 50/50 D20/pyridine, with subsequent reduction of the aldehyde with NaBH4. The 6-furanoid form was isolated from the I-lyxo by-product by reverse phase HPLC. Applied to pyrimidine 2′-deoxyribonucleosides, this method was shown to give deuterated 2′-deoxycytidine and thymidine in good yield.     

Lectin-induced inhibition of plasma membrane 5′-nucleotidase: Sensitivity of purified enzyme

To determine whether the lectin-induced inhibition of plasma membrane 5′-nucleotidase resulted from direct interaction of the lectin with the enzyme or indirectly from a membranous change due to lectin binding to other membrane glycoproteins, the enzyme was purified and its sensitivity tested in the absence of other membrane components. A 5000 fold purification was achieved by solubilization in Lubrol PX followed by gel filtration (Sephadex G-100), anion exchange (DEAE-Biogel A) and selective adsorption (hydroxylapatite) chromatography. The purified enzyme was even more sensitive to inhibition by high concentrations of concanavalin A, wheat germ agglutinin or Rincinus communis agglutinin than was the membrane-bound enzyme indicating that inhibition is due to direct binding of the lectins to the glycoprotein enzyme itself. Divalent succinyl Con A inhibited neither form of the enzyme suggesting the need for crosslinking for inhibition by the native lectin. The purified enzyme could not be activated by low concentrations of lectins which stimulated the membrane bound enzyme.     

Difference in the Cyclic Adenosine 3′,5′-Monophosphate Levels in Normal and Transformed Cells

CYCLIC 3′5′-adenosine monophosphate (cyclic AMP) regulates many physiological phenomena^1,2. Cellular morphology changes when the dibutyryl derivative of cyclic AMP is added in vitro to the nutrient media of cultured mammalian cells^3–6. Dibutyryl cyclic AMP has also been shown to restore controlled growth to transformed cells³, change the cell's surface architecture^3,7 and induce axon formation⁸ with an accompanied increase in acetylcholinesterase activity⁹ in neuroblastoma cells growing in culture. These effects suggest that the cyclic AMP moiety may have some basic regulatory action on cell growth and cell specialization.     

Cloning and sequencing of inulinase and β-fructofuranosidase genes of a deep-sea Microbulbifer species and properties of recombinant enzymes

An inulinase-producing Microbulbifer sp. strain, JAM-3301, was isolated from a deep-sea sediment. An inulin operon that contained three open reading frames was cloned and sequenced. Two of the three genes were expressed. One product was an endo-inulinase, and the other was a β-fructofuranosidase. Both enzymes worked together to effectively degrade inulin.     

Diversity and heavy metal tolerance of endophytic fungi from six dominant plant species in a Pb–Zn mine wasteland in China

The diversity and metal tolerance of endophytic fungi from six dominant plant species in a Pb–Zn mine wasteland in Yunnan, China were investigated. Four hundred and ninety-five endophytic fungi were isolated from 690 tissue segments. The endophytic fungal colonization extent and isolation extent ranged from 59 % to 75 %, and 0.42–0.93, respectively, and a positive correlation was detected between them. Stems harboured more endophytic fungi than leaves in each plant species, and the average colonization extent of stems was 82 %, being significantly higher than that of leaves (47 %) (P ≤ 0.001, chi-square test). The fungi were identified to 20 taxa in which Phoma, Alternaria and Peyronellaea were the dominant genera and the relative frequencies of them were 39.6 %, 19.0 % and 20.4 %, respectively. Metal tolerance test showed that 3.6 mM Pb²⁺ or 11.5 mM Zn²⁺ exhibited the greatest toxicity to some isolates and they did not grow on the metal-amended media. In contrast, some isolates were growth stimulated in the presence of tested metals. The isolates of Phoma were more sensitive to Zn²⁺ than the isolates of Alternaria and Peyronellaea. However, the sensitivity of isolates to Pb²⁺ was not significantly different among Phoma, Alternaria, Peyronellaea and other taxa (P > 0.05, chi-square test). Our results suggested that fungal endophyte colonization in Pb–Zn polluted plants is moderately abundant and some isolates have a marked adaptation to Pb²⁺ and Zn²⁺ metals, which has a potential application in phytoremediation in this area.     

Protein kinase activity stimulated by adenosine 3′:5′-cyclic monophosphate in synaptic-membrane fragments from ox brain. Inhibition of intrinsic activity by free and membrane-bound calcium ions

1. Cyclic AMP-stimulated protein kinase activity phosphorylating intrinsic substrates in preparations of synaptic-membrane fragments from ox cerebral cortex was examined in relation to (a) the content of membrane-bound Ca(2+) in the preparations and (b) added Ca(2+) in the assay medium. 2. Centrifugal washing of synaptic-membrane fragments with buffered ethane dioxybis(ethylamine)tetra-acetate solutions decreased bound Ca(2+) from 2.8+/-0.4 (s.d.) to 0.9+/-0.3nmol/mg of protein. In washed preparations basal protein kinase activity was increased by about 40% and the cyclic AMP-stimulated activity by about 15%. Addition of Ca(2+) in the concentration range 5-50mum to the assay medium progressively inhibited the kinase activity of the washed preparations; in this range of Ca(2+) concentration the basal activity was inhibited more than the stimulated activity. 3. In unwashed preparations concentrations of Ca(2+) above 100mum inhibited the cyclic AMP-stimulated activity more than the basal activity. 4. The inhibitory effect of several concentrations of Ca(2+) was examined in relation to cyclic AMP concentration; no evidence for competition between Ca(2+) and cyclic AMP for a site on the enzyme was observed.     

Isolation and Identification of 5′-Methylthioadenosine Sulfoxide from Human Urine

Abstract

An adenine nucleoside isolated from human urine has been identified by mass spectra and other techniques as 5′-deoxy-5′-methyl-thioadenosine sulfoxide. Elevated levels (3–5 nmols/μmol creatinine) were noted in two children with severe combined immunodeficiency.     

Continuous production of 5′-ribonucleotides from yeast RNA by hydrolysis with immobilized 5′-phosphodiesterase and 5′-adenylate deaminase

The production of 5-IMP and 5-GMP by enzymatic conversion from RNA using a continuous two packed-bed reactor was investigated. 5-Phosphodiesterase (5PD) and 5-adenylate deaminase (5AD) were immobilized in an acrylic resin to produce derivatives with about 15 U/g of support. The kinetic properties of the enzymes were described by Michaelis-Menten models: no significant differences were found in the K _m value of the free and immobilized 5AD (60 and 20 m, respectively), whereas for 5PD the K _m value was one order of magnitude higher for the immobilized enzyme (4.85 mg RNA/ml), probably due to diffusional limitations. Both enzymes remained stable after 8 h of use in a continuous packed-bed reactor whereas the half lives of the free enzymes were 193 min and 240 min at 40°C and 70°C for 5AD and 5PD, respectively. A procedure is proposed for the design of a continuous two packed-bed column process.F. Olmedo and F. Iturbe are with the Depto. de Alimentos y Biotecnologia, Facultad de Química, UNAM, México 04510, D.F., Mexico. J. Gomez-Hernández is with the Depto. de Biotecnología, UAM-1, Apdo. Postal 55-535, México 09340, D.F., Mexico. A. López-Munguía is with the Instituto de Biotecnología, Apartado Postal 510-3, Cuernavaca, Mor. 62271, Mexico     

The 5′-Nor Aristeromycin Analogues of 5′-Deoxy-5′-Methylthioadenosine and 5′-Deoxy-5′-Thiophenyladenosine

To extend the potential of 5′-noraristeromycin (and its enantiomer) as potential antiviral candidates, the enantiomers of the carbocyclic 5′-nor derivatives of 5′-methylthio-5′-deoxyadenosine and 5′-phenylthio-5′-deoxyadenosine have been synthesized and evaluated. None of the compounds showed meaningful antiviral activity.     

Inhibition of the synthesis of polyamines and macromolecules by 5′-methylthioadenosine and 5′-alkylthiotubercidins in BHK21 cells

5′-Methylthioadenosine and four 5′-alkylthiotubercidins were tested for their ability to inhibit polyamine synthesis in vitro and to decrease polyamine concentration and prevent growth of baby-hamster-kidney (BHK21) cells. 5′-Methylthioadenosine and 5′-methylthiotubercidin decreased the activity of spermidine synthase from brain to roughly the same extent, whereas brain spermine synthase was much more strongly inhibited by 5′-methylthioadenosine compared with 5′-methylthiotubercidin. These nucleoside derivatives also inhibited the growth of BHK21 cells and increased the concentration of putrescine. 5′-Methylthioadenosine decreased cellular spermine concentration, whereas 5′-methylthiotubercidin lowered the concentration of spermidine. The activities of ornithine decarboxylase and S-adenosylmethionine decarboxylase were enhanced in cells grown in the presence of 5′-methylthiotubercidin. The growth inhibition produced by these nucleoside derivatives was not reversed by exogenous spermidine or spermine. 5′-Ethylthiotubercidin, 5′-propylthiotubercidin and 5′-isopropylthiotubercidin did not appreciably inhibit spermidine or spermine synthase in vitro or decrease the cellular polyamine content, but effectively prevented the growth of BHK21 cells. All nucleoside derivatives at concentrations of 0.2–1 mm caused a rapid inhibition of protein synthesis. It is concluded that the growth inhibition produced by 5′-methylthioadenosine and 5′-alkylthiotubercidins was not primarily due to polyamine depletion but other target sites, for instance the cellular nucleotide pool, cell membranes etc. must be considered.     

Purification and properties of adenylyl sulphate:ammonia adenylyltransferase from Chlorella catalysing the formation of adenosine 5′-phosphoramidate from adenosine 5′-phosphosulphate and ammonia

Extracts of Chlorella pyrenoidosa, Euglena gracilis var. bacillaris, spinach, barley, Dictyostelium discoideum and Escherichia coli form an unknown compound enzymically from adenosine 5′-phosphosulphate in the presence of ammonia. This unknown compound shares the following properties with adenosine 5′-phosphoramidate: molar proportions of constituent parts (1 adenine:1 ribose:1 phosphate:1 ammonia released at low pH), co-electrophoresis in all buffers tested including borate, formation of AMP at low pH through release of ammonia, mass and i.r. spectra and conversion into 5′-AMP by phosphodiesterase. This unknown compound therefore appears to be identical with adenosine 5′-phosphoramidate. The enzyme that catalyses the formation of adenosine 5′-phosphoramidate from ammonia and adenosine 5′-phosphosulphate was purified 1800-fold (to homogeneity) from Chlorella by using (NH₄)₂SO₄ precipitation and DEAE-cellulose, Sephadex and Reactive Blue 2–agarose chromatography. The purified enzyme shows one band of protein, coincident with activity, at a position corresponding to 60000–65000 molecular weight, on polyacrylamide-gel electrophoresis, and yields three subunits on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis of 26000, 21000 and 17000 molecular weight, consistent with a molecular weight of 64000 for the native enzyme. Isoelectrofocusing yields one band of pI4.2. The pH optimum of the enzyme-catalysed reaction is 8.8. ATP, ADP or adenosine 3′-phosphate 5′-phosphosulphate will not replace adenosine 5′-phosphosulphate, and the apparent K_m for the last-mentioned compound is 0.82mm. The apparent K_m for ammonia (assuming NH₃ to be the active species) is about 10mm. A large variety of primary, secondary and tertiary amines or amides will not replace ammonia. One mol.prop. of adenosine 5′-phosphosulphate reacts with 1 mol.prop. of ammonia to yield 1 mol.prop. each of adenosine 5′-phosphoramidate and sulphate; no AMP is found. The highly purified enzyme does not catalyse any of the known reactions of adenosine 5′-phosphosulphate, including those catalysed by ATP sulphurylase, adenosine 5′-phosphosulphate kinase, adenosine 5′-phosphosulphate sulphotransferase or ADP sulphurylase. Adenosine 5′-phosphoramidate is found in old samples of the ammonium salt of adenosine 5′-phosphosulphate and can be formed non-enzymically if adenosine 5′-phosphosulphate and ammonia are boiled. In the non-enzymic reaction both adenosine 5′-phosphoramidate and AMP are formed. Thus the enzyme forms adenosine 5′-phosphoramidate by selectively speeding up an already favoured reaction.