Measurement of Microbial Activity and Growth in the Ocean by Rates of Stable Ribonucleic Acid Synthesis

A relatively simple and extremely sensitive technique for measuring rates of stable ribonucleic acid (RNA) synthesis was devised and applied to bacterial cultures and seawater samples. The procedure is based upon the uptake and incorporation of exogenous radiolabeled adenine into cellular RNA. To calculate absolute rates of synthesis, measurements of the specific radioactivity of the intracellular adenosine 5′-triphosphate pools (precursor to RNA) and of the total amount of radioactivity incorporated into stable cellular RNA per unit time are required. Since the rate of RNA synthesis is positively correlated with growth rate, measurements of RNA synthesis should be extremely useful for estimating and comparing the productivities of microbial assemblages in nature. Adenosine 5′-triphosphate, adenylate energy charge, and rates of stable RNA synthesis have been measured at a station located in the Columbian Basin of the Caribbean Sea. A subsurface peak in RNA synthesis (and therefore growth) was located within the dissolved oxygen minimum zone (450 m), suggesting in situ microbiological utilization of dissolved molecular oxygen. Calculations of the specific rates of RNA synthesis (i.e., RNA synthesis per unit of biomass) revealed that the middepth maximum corresponded to the highest specific rate of growth (420 pmol of adenine incorporated into RNA·day⁻¹) of all depths sampled, including the euphotic zone. The existence of an intermediate depth zone of active microbial growth may be an important site for nutrient regeneration and may serve as a source of reduced carbon for mesopelagic and deep sea environments.     

ATP Citrate Lyase from Germinating Castor Bean Endosperm: Localization and some Properties

ATP citrate lyase (EC 4.1.3.8) has been found in crude extracts from endosperm tissue of germinating castor bean and shows its maximum activity in 4- to 5-day-old seedlings. A strict requirement for coenzyme A and adenosine 5′-triphosphate was demonstrated. The pH optimum for the reaction is around 7.5. The unstable enzyme can be stabilized by freezing and addition of citrate and glycerol. (−)-Hydroxycitrate is a potent inhibitor. The molecular weight is about 400,000. The adenosine 5′-triphosphate citrate lyase is localized in the plastids, where it possibly plays a role in providing acetyl coenzyme A for lipid biosynthesis.     

Effect of Glucose and Adenosine Phosphates on Production of Extracellular Carbohydrases of Alternaria solani

Production of carbohydrases by Alternaria solani is inhibited by glucose under low growth conditions. In an enriched medium, glucose has little effect on the production of polygalacturonase and cellulase while it still suppresses production of β-glucosidase. Low levels of all three enzymes were produced in the absence of their respective substrates. Such regulation has been found with many organisms. However, far greater production of these carbohydrases occurred with additions of adenosine phosphates to the growth media. Highest stimulation of enzyme production was by adenosine 5′-phosphate. Adenosine 5′-triphosphate and cyclic 3′, 5′-adenosine monophosphate gave lesser amounts. Starvation appears to induce production of extracellular carbohydrases and adenosine 5′-phosphate may have a role in the starvation process.     

Isolation of uridine 5'-pyrophosphate glucuronic Acid pyrophosphorylase and its assay using p-pyrophosphate

A procedure was devised to detect and assay uridine 5′-pyrophosphate (UDP)-glucuronic acid pyrophosphorylase in plant extracts. Substrates are UDP-glucuronic acid and ³²P-pyrophosphate, and the ³²P-uridine 5′-triphosphate produced is selectively adsorbed to charcoal. The charcoal adsorption procedure is a modification of that used to determine ³²P-adenosine 5′-triphosphate produced by adenosine 5′-pyrophosphate glucose pyrophosphorylase, and the modification greatly improves the retention of uridine 5′-triphosphate.     

Turnip Yellow Mosaic Virus RNA as a Substrate of the Transfer RNA Nucleotidyltransferase II. Incorporation of Cytidine 5'-Monophosphate and Determination of a Short Nucleotide Sequence at the 3' End of the RNA

Turnip yellow mosaic virus (TYMV) RNA treated with snake venom phosphodiesterase accepts cytidine 5′-monophosphate and adenosine 5′-monophosphate (AMP) when it is incubated in the presence of cytidine 5′-triphosphate (CTP), adenosine 5′-triphosphate, and Escherichia coli transfer RNA nucleotidyltransferase; untreated TYMV RNA accepts only AMP. When α ³²PCTP was used for terminal labeling, the nearest neighbor analyses and the anallyses after action of various nucleases showed that the sequence of five nucleotides at the 3′ end of TYMV RNA is: pGpCpApCpC. A nuclease present in commerical preparations of snake venom phosphodiesterase leads to the fragmentation of TYMV RNA, the 3′ end of which is found in a fragment having a sedimentation constant close to 5s.     

Formation of adenosine 5'-phosphorofluoridate and the assay of adenyl cyclase in barley seeds

Barley seed (Hordeum vulgare L.) homogenates contain an apparent enzymatic activity which catalyzes the synthesis of adenosine 5′-phosphorofluoridate from magnesium-adenosine 5′-triphosphate and sodium fluoride. Formation of this compound may interfere with some adenyl cyclase assays which use fluoride as a component of the incubation medium. Neither adenyl cyclase activity nor endogenous adenosine 3′: 5′-monophosphate was detected in barley seed homogenates or extracts.     

Purification and Regulatory Properties of Fructose 1,6-Diphosphatase from Hydrogenomonas eutropha

Fructose diphosphatase of Hydrogenomonas eutropha H 16, produced during autotrophic growth, was purified 247-fold from extracts of cells. The molecular weight of the enzyme was estimated to be 170,000. The enzyme showed a pH optimum of 8.5 in both crude extracts and purified preparation. The shape of the pH curve was not changed in the presence of ethylenediaminetetraacetic acid. The enzyme required Mg²⁺ for activity. The MgCl₂ saturation curve was sigmoidal and the degree of positive cooperativity increased at lower fructose diphosphate concentrations. Mn²⁺ can replace Mg²⁺, but maximal activity was lower than that observed with Mg²⁺ and the optimal concentration range was narrow. The fructose diphosphate curve was also sigmoidal. The purified enzyme also hydrolyzed sedoheptulose diphosphate but at a much lower rate than fructose diphosphate. The enzyme was not inhibited by adenosine 5′-monophosphate but was inhibited by ribulose 5-phosphate and adenosine 5′-triphosphate. Adenosine 5′-triphosphate did not affect the degree of cooperativity among the sites for fructose diphosphate. The inhibition by adenosine 5′-triphosphate was mixed and by ribulose 5-phosphate was noncompetitive. An attempt was made to correlate the properties of fructose diphosphatase from H. eutropha with its physiological role during autotrophic growth.     

The preparation of adenosine 5′-pyrophosphate by a non-enzymic method

1. A non-enzymic method for the preparation of adenosine 5′-diphosphate is described, in which the terminal phosphate of adenosine 5′-triphosphate is transferred to methanol in the presence of hydrochloric acid. The final purified product can be obtained in 60% yield. 2. Experiments with [¹⁴C]methanol showed that no methylation of the adenosine diphosphate occurs during the reaction. 3. Confirmation that the pyrophosphate moiety of the adenosine diphosphate produced was in the 5′-position was obtained by: (a) periodate oxidation; (b) treatment with apyrase and examination of the resulting adenylic acid isomer by paper chromatography. 4. The method appears to be generally applicable to the preparation of nucleoside 5′-diphosphates from the corresponding nucleoside 5′-triphosphates.     

The mechanism of ethylene and cyanide action in triggering the rise in respiration in potato tubers

Ethylene and cyanide induce a sharp increase in respiration in potato tubers (Solanum tuberosum, var. Russet) attended by changes in the glycolytic intermediates which indicate that both gases enhance glycolysis. The level of sucrose also increases in response to both treatments. The data are taken to indicate that both cyanide and ethylene either activate or affect the link between the conventional electron transport chain and the cyanide-insensitive path. It is further proposed that this activation may well be the primary event leading to the rise in respiration. Ethylene increases the level of adenosine 5′-triphosphate and it is suggested that because of the 4- to 6-fold increase in the rate of electron flux through site I, which continues to operate in the over-all cyanide-insensitive path, the absolute levels of adenosine 5′-triphosphate will also be expected to increase in the presence of cyanide. The increase in sucrose content is considered to be the consequence of the rise in adenosine 5′-triphosphate concentration.     

Diacylglycerol kinase from suspension cultured plant cells : characterization and subcellular localization

Diacylglycerol kinase (adenosine 5′-triphosphate:1,2-diacylglycerol 3-phosphotransferase, EC 2.7.1.107), purified from suspension cultured Catharanthus roseus cells (J Wissing, S Heim, KG Wagner [1989] Plant Physiol 90: 1546-1551), was further characterized and its subcellular location was investigated. The enzyme revealed a complex dependency on lipids and surfactants; its activity was stimulated by certain phospholipids, with phosphatidylinositol and phosphatidylglycerol as the most effective species, and by deoxycholate. In the presence of Triton X-100, used for its purification, a biphasic dependency upon diacylglycerol was observed and the apparent Michaelis constant values for diacylglycerol decreased with decreasing Triton concentration. The enzyme accepted both adenosine 5′-triphosphate and guanosine 5′-triphosphate as substrate and showed rather low apparent inhibition constant values for all nucleoside diphosphates tested. Diacylglycerol kinase is an intrinsic membrane protein and no activity was found in the cytosol. An investigation of different cellular membrane fractions confirmed its location in the plasma membrane.     

Further studies on the bicarbonate stimulation of photophosphorylation in isolated chloroplasts

The bicarbonate effect in stimulating the rate of photophosphorylation by isolated spinach (Spinacia oleracea var. Virginia blight-resistant savoy) chloroplasts at a pH below the optimum has been re-examined. Its seasonal nature may be related to the hormonal status of the plants. Bicarbonate anions stimulate adenosine 5′-triphosphate synthesis if added in the final, adenosine 5′-triphosphate-forming stage of either a postillumination or an acid-base experiment. They also stimulate the membrane-bound, Mg²⁺-dependent adenosine 5′-triphosphatase of chloroplasts, and the Ca²⁺-dependent adenosine 5′-triphosphatase of detached coupling factor. These and other data point to the interaction between energized thylakoid membranes and the coupling factor as the probable site of action of bicarbonate anions when they stimulate photophosphorylation.     

Photoactivation of NAD Kinase through Phytochrome: Phosphate Donors and Cofactors

The specificities of phosphate donors and the effects of metal chelating agents and divalent metal ions on NAD kinase activation by phytochrome-far red-absorbing form (Pfr) were examined. ATP was the most efficient phosphorylating agent. Uridine 5′-triphosphate, cytidine 5′-triphosphate (CTP), inosine 5′-triphosphate, and guanosine 5′-triphosphate in this order caused significant phosphorylation in the dark. Under red light, striking photoactivation of NAD kinase was obtained with ATP and subsequently CTP.     

Oxaloacetate Synthesis in Butyrivibrio fibrisolvens

Phosphoenolpyruvate carboxykinase (adenosine 5′-triphosphate) was the only enzyme capable of carboxylating pyruvate or phosphoenolpyruvate that could be demonstrated in sonicated cells or cell-free extracts of a group 1 butyrivibrio.     

3'-Azido-2',3'-dideoxynucleoside 5'-triphosphates inhibit telomerase activity in vitro, and the corresponding nucleosides cause telomere shortening in human HL60 cells

Telomerase adds telomeric DNA repeats to the ends of linear chromosomal DNA. 3′-Azido-3′-deoxythymidine 5′-triphosphate (AZTTP) is a known telomerase inhibitor. To obtain more selective and potent inhibitors that can be employed as tools for studying telomerase, we investigated the telomerase-inhibitory effects of purine nucleosides bearing a 3′-down azido group: 3′-azido-2′,3′-dideoxyguanosine (AZddG) 5′-triphosphate (AZddGTP), 3′-azido-2′,3′-dideoxy-6-thioguanosine (AZddSG) 5′-triphosphate (AZddSGTP), 3′-azido-2′,3′-dideoxyadenosine (AZddA) 5′-triphosphate (AZddATP) and 3′-azido-2′,3′-dideoxy-2-aminoadenosine (AZddAA) 5′-triphosphate (AZddAATP). Of these, AZddGTP showed the most potent inhibitory activity against HeLa cell telomerase. AZddGTP was significantly incorporated into the 3′-terminus of DNA by partially purified telomerase. However, AZddGTP did not exhibit significant inhibitory activity against DNA polymerases α and δ, suggesting that AZddGTP is a selective inhibitor of telomerase.

We also investigated whether long-term treatment with these nucleosides could alter telomere length and growth rates of human HL60 cells in culture. Southern hybridization analysis of genomic DNA prepared from cells cultured in the presence of AZddG and AZddAA revealed reproducible telomere shortening.

     

Assessment of Microbial Fouling in an Ocean Thermal Energy Conversion Experiment

A project to investigate biofouling, under conditions relevant to ocean thermal energy conversion heat exchangers, was conducted during July through September 1977 at a site about 13 km north of St. Croix (U.S. Virgin Islands). Seawater was drawn from a depth of 20 m, within the surface mixed layer, through aluminum pipes (2.6 m long, 2.5-cm internal diameter) at flow velocities of about 0.9 and 1.8 m/s. The temperature of the seawater entering the mock heat exchanger units was between 27.8 and 28.6°C. After about 10 weeks of exposure to seawater, when their thermal conductivity was reported to be significantly impaired, the pipes were assayed for the accumulation of biological material on their inner surfaces. The extent of biofouling was very low and independent of flow velocity. Bacterial populations, determined from plate counts, were about 10⁷ cells per cm². The ranges of mean areal densities for other biological components were: organic carbon, 18 to 27 μg/cm²; organic nitrogen, 1.5 to 3.0 μg/cm²; adenosine 5′-triphosphate, 4 to 28 ng/cm²; carbohydrate (as glucose in the phenol assay), 3.8 to 7.0 μg/cm²; chlorophyll a, 0.2 to 0.8 ng/cm². It was estimated from the adenosine 5′-triphosphate and nitrogen contents that the layer of live bacteria present after 10 weeks was only of the order of 1μm thick. The C/N ratio of the biological material suggested the presence of extracellular polysaccharidic material. Such compounds, because of their water-retaining capacities, could account for the related increase in thermal resistance associated with the pipes. This possibility merits further investigation, but the current results emphasize the minor degree of biofouling which is likely to be permissible in ocean thermal energy conversion heat exchangers.     

Biomass,production and activity of bacteria in the Black Sea,with special reference to chemosynthesis and the sulfur cycle

Abundance, morphological composition, vertical distribution, production and activity of total bacterioplankton and its specific groups in the Black Sea were investigated in August–September 1989. The total bacterioplankton was highest in the upper mixed layer (0.7–1 × 10⁶ cells ml^–1), corresponding to that in mesotrophic basins. In the N-E shallow part of the sea it attained 3 × 10⁶. Below the thermocline (50–100 m) the total number of bacteria decreased to 0.2–0.4 × 10⁶ ml^–1. In the redox gradient zone (zone of O₂-H₂S interface), it increased again. In deep anoxic waters the bacterioplankton, numbering 0.15–0.2 × 10⁶ ml^–1, was functionally inactive. Its biomass was 12–40 mg C m^–3 in the upper mixed layer, 5–10 mg C m^–3 in the intermediate cold layer (40–100 m depth), and 10–20 mg C^–3 in the redox zone. Maximum production rates occurred in the upper mixed layer (8–20 mg C^–3 d^–1) and in the redox-zone, 80–90% of it was due to chemosynthesis of thiobacilli. Below 200 m, microbial production decreased to about zero in the anoxic zone. Maximum activity of heterotrophic bacteria was recorded in the upper mixed layer, while thiobacilli and methaneoxidezing bacteria were most active in the redox-zone. Here, the maximum rates of H₂S and of thiosulfate oxidation, as well as maximum sulfate reduction were recorded. Chemical oxidation of H₂S was dominant. These results are discussed with respect to the present ecological situation of the Black Sea.     

Identification of Functionally Important Residues of the Rat P2X4 Receptor by Alanine Scanning Mutagenesis of the Dorsal Fin and Left Flipper Domains

Crystallization of the zebrafish P2X4 receptor in both open and closed states revealed conformational differences in the ectodomain structures, including the dorsal fin and left flipper domains. Here, we focused on the role of these domains in receptor activation, responsiveness to orthosteric ATP analogue agonists, and desensitization. Alanine scanning mutagenesis of the R203-L214 (dorsal fin) and the D280-N293 (left flipper) sequences of the rat P2X4 receptor showed that ATP potency/efficacy was reduced in 15 out of 26 alanine mutants. The R203A, N204A, and N293A mutants were essentially non-functional, but receptor function was restored by ivermectin, an allosteric modulator. The I205A, T210A, L214A, P290A, G291A, and Y292A mutants exhibited significant changes in the responsiveness to orthosteric analog agonists 2-(methylthio)adenosine 5′-triphosphate, adenosine 5′-(γ-thio)triphosphate, 2′(3′-O-(4-benzoylbenzoyl)adenosine 5′-triphosphate, and α,β-methyleneadenosine 5′-triphosphate. In contrast, the responsiveness of L206A, N208A, D280A, T281A, R282A, and H286A mutants to analog agonists was comparable to that of the wild type receptor. Among these mutants, D280A, T281A, R282A, H286A, G291A, and Y292A also exhibited increased time-constant of the desensitizing current response. These experiments, together with homology modeling, indicate that residues located in the upper part of the dorsal fin and left flipper domains, relative to distance from the channel pore, contribute to the organization of the ATP binding pocket and to the initiation of signal transmission towards residues in the lower part of both domains. The R203 and N204 residues, deeply buried in the protein, may integrate the output signal from these two domains towards the gate. In addition, the left flipper residues predominantly account for the control of transition of channels from an open to a desensitized state.     

Distribution and breeding biology of offshore pelagic cyprinids and catfish in Lake Malawi/Niassa

Synopsis Lake Malawi/Niassa is a permanently stratified lake, consisting of an oxygenated layer of 230 m depth that overlies an anoxic zone that extends to the lake bottom at a maximum depth of over 700 m. Some fish are found throughout the oxygenated zone of the offshore waters, and lead a pelagic existence, although many of the species form part of the demersal community in shallower waters where the lake-bed is oxygenated. This paper reports on the distribution of cyprinids and catfish at six offshore locations, sampled with a mid-water trawl and gillnets, along the north-south axis of the lake. These two groups formed, respectively, 5% and 13% of the offshore fish biomass in the trawl catches. The offshore cyprinids comprised the small lake-spawningEngraulicypris sardella, the only species to have pelagic larvae, and the larger river-spawningOpsaridium microcephalum andO. microlepis. These cyprinids occurred mainly in the upper 100 m of the water column. The biomass of both larvae and adults ofE. sardella showed considerable fluctuations over the two years of study. The spawning site ofE. sardella remains a mystery, but is no longer believed to be in the offshore pelagic zone. The most abundant catfish was the mochokidSynodontis njassae, that exhibited diurnal movements from just above the oxic-anoxic boundary layer during the day to the surface layers at night. The clariid catfish of the genusBathyclarias were caught infrequently offshore, but owing to their large size, they could form a significant part of the biomass. Their abundance was difficult to quantify, as it was believed that the majority are active in the near-surface layers and were under-sampled by the trawl and gillnets. Information on some aspects of the breeding biology is included in the paper, although our knowledge in this area is very incomplete.     

Adenosine triphosphatase in isolated membranes of Staphylococcus aureus

The preparation of cytoplasmic membranes from suspensions of Staphylococcus aureus lysed by an enzyme recently isolated in these laboratories is described. These membranes contained: protein, 34.4%; ribonucleic acid, 6.6%; lipids, 34.5%; and total phosphorus, 1.4%. Such membranes exhibited adenosine 5′-triphosphatase (E.C. 3.6.1.3) activity, liberating orthophosphate at an initial rate of 0.53 μmole per min per mg of protein under optimal conditions. The enzyme was Mg⁺⁺-dependent and K⁺- or Na⁺-stimulated. Maximal activity was observed with a molar adenosine 5′-triphosphate (ATP) to Mg⁺⁺ ratio of 1. One mole of orthophosphate was liberated per mole of ATP; the other product of digestion was adenosine 5′-diphosphate. Inorganic pyrophosphate and the 5′-triphosphates of guanosine, uridine, and cytidine were also attacked by membrane preparations, but more slowly than ATP. Ouabain, p-chloromercuribenzoate, and 2,4-dinitrophenol did not alter adenosine triphosphatase activity, whereas both Atebrine and chlorpromazine were inhibitory.     

Localization of an Amikacin 3′-Phosphotransferase in Escherichia coli

A plasmid-encoded enzyme reported by us to phosphorylate amikacin in a laboratory strain of Escherichia coli has been localized in the bacterial cell. More than 88% of this amikacin phosphotransferase (APH) activity was retained in spheroplasts formed by ethylenediaminetetraacetate-lysozyme treatment of an APH-containing E. coli transconguant known to form spheroplasts readily. By comparison, the spheroplasts retained 94% of deoxyribonucleic acid polymerase I and 98% of glutamyl-transfer ribonucleic acid synthetase, two internal markers, whereas less than 10% of the activity of a periplasmic marker, acid phosphatase, was present in spheroplasts. Treatment of whole cells of the transconjugant with chemical probes incapable of crossing the plasma membrane obliterated acid phosphatase activity, whereas the internal markers deoxyribonucleic acid polymerase I, glutamyl-transfer ribonucleic acid synthetase, and β-galactosidase were virtually unaffected after treatment for 5 min; more than 60% of the APH activity remained. As a control, similar chemical treatment of sonic extracts, in which enzymes were not protected by bacterial compartmentalization, produced more extensive reduction in the activities of all test enzymes, including APH. Spheroplasts preincubated with adenosine triphosphatase were shown by thin-layer chromatography to phosphorylate amikacin. Spheroplasts of cells grown in the presence of H₃³²PO₄ were shown to utilize internally generated adenosine 5′-triphosphate in the phosphorylation of amikacin. The absence of ³²P-phosphorylated amikacin after incubation of [γ-³²P]adenosine 5′-triphosphate with spheroplasts confirmed that exogenous adenosine 5′-triphosphate was not used in the reaction. These results suggest an internal location for APH. This conclusion has implications for the role of such enzymes in aminoglycoside resistance of gram-negative bacteria.