Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.     

RNA synthesis during morphogenesis of the fungusMucor racemosus

Bacteroides succinogenes produces acetate and succinate as major products of carbohydrate fermentation. An investigation of the enzymes involved indicated that pyruvate is oxidized by a flavin-dependent pyruvate cleavage enzyme to acetyl-CoA and CO₂. Active CO₂ exchange is associated with the pyruvate oxidation system. Reduction of flavin nucleotides is CoASH-dependent and does not require ferredoxin. Acetyl-CoA is further metabolized via acetyl phosphate to acetate and ATP. Reduced flavin nucleotide is used to reduce fumarate to succinate by a particulate flavin-specific fumarate reductase reaction which may involve cytochrome b. Phosphoenolpyruvate (PEP) is carboxylated to oxalacetate by a GDP-specific PEP carboxykinase. Oxalacetate, in turn, is converted to malate by a pyridine nucleotide-dependent malate dehydrogenase. The organism has a NAD-dependent glyceraldehyde-3-phosphate dehydrogenase. The data suggest that reduced pyridine nucleotides generated during glycolysis are oxidized in malate formation and that the electrons generated during pyruvate oxidation are used to reduce fumarate to succinate.     

Variations in short term products of inorganic carbon fixation in exponential and stationary phase cultures of Aphanocapsa 6308

Aphanocapsa 6308 metabolizes both NaHCO₃ and Na₂CO₃. The short term incorporation (5-s) metabolic pattern and the patterns of incorporation of bicarbonate for exponential versus stationary phase cultures differ, however. Cells were equilibrated for 10 min in air and distilled water prior to injection of either NaH¹⁴CO₃ at pH 8.0, or Na₂ ¹⁴CO₃ at pH 11.0. Hot ethanol extracts were analyzed via paper chromatography and autoradiography for products of CO₂ fixation. At 5 s, malate (51.5%) predominates slightly as a primary bicarbonate fixation product over 3-phosphoglycerate (40.3%); 3-phosphoglycerate is the primary product of carbonate fixation. At 60 s, the carbonate and bicarbonate labelling patterns are similar. Cells in stationary phase fix in 5 s a greater proportion of bicarbonate into malate (36% vs. 14% for 3-phosphoglycerate) than do cells in exponential growth. Likewise, 60 s incorporations show a large amount of bicarbonate fixed into aspartate (30.9%) in stationary phase cells over that of exponential phase (11.6%). These data suggest an operative C₄ pathway for purposes not related to carbohydrate synthesis but rather as compensation for the incomplete tricarboxylic acid cycle in cyanobacteria. The enhancement of both aspartate fixation and CO₂ fixation into citrulline in stationary phase correlates with an increase in cyanophycin granule production which requires both aspartate and arginine.Nonstandard Abbreviations 3-PGA 3-phosphoglyceric acid - TCA tricarboxylic acid     

Modulation of platelet responsiveness through selective phosphorylation of plasma membrane proteins: Antagonistic eeffects of cyclic AMP and cyclic GMP

³²P phosphorylation of plasma membranes from human blood platelets, under conditions that closely resemble physiological ones (endogeneous phosphate donors and intact platelets in homologous plasma), result in the incorporation of the label mainly in a membrane glycoprotein of apparently high molecular weight (greater than 400 000). Dibutyryl cyclic AMP, an inhibitor of platelet aggregation, specifically increases the degree of phosphorylation of this glycoprotein. Moreover, it has been found that prostaglandin E₁ one of the most potent inhibitors of platelet aggregation which also increases phosphorylation of the same glycoprotein, is significantly more effective than cyclic AMP.Cyclic GMP does not have any apparent effect on platelet aggregation. However, incubation of platelet-rich plasma with both cyclic GMP and cyclic AMP results in a partial recovery of the platelet responsiveness towards ADP-induced aggregation. Coincidently, the degree of phosphorylation of the high molecular weight glycoprotein under these conditions, although still higher than in controls (no nucleotides added), is significantly decreased as compared with cyclic AMP-treated cells. Furthermore, cyclic GMP inhibits the cyclic AMP-dependent protein kinase activity in isolated platelet plasma membranes.These results suggest a central role for this membrane phosphoglycoprotein in the triggering of platelet aggregation and, furthermore, suggest that modulation of its degree of phosphorylation may be exerted through some cyclic AMP/cyclic GMP relationship, which in the basal state might be critical for platelet responsiveness.     

Purine-Excretory Nature of Refractile Bodies in the Marine Ciliate Parauronema acutum*

SYNOPSIS. A method was developed for the isolation and purification of crystalline, highly refractile bodies found in the cytoplasm of a symbiote-free strain of the marine hymenostome ciliate, Parauronema acutum, strain 110–3. Chemical analysis of the purified refractile bodies revealed an abundance of the purines, hypoxanthine and guanine. It was evident from studies involving the use of ¹⁴C-labeled precursors that both hypoxanthine and guanine are derived from higher purine derivatives. We postulate that these bodies are excretory in function and that guanine and hypoxanthine are major endproducts of purine metabolism of P. acutum.     

Effect of Acetate on Esterase C Activity During the Growth Cycle of Paramecium*

SYNOPSIS Enhanced esterase C activity could be demonstrated by starch gel electrophoresis in various stocks of Paramecium spp. (P. primaurelia stocks 90 and 540, P. biaurelia stock 93, P. tetraurelia stock 29. P. pentaurelia stock 87, P. octaurelia stocks 31 and 300, and P. multimicronucleatum species 3, stock 8 MO) grown in Adaptation Medium. This esterase, however, was barely detectable when they were cultivated in Axenic Medium. Addition of trypticase to Adaptation Medium resulted in reduction of esterase C in the ciliates. This effect is ascribable to Na acetate present in trypticase. Since esterase C increased with the decrease in acetate concentration (as estimated by gas-liquid chromatography) during growth of Paramecium, acetate appears to be utilized by the cells. Sensitivity of esterase C to acetate occurs in all 6 species of Paramecium examined. Different stocks within a species may have different levels of sensitivity; in one case this is genetically determined. The results emphasize the importance of controlling and manipulating growth conditions for the assessment of inter- and intraspecies variations in the isozymes of Paramecium.     

Biosynthesis of prostaglandins and thromboxane B2 by fetal lung homogenates

The conversion of arachidonic acid to prostaglandins (PG's) and thromboxane B₂ (TXB₂) was investigated in homogenates from fetal and adult bovine and rabbit lungs. Adult bovine lungs were very active in converting arachidonic acid (100 μg/g tissue) to both PGE₂ (10.7 μg/g tissue) and TXB₂ (6.2 μ/g tissue). Smaller amounts of PGF_2α (0.9 μ/g) and 6-oxoPGF_1α were formed. Homogenates from fetal calf lungs during the third trimester of pregnancy were quite active in converting arachidonic acid to PGE₂, but formed very little TXB₂, PGF_2α or 6-oxoPGF_1α. Homogenates from rabbit lungs converted arachidonic acid (100 μg/g) mainly to PGE₂, both before and after birth. The amount of PGE₂ formed increased during gestation to a maximum of about 6 μg/g tissue at 28 days of gestation. It then decreased to a minimum (1.5 μg/g) which was observed 8 days after birth, followed by an increase to about 4 μg/g in older rabbits.     

The role of the nicotinamide and adenine subsites in the negative co-operativity of coenzyme binding to glyceraldehyde-3-phosphate dehydrogenase.

The interaction of 3-aminopyridine-adenine dinucleotide, an NAD ⁺ 2 analogue which is fluorescent at the pyridine end of the molecule, with rabbit muscle glyceraldehyde-3-phosphate dehydrogenase was investigated. The fluorescence properties of the AAD⁺ molecule were used to monitor the nicotinamide subsites ou the GPDHase tetramer, the fluorescent aminopyridine moiety of the molecule serving as an intrinsic probe. Although the binding of AAD⁺ wag found to be negatively co-operative, no conformational changes induced at the nicotinamide subsite upon coenzyme binding were found to be transmitted to neighboring subunits. These findings, in conjunction with our earlier findings and with the observation that different NAD⁺ analogues which differ in the chemistry of the pyridine moiety bind with different extents of co-operativity, enable us to offer specific roles for the nicotinamide and the adenine subsites in generating the negative co-operativity.It is suggested that the structure of the pyridine moiety of the coenzyme controls the mode of binding of the pyridine moiety to the nicotinamide subsite. This, in turn, controls the orientation of the adenine moiety with respect to its subsite, thereby determining the mode of the interactions between the adenine and its binding domain. As the propagation of conformational changes caused by these interactions to neighboring subunits is believed to be the cause of the negative co-operativity exhibited by this enzyme towards coenzyme binding, the structure of the pyridine moiety controls this phenomenon.     

The role of GTP in the activation of adenylate cyclase.

An attempt is made to integrate the knowledge on the role of hormones and guanyl nucleotides in regulating adenylate cyclase into a single molecular model. It is suggested that the hormone catalyzes the activation of the enzyme adenylate cyclase by facilitating the conversion of the enzyme from its inactive state to its active form. The hormone is also responsible for the termination of the signal namely the deactivation of the enzyme by inducing the hydrolysis of GTP at its regulatory site. The relative rates of these two processes determine the steady state concentration of the active form of the enzyme. The model also explains the difference in behaviour between GTP and its non-hydrolyzable analogs GppNHp and GTPγS.