Contextual constraints on codon pair usage: structural and biological implications

Complementary DNA sequence data of 278 protein coding genes from prokaryotic systems have been analysed at the level of near neighbour codon pairs. Our analysis points out that constraints exist even at the level of near neighbour codon pairs. These constraints are in addition to those which arise due to relative levels of tRNA. Codon pairs, which in the data base have different occurrence values from their expected values, neither have common secondary structure nor do have better stabilization due to high base stacking. Our study points out that there are strong interaction between constituent codons in these codon pairs. These strongly interacting codon pairs, we suggest, are involved in the formation of three dimensional structural elements of cDNA/mRNA and interact with ribosome and thus modulate translation.     

Construction of a new yeast cloning vector containing autonomous replication sequences from Candida utilis.

DNA sequences from the Candida utilis genome which, when cloned into a yeast integration plasmid (YIp5), confer on YIp5 the ability to replicate autonomously in Saccharomyces cerevisiae are described. Several recombinant plasmids which transform S. cerevisiae YNN27 to Ura3+ with an efficiency of 2 X 10(3) transformants per microgram of DNA were obtained. One of the recombinant plasmids, pHMR22 (6.6 kilobases) contains ars (autonomous replication sequence), which is homologous with two different DNA fragments of the C. utilis genome but has no detectable homology to total DNA from Candida albicans, Pachysolen tannophilus, or S. cerevisiae. Restriction and subcloning analyses of pHMR22 showed that Sau3A destroys the functions of cloned ars whereas there are no BamHI, PstI, SalI, HindIII, EcoRI, or PvuII sites in the region of ars which is required for its functional integrity. Thus, pHMR22 appears to be a useful vector for cloning desired genes in S. cerevisiae.     

Productivity and nutrient uptake of water hyacinth,Eichhornia crassipes I. Effect of nitrogen source

Water hyacinth,Eichhornia crassipes, growth and nutrient uptake rates, as influenced by different N sources and N transformations, were measured using microcosm aquaculture systems. Net productivity was highest in the system receiving equal amounts of NH₄ ⁺ and NO₃ ^- (at 10 mg N 1^-1 each) and decreased in the order of NO₃ ^-, NH₄ ⁺, urea (added at 20 mg N 1^-1 each), and methane digestor effluent (at 6 mg N 1^-1). During the first 7-wk study (average ambient air temperature was 26–28°C), biomass yields were in the range of 19–53 g dry wt m^-2 day^-1, while between the 8th and 12th wk (average ambient air temperature was 16–22°C), biomass yields were in the range of 10–33 g dry wt m^-2 day^-1. In the systems with either NH₄ ⁺ or NO₃ ^-, or both added in equal proportions, about 14–20% of the total yield was contributed by roots, whereas in the system with urea and digestor effluent, roots contributed about 23 and 44% of the total yield, respectively. Nitrogen and P uptake per unit area followed trends similar to biomass yields. Nitrogen uptake rates were in the range of 533–2, 161 mg N m^-2 day^-1 for the systems receiving NH₄ ⁺, NO₃ ^-, and urea, while uptake rates were in the range of 124–602 mg N m^-2 day^-1 for the system receiving methane digestor effluent. Phosphorus uptake rates were found to be in the range of 59–542 mg P m^-2 day^-1. Under the most favorable conditions, maximum recorded biomass yield was 53 g dry wt m^-2 day^-1, with N and P removal rate of 2,161 mg N m^-2 day^-1 and 542 mg P m^-2 day^-1, indicating the potential of water hyacinth to produce large amounts of biomass which can be potentially used as a feedstock to produce methane.     

The role of cardiolipin as an acyl donor in dog heart N-acylethanolamine phospholipid biosynthesis

N-Acylethanolamine phospholipids were produced from endogenous substrates with dog heart mitochondrial and microsomal preparations. With mitochondria the N-acyl group contained 13.8% linoleate, with microsomes only 3.6%. Cardiolipin comprised 18.5% of mitochondrial and 3.3% of microsomal lipid P and contained 93.7 and 72.4% linoleic acid, respectively. Incubation of dog heart subcellular fractions with [1-14C]linoleoyl cardiolipin in the presence of Ca2+ resulted in the formation of N-acylethanolamine phospholipids labeled primarily in the N-acyl and 1-O-acyl moieties. The data indicate that cardiolipin is the major source of linoleic acid used in the N-acylation of ethanolamine phospholipids by transacylase activity.     

Isolation and functional characterization of hydrocarbon emulsifying and solubilizing factors produced by a Pseudomonas species

Pseudomonas PG-1 cultivated on pristane produced in good amount a heat-stable polymeric substance which showed strong hydrocarbon emulsifying and solubilizing properties. The substance was isolated in crude form and was found to contain 34% protein, 16% carbohydrate, and 40% lipid. The hydrocarbon solubilizing activity of the isolate was strongly inhibited by EDTA but the chelating agent had no effect on the hydrocarbon emulsifying activity. Both activities of the isolate were strongly inhibited by chymotrypsin treatment indicating the importance of the protein moiety for its activity. Hydrocarbon solubilization by the isolate showed a certain degree of specificity to pristane in modest agitation generally used in microbial cultivation, but this specificity was lost by vigorous agitation in a Waring blender. It was proposed that in the first case, solubilization was effected by a solubilizing factor specific to pristane, whereas in the latter case, nonspecific solubilization occurred due to the action of the emulsifying factor. The rate of pristane solubilization by heat-treated culture broth under the conditions of agitation used in cultivation (rotary shaker, 120 rpm) was found to be ca. 750 mg L(-1) h(-1) which was much larger than the maximal pristane uptake rate of 170 mg L(-1) h(-1) observed during microbial growth on the substrate. It was concluded that hydrocarbon solubilization could satisfactorily account for the substrate uptake and growth.     

Tissue-specific expression of the rat glutathione S-transferases

Tissue-specific patterns of rat glutathione S-transferase expression have been demonstrated by in vitro translation of purified poly(A) RNAs and by protein purification. Poly(A) RNAs from six rat tissues including heart, kidney, liver, lung, spleen, and testis were used to program in vitro translation with the rabbit reticulocyte lysate system and [35S]methionine. The glutathione S-transferase subunits synthesized in vitro were purified from the translation products by affinity chromatography on S-hexylglutathione-linked Sepharose 6B columns. The affinity bound fractions were analyzed by Na dodecyl SO4-polyacrylamide gel electrophoresis and fluorography. A subunit of Mr = 22,000 detected in the in vitro translation products of poly(A) RNAs from heart, kidney, lung, spleen, and testis is missing from the translation products of liver poly(A) RNAs. This Mr = 22,000 subunit is present only in the anionic glutathione S-transferase fraction purified from rat heart, kidney, lung, spleen, and testis. Purified anionic glutathione S-transferase from rat liver does not contain this subunit. The relative specific activities toward a dozen different substrates also demonstrate the nonidentity between liver and kidney anionic glutathione S-transferases. In addition, among the glutathione S-transferase subunits expressed in the liver, some of them could not be detected in the other tissues investigated. Our results indicate that tissue-specific expression of rat glutathione S-transferases may occur pretranslationally.     

Biosynthesis of N-acylethanolamine phospholipids by dog brain preparations

Abstract: Dog brain homogenates and subcellular preparations incubated in the presence of Ca²⁺ produced a new phospholipid that was isolated and identified by its infrared spectrum and by chemical degradation as a mixture of 1, 2-diacyl, alkenylacyl, and alkylacyl sn -glycero-3-phospho ( N -acyl)ethanolamines, 50, 45, and 5%, respectively. The N -acyl groups consisted almost exclusively of 16:0, 18:0, and 18:1 fatty acids. Formation of N -acylethanolamine phospholipids from endogenous substrates was linear for about 90 min at approximately 4.5 nmol/h/mg protein and exhibited a pH optimum of 10. Biosynthetic activity was associated with particulate fractions, primarily microsomes, synaptosomes, and mitochondria, but not with myelin. In each case, small amounts (∼0.5 nmol/h/mg protein) of long-chain N -acylethanolamines were also produced. Incubation of dog brain microsomes with 1,2-di[1'-¹⁴C]palmitoyl glycero-phosphocholine yielded N -acylethanolamine phospholipids labeled at both N -acyl (55%) and O -acyl (45%) moieties. It appears that dog brain organelles may contain a phosphatidylethanolamine N -acyl transferase (transacylase) analogous to that recently demonstrated in the myocardial tissue.     

Photosynthetic Units and Carbon Assimilation in Leaves of Grain Sorghum under Different Light Intensities

The Cyt f and P700 contents in leaves of three Sorghum, varietieswere measured, in relation to their carbon assimilation, underdifferent light intensities during growth. At the maximum irradiationused (1,800 µE m^–2 s^–1) the ratio of P700to Cyt f was close to unity, whereas under low irradiation (450µE m^–2 s^–1) the ratio of P700 to Cyt f rangedfrom two to three. A strikingly positive correlation existedbetween the P700 contents of the leaves and their rates of carbondioxide fixation, dry matter production and Cyt f contents,only when the plants were grown under high light intensities.The P700 content of the leaves in plants grown under low irradiationwas unrelated to the contents of Cyt f. Thus, at a high lightintensity there is a close relationship between the Cyt f andP700 levels, but at low intensities the amounts of electroncarriers and the reaction centre are independent. (Received March 7, 1983; Accepted August 24, 1983)     

Preparation of oligodeoxyribonucleoside methylphosphonates on a polystyrene support.

An efficient procedure is described for synthesizing deoxyribonucleoside methylphosphonates on polystyrene polymer supports which involves condensing 5'-dimethoxytrityldeoxynucleoside 3'-methylphosphonates. The oligomers are removed from the support and the base protecting groups hydrolyzed by treatment with ethylenediamine in ethanol, which avoids hydrolysis of the methylphosphonate linkages. Two types of oligomers were synthesized: those containing only methylphosphonate linkages, d-Np(Np)nN, and those which terminate with a 5' nucleotide residue, dNp (Np)nN. The latter oligomers can be phosphorylated by polynucleotide kinase, and are separated by polyacrylamide gel electrophoresis according to their chain length. Piperdine randomly cleaves the oligomer methylphosphonate linkages and generates a series of shorter oligomers whose number corresponds to the length of the original oligomer. Apurinic sites introduced by acid treatment spontaneously hydrolyze to give oligomers which terminate with free 3' and 5' OH groups. These reactions may be used to characterize the oligomers.