Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes

Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7–3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5–9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 (estimated from the melanogaster species subgroup) or 2.9 (estimated from the obscura group) times higher in mitochondrial genes than in nuclear genes. Synonymous transversions in mitochondrial genes occurred at an approximately equivalent rate to those in the fastest nuclear genes. This last result is not consistent with the hypothesis that the difference in turnover rates between mitochondrial and nuclear genomes is the major factor determining higher synonymous substitution rates in mtDNA. We conclude that the difference in synonymous substitution rates is due to a combination of two factors: a higher transitional mutation rate in mtDNA and constraints on nuclear genes due to selection for codon usage. Received: 27 November 1996 / Accepted: 8 May 1997     

Endogenous ligands of rat lung beta-galactoside-binding protein (galaptin) isolated by affinity chromatography on carboxyamidomethylated-galaptin-Sepharose.

Rat lung beta-galactoside-binding protein (galaptin) is developmentally regulated during postnatal lung development. In common with other vertebrate galaptins, it is very labile when purified and dependent on the presence of exogenous thiol reagents. Reaction of rat lung galaptin with iodoacetamide resulted in a stable active carboxyamidomethylated galaptin that could be coupled to Sepharose. The resultant affinity matrix bound asialoglycoproteins, and these could be quantitatively eluted with disaccharide haptens. The carboxyamidomethylated-galaptin-Sepharose affinity matrix was used to search for endogenous ligands in 13-day-rat lung. Cytosolic fractions of developing rat lung contained no moieties that could be specifically eluted with disaccharide hapten. Only when membranous fractions were extracted with 1% Triton were glycoproteins solubilized that bound to the affinity matrix and could be specifically eluted with disaccharide hapten. The eluted glycoproteins were potent inhibitors of galaptin binding to asialo-orosomucoid. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis identified these glycoproteins as being of high Mr, with three components of Mr 160000-200000 and a smaller component of Mr 75000. This is the first evidence for specific membrane-associated glycoproteins being the ligands of rat lung galaptin.     

Photoreceptor membrane breakdown in the spider Dinopis: GERL differentiation in the receptors

Summary In the spider Dinopis, retinae of the posterior median eyes synthesise new photoreceptor membrane in bulk at dusk and destroy it at dawn (Blest, 1978). During the dawn period, there is a rapid, anticipatory differentiation of unusual organelles from the rough endoplasmic reticulum (RER) in the intermediate segments of the receptors. This system is classified as GERL. Its products appear to play a role in the autolysis of photoreceptor membrane. Consistent topographical relationship to Golgi bodies has not been determined. Circumscribed regions of RER whorls first reorganise to yield fenestrated profiles; these differentiate further to a number of structures by condensation and loss of ribosomes. Smooth tubular profiles are termed rigid tubules to indicate their probable homology with the rigid lamellae of vertebrate secretory cells. More complex smooth multilocular bodies are also produced. Evidence is discussed which implies that both rigid tubules and multilocular bodies give rise to condensing vacuoles. These, in turn, pinch off coated vesicles assembled as Nebenkerne. Some rigid tubules are transported to the interrhabdomeral cytoplasm of the receptive segments. At late stages of differentiation, rigid tubules, multilocular bodies and Nebenkerne give strong, positive responses to zinc iodide-osmium tetroxide (ZIO) treatment; early stages and both cis and trans Golgi components do not. GERL differentiation is independent of immediate illumination of the retina at dawn. It is suggested to mediate the lysis of membrane degradation products by the production of hydrolases.We thank Professor D.T. Anderson F.R.S. for our use of field facilities at the Crommelin Biological Field Station of Sydney University at Warrah, Pearl Beach, N.S.W., and Andrew and Sally Austin and Sally Stowe for help in the field. We are indebted to Rod Whitty and the Electron Microscopy Unit for advice and support throughout these studies     

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.     

Active and passive cation transport and L antigen hertogeneity in low potassium sheep red cells

Several lines of experimental evidence are presented suggesting that the L antigens in low potassium (LK) sheep red cells are associated with separate Na(+)K(+) pump flux is distinct from the action of anti-L(l) on K(+) leak flux, implying that K(+) leak transport sites may not be converted into active pumps by the L antiserum. Treatment of LK red cells with trypsin completely abolished both the stimulation of K(+) pump flux and the enhancement of the rate of ouabain binding brought about by anti- L. That this effect is due to a total destruction of the L(p) determinant associated with the LK pump was evident from the complete failure of anti-L(p) to bind to trypsinized LK red cells. The L(p) antigen can be effectively protected against the trypsin attack by prior incubation with anti-L, indicating that the sites for antibody binding and trypsin action may be closely adjacent at the structural level. Trypsin treatment, however, did not interfere with anti-L(l) reducing ouabain insensitive K(+) leak influx, nor did it prevent binding of anti-L(ly), the hemolytically active L antibody which is probably identical with anti-L(l). The functional independence of the L(p) and L(l) sites was documented by the observation that anti-L(l) still reduced K(+) leak influx in LK cells with experimentally induced high potassium concentrations, at which K(+) pump flux is fully suppressed, whether or not anti-L(p) was binding to the L(p) antigen associated with the LK pump.     

Biliary excretion of warfarin metabolites and their metabolism by rat gut flora.

The bile was determined to be the major excretory route for ¹⁴C-warfarin in the rat with approximately 10% of the administered dose excreted within 5 hours after injection. Relatively little radioactivity appeared in the faces, indicating that considerable enterohepatic recycling was taking place. Less than 4% of the radioactivity in the bile could be extracted with organic solvents. Following incubation of the bile with β-glucuronidase or rat gut flora, however, the bulk of the radioactivity was extractable. The extent of gut flora-mediated hydrolysis of these polar biliary warfarin conjugates was approximately the same as obtained with β-glucuronidase. Approximately $\text{1}\text{3}$ of the gut flora-hydrolyzable conjugates were labile and subject to nonenzymatic hydrolysis at 37 C for 24 h. Chromatographic examination of the extracts from β-glucuronidase-treated bile revealed the presence of warfarin and 4′-, 6-, 7-, and 8-hydroxywarfarin. Warfarin and 7-hydroxywarfarin were the most abundant metabolites in the extracts.     

Comparison of EC broth and medium A-1 for the recovery of Escherichia coli from frozen shucked snow crab.

Two variations of the multiple-tube fermentation technique were used to enumerate fecal coliforms in commercially processed, frozen crab meat. These were the EC confirmation test and a more rapid method that requires medium A-1. The method with medium A-1 was more specific than the EC confirmation test for detecting Escherichia coli type 1. E. coli was isolated from 84% of the positive medium A-1 tubes, whereas it was isolated from only 64% of the positive tubes of EC broth. When samples of crab meat were inoculated with known amounts of E. coli, better estimates of the known numbers were obtained by the medium A-1 method. Several species of nonfecal coliforms were isolated from cultures in EC broth. These belonged to the genera Klebsiella, Citrobacter, Enterobacter, and Serratia. Apparently these strains were naturally adapted to growth at an elevated temperature because the majority were able to grow at 44.5 degrees C when retested in EC broth. Fewer species of nonfecal coliforms were isolated from medium A-1. Those that were isolated belonged to the genera Citrobacter and Enterobacter.     

Structural changes in (Na+ + K+)-ATPase accompanying detergent inactivation

Structural changes in the purified $\text{(}\text{Na}{}^{\mathrm{+}}\text{+ K}{}^{\mathrm{+}}\text{)-ATPase}$ accompanying detergent inactivation were investigated by monitoring changes in light scattering, intrinsic protein fluorescence, and tryptophan to β-parinaric acid fluorescence resonance energy transfer. Two phases of inactivation were observed using the non-ionic detergents, digitonin, Lubrol WX and Triton X-100. The rapid phase involves detergent monomer insertion but little change in protein structure or little displacement of closely associated lipids as judged by intrinsic protein fluorescence and fluorescence resonance energy transfer. Lubrol WX and Triton X-100 also caused membrane fragmentation during the rapid phase. The slower phase of inactivation results in a completely inactive enzyme in a particle of 400 000 daltons with 20 mol/mol of associated phospholipid. Fluorescence changes during the course of the slow phase indicate some dissociation of protein-associated lipids and an accompanying protein conformational change. It is concluded that non-parallel inhibition of $\text{(}\text{Na}{}^{\mathrm{+}}\text{+ K}{}^{\mathrm{+}}\text{)-ATPase}$ and $\text{p-}\text{nitrophenylphosphate}$ activity by digitonin (which occurs during the rapid phase of inactivation) is unlikely to require a change in the oligomeric state of the enzyme. It is also concluded that at least 20 mol/mol of tightly associated lipid are necessary for either $\text{(}\text{Na}{}^{\mathrm{+}}\text{+ K}{}^{\mathrm{+}}\text{)-ATPase}$ or $\text{p-}\text{nitrophenylphosphatase}$ activity and that the rate-limiting step in the slow inactivation phase involves dissociation of an essential lipid.     

Structural changes in (Na+ + K+)-ATPase accompanying detergent inactivation

Structural changes in the purified (Na+ + K+)-ATPase accompanying detergent inactivation were investigated by monitoring changes in light scattering, intrinsic protein fluorescence, and tryptophan to beta-parinaric acid fluorescence resonance energy transfer. Two phases of inactivation were observed using the non-ionic detergents, digitonin, Lubrol WX and Triton X-100. The rapid phase involves detergent monomer insertion but little change in protein structure or little displacement of closely associated lipids as judged by intrinsic protein fluorescence and fluorescence resonance energy transfer. Lubrol WX and Triton X-100 also caused membrane fragmentation during the rapid phase. The slower phase of inactivation results in a completely inactive enzyme in a particle of 400 000 daltons with 20 mol/mol of associated phospholipid. Fluorescence changes during the course of the slow phase indicate some dissociation of protein-associated lipids and an accompanying protein conformational change. It is concluded that non-parallel inhibition of (Na+ + K+)-ATPase and p-nitrophenylphosphate activity by digitonin (which occurs during the rapid phase of inactivation) is unlikey to require a change in the oligomeric state of the enzyme. It is also concluded that at least 20 mol/mol of tightly associated lipid are necessary for either (Na+ + K+)-ATPase or p-nitrophenylphosphatase activity and that the rate-limiting step in the slow inactivation phase involves dissociation of an essential lipid.