Hypervariable and Highly Divergent Intron–Exon Organizations in the Chordate Oikopleura dioica

Oikopleura dioica is a pelagic tunicate with a very small genome and a very short life cycle. In order to investigate the intron–exon organizations in Oikopleura, we have isolated and characterized ribosomal protein EF-1, Hox, and -tubulin genes. Their intron positions have been compared with those of the same genes from various invertebrates and vertebrates, including four species with entirely sequenced genomes. Oikopleura genes, like Caenorhabditis genes, have introns at a large number of nonconserved positions, which must originate from late insertions or intron sliding of ancient insertions. Both species exhibit hypervariable intron–exon organization within their -tubulin gene family. This is due to localization of most nonconserved intron positions in single members of this gene family. The hypervariability and divergence of intron positions in Oikopleura and Caenorhabditis may be related to the predominance of short introns, the processing of which is not very dependent upon the exonic environment compared to large introns. Also, both species have an undermethylated genome, and the control of methylation-induced point mutations imposes a control on exon size, at least in vertebrate genes. That introns placed at such variable positions in Oikopleura or C. elegans may serve a specific purpose is not easy to infer from our current knowledge and hypotheses on intron functions. We propose that new introns are retained in species with very short life cycles, because illegitimate exchanges including gene conversion are repressed. We also speculate that introns placed at gene-specific positions may contribute to suppressing these exchanges and thereby favor their own persistence.Supplementary material () is available for this article.     

FTIR analysis of cellulose treated with sodium hydroxide and carbon dioxide

Cellulose samples treated with sodium hydroxide (NaOH) and carbon dioxide in dimethylacetamide (DMAc) were analyzed by FTIR spectroscopy. Absorbance of hydrogen-bonded OH stretching was considerably decreased by the treatment of NaOH and carbon dioxide. The relative absorbance ratio (A(4000-2995)/A(993)) represented the decrease of absorbance as a criterion of hydrogen-bond intensity (HBI). The absorbance of the band at 1430cm(-1) due to a crystalline absorption was also decreased by NaOH treatment. The absorbance ratio of the bands at 1430 and 987-893cm(-1) (A(1430)/A(900)), adopted as crystallinity index (CI), was closely related to the portion of cellulose I structure. With the help of FTIR equipped with an on-line evacuation apparatus, broad OH bending due to bound water could be eliminated. FTIR spectra of the carbon dioxide-treated cellulose samples at 1700-1525cm(-1) were divided into some bands including 1663, 1635, 1616, and 1593cm(-1). The broad OH bending due to bound water at 1641-1645cm(-1) was resolved to two bands at 1663 and 1635cm(-1). As a trace of DMAc, the band at 1616cm(-1) is disappeared by washing for the cellulose treated with carbon dioxide (Cell 1-C and Cell 2/60-C). The decrease of HBI, the easy removal of DMAc, and the band at 1593cm(-1) supported the introduction of new chemical structure in cellulose. The bands shown at 1593 and 1470cm(-1) was assigned as hydrogen-bonded carbonyl stretching and O-C-O stretching of the carbonate ion.     

Batch and fed-batch production of coenzyme Q10 in recombinant Escherichia coli containing the decaprenyl diphosphate synthase gene from Gluconobacter suboxydans

Coenzyme Q₁₀ (CoQ₁₀) is a quinine consisting of ten units of the isoprenoid side-chain. Because it limits the oxidative attack of free radicals to DNA and lipids, CoQ₁₀ has been used as an antioxidant for foods, cosmetics and pharmaceuticals. Decaprenyl diphosphate synthase (DPS) is the key enzyme for synthesis of the decaprenyl tail in CoQ₁₀ with isopentenyl diphosphate. The ddsA gene coding for DPS from Gluconobacter suboxydans was expressed under the control of an Escherichia coli constitutive promoter. Analysis of the cell extract in recombinant E. coli BL21/pACDdsA by high performance liquid chromatography and mass spectrometry showed that CoQ₁₀ rather than endogenous CoQ₈ was biologically synthesized as the major coenzyme Q. Expression of the ddsA gene with low copy number led to the accumulation of CoQ₁₀ to 0.97 mg l^–1 in batch fermentation. A high cell density (103 g l^–1) in fed-batch fermentation of E. coli BL21/pACDdsA increased the CoQ₁₀ concentration to 25.5 mg l ^–1 and its productivity to 0.67 mg l^–1 h^–1, which were 26.0 and 6.9 times higher than the corresponding values for batch fermentation.     

Solid-phase refolding of cyclodextrin glycosyltransferase adsorbed on cation-exchange resin

Expression with a fusion partner is now a popular scheme to produce a protein of interest because it provides a generic tool for expression and purification. In our previous study, a strong polycationic tail has been harnessed for an efficient purification scheme. Here, the same polycation tail attached to a protein of interest is shown to hold versatility for a solid-phase refolding method that utilizes a charged adsorbent as a supporting material. Cyclodextrin glycosyltransferase (CGTase) fused with 10 lysine residues at the C-terminus (CGTK10ase) retains the ability to bind to a cation exchanger even in a urea-denatured state. When the denatured and adsorbed CGTK10ase is induced to refold, the bound CGTK10ase aggregates little even at a g/L range. The renatured CGTK10ase can also be simply recovered from the solid support by adding high concentration of NaCl. The CGTK10ase refolded on a solid support retains specific enzyme activity virtually identical to that of the native CGTK10ase. Several factors that are important in improving the refolding efficiency are explored. Experimental results indicate that nonspecific electrostatic interactions between the charge of the ion exchanger and the local charge of CGTase other than the polycationic tag should be reduced to obtain higher refolding yield. The solid-phase refolding method utilizing a strong polycationic tag resulted in a remarkable increase in the refolding performance. Taken together with the previous report in which a series of polycations were explored for efficient purification, expression of a target protein fused with a strong polycation provides a straightforward protein preparation scheme.     

Role of the connectivity of secondary structure segments in the folding of alpha(1)-antitrypsin

The native form of serpins (serine protease inhibitors) is metastable, which is critical to their biological functions. Spontaneous conversion from the native form of serpins into a more stable conformation, called the "latent" form, is restricted. To examine whether the connectivity of strand 1 of beta-sheet C to the hydrophobic core is critical to the serpin's preferential folding to the metastable native conformation, we designed a circularly-permuted mutant of alpha(1)-antitrypsin, the prototype serpin, in which strand 1C is disconnected from the hydrophobic core. Conformation of the circular permutant was similar to that of the latent form, as revealed by equilibrium unfolding, limited proteolysis, and spectroscopic properties. Our results support the notion that rapid folding of the hydrophobic core with concomitant incorporation of strand 1C into beta-sheet C traps the serpin molecule into its native metastable conformation.