Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme

Metal ions are essential cofactors for various ribozymes. Here we dissect the roles of metal ions in an aminoacyl-tRNA synthetase-like ribozyme (ARS ribozyme), which was evolved in vitro. This ribozyme can charge phenylalanine on tRNA in cis, where it is covalently attached to the 5′-end of tRNA (i.e. a form of precursor tRNA), as well as in trans, where it can act as a catalyst. The presence of magnesium ion is essential for this ribozyme to exhibit full catalytic activity. Metal-dependent kinetics, as well as structural mappings using Tb³⁺ in competition with Mg²⁺ or Co(NH₃)₆³⁺, identified two potential metal-binding sites which are embedded near the tRNA-binding site. The high affinity metal-binding site can be filled with either Mg²⁺ or Co(NH₃)₆³⁺ and thus the activity relies on a metal ion that is fully coordinated with water or ammonium ions. This site also overlaps with the amino acid-binding site, suggesting that the metal ion plays a role in constituting the catalytic core. The weak metal-binding site is occupied only by a metal ion(s) that can form innersphere contacts with ligands in the ribozyme and, hence, Mg²⁺ can enhance ribozyme activity, but Co(NH₃)₆³⁺ cannot. The experiments described in this work establish the roles of metal ions that have distinct coordination properties in the ARS ribozyme.     

Minihelix-loop RNAs: minimal structures for aminoacylation catalysts

We report here an in vitro selected ribozyme, KL17, which is active in charging amino acids on its own 5′-OH group. The ribozyme consists of two catalytic domains, one of which (consisting of P5/P6/L6) recognizes amino acid substrates based on the steric environment of the side chain, whereas the other recognizes an aminoacylated oligonucleotide. The secondary structure of this ambidextrous ribozyme arranges into a pseudoknot, where L6 docks onto the 3′-terminal single-stranded region. The formation of this pseudoknot structure brings the P6 region, in which the essential catalytic core is most likely embedded, into the proximity of the 5′-OH group. Our studies show that the P6–L6 domain can be separated from the main body of KL17 and the derived P6–L6 minihelix-loop RNA can act as a trans-aminoacylation catalyst. In this report, we also compare this ribozyme with an analogous aminoacylation system previously characterized in our laboratory and illuminate the similarities and differences between these catalytic systems.     

Immunohistochemical localization of acyl-CoA hydrolase/thioesterase multigene family members to rat epithelia

Acyl-CoA hydrolases cleave acyl-CoA thioesters to free fatty acids and coenzyme A. The potency of these enzymes may serve to modulate cellular levels of acyl-CoAs to affect various cellular functions, including lipid metabolism. In this study, we investigated the tissue distribution of this multigene family of enzymes, focusing on cytosolic (CTE-I) and mitochondrial acyl-CoA thioesterases (MTE-I) in adult rats, using an anti-CTE-I antibody which recognizes both the isoforms. Western blotting detected them mainly in organs closely related to fatty acid oxidation, of which kidney contained the highest levels of both enzymes. Immunohistochemistry localized the enzymes primarily in the proximal tubules, where a large energy demand is expected and fatty acids represent a major fuel, correlating well with the intrarenal distribution of peroxisomal beta-oxidation. In situ hybridization suggested colocalization of CTE-I and MTE-I in the kidney. The immunoreactivity was also found in various epithelial tissues in the body, including Harderian gland and sebaceous gland. These results demonstrated the distribution of CTE-I and MTE-I in a wide variety of rat tissues, primarily characterized by an epithelial localization, being consistent with their involvement in fatty acid metabolism.     

A tRNA aminoacylation system for non-natural amino acids based on a programmable ribozyme

The ability to recognize tRNA identities is essential to the function of the genetic coding system. In translation aminoacyl-tRNA synthetases (ARSs) recognize the identities of tRNAs and charge them with their cognate amino acids. We show that an in vitro evolved ribozyme can also discriminate between specific tRNAs, and can transfer amino acids to the 3' ends of cognate tRNAs. The ribozyme interacts with both the CCA-3' terminus and the anticodon loop of tRNA(fMet), and its tRNA specificity is controlled by these interactions. This feature allows us to program the selectivity of the ribozyme toward specific tRNAs, and therefore to tailor effective aminoacyl-transfer catalysts. This method potentially provides a means of generating aminoacyl tRNAs that are charged with non-natural amino acids, which could be incorporated into proteins through cell-free translation.     

Aquaporin isoforms responsive to salt and water stresses and phytohormones in radish seedlings

Aquaporins in the plasma and vacuolar membranes play a key role in the intercellular and intracellular water transport in plants. First, we quantitated the absolute amounts for mRNAs of eight aquaporin isoforms in hypocotyls of radish seedlings. Then, we investigated the effects of salt and water stresses (150 mM NaCl, 300 mM mannitol and 20% polyethylene glycol) and phytohormones (gibberellic acid, abscisic acid and brassinolide) on the mRNA and protein levels of aquaporins in the plasma membrane (RsPIP1-1, 1-2, 1-3, 2-1, 2-2 and 2-3) and vacuolar membrane (RsTIP1-1 and 2-1). The mRNA and protein levels of RsTIP1-1, RsTIP2-1, RsPIP1-1, RsPIP1-2 and RsPIP1-3 were comparatively constant. In contrast, mannitol treatment altered the mRNA levels of RsPIP2-1, RsPIP2-2 and RsPIP2-3 in roots. Immunoblot analysis showed that the RsPIP2-1 protein level was increased by NaCl treatment and decreased by treatment with mannitol and polyethylene glycol. Gibberellic acid and abscisic acid suppressed the levels of mRNAs of RsPIP2-1, RsPIP2-2 and RsPIP2-3 and the protein level of RsPIP2-1 in roots. On the other hand, the protein levels of RsPIP1-group members and RsTIPs were scarcely changed by these phytohormones. In the case of hypocotyls and cotyledons, the mRNA and protein levels of eight isoforms were not markedly affected by any treatment. These results indicate that aquaporins in the root, especially the RsPIP2 group, may be a stress responsive type of aquaporin at least in the protein level.     

Characterization and Identification of Asexual Strains of Pythium Associated with Root Rot of Rose in Japan

This study was conducted to survey the distribution of asexual isolates of Pythium in rose production and to characterize and identify them. Asexual isolates with proliferating globose sporangia belong to group P according to the key of van der Plaats‐Niterink (1981; Monograph of the genus Pythium. Studies in Mycology, Vol. 21, Centraalbueau Voor Schimmelcultures, Baarn, The Netherlands). Group P isolates were recovered from rotted roots of both cutting and miniature roses cultured in rock wool and ebb‐and‐flow culture systems, respectively, throughout the main rose production area of Japan. The typical feature of the P group isolates was that they could grow fast at high temperature, at least 30 mm per 24 h at 35°C. There was no difference between the P group isolates and P. helicoides in morphology and size of sporangia and sporangial germination mode. The symptoms caused by the group P isolates were root rot, followed by leaf blight and plant death in severe cases. In restriction fragment length polymorphism analysis of the rDNA‐ITS region, the banding patterns with five of six enzymes were identical between group P and P. helicoides, the only difference being seen with HhaI. In direct amplification analysis of minisatellite‐region DNA with M13 primer, group P and P. helicoides shared three of five distinct bands. In contrast, P. oedochilum and P. ostracodes showed different banding patterns except for each one band. The results suggest that the group P isolates obtained from rose root rot may be asexual strains of P. helicoides.     

Increased uncoupling protein-2 and -3 gene expressions in skeletal muscle of STZ-induced diabetic rats

Streptozotocin (STZ)-induced diabetic animals are vulnerable to cold stress. Uncoupling proteins (UCPs) play an important role in regulating thermogenesis. We investigated the gene expressions of UCPs in brown adipose tissue (BAT), white adipose tissue (WAT), liver and gastrocnemius muscle of STZ-diabetic rats using Northern blot. UCP-1, -2 and -3 mRNA expressions in BAT were all remarkably lower in STZ-diabetic rats than those in control rats. Both UCP-2 and -3 gene expressions in gastrocnemius muscle were substantially elevated in STZ-diabetic rats and insulin treatment restored UCP gene expressions to normal levels. These results suggest that in STZ-diabetic rats, the overexpression of UCP-2 and UCP-3 in skeletal muscle provides a defense against hypothermogenesis caused by decreased UCPs in BAT.     

Fuzzy control of ethanol concentration its application to maximum glutathione production in yeast fed-batch culture

A fuzzy logic controller (FLC) for the control of ethanol concentration was developed and utilized to realize the maximum production of glutathione (GSH) in yeast fedbatch culture. A conventional fuzzy controller, which uses the control error and its rate of change in the premise part of the linguistic rules, worked well when the initial error of ethanol concentration was small. However, when the initial error was large, controller overreaction resulted in an overshoot.An improved fuzzy controller was obtained to avoid controller overreaction by diagnostic determination of "glucose emergency states" (i.e., glucose accumulation or deficiency), and then appropriate emergency control action was obtained by the use of weight coefficients and modification of linguistic rules to decrease the overreaction of the controller when the fermentation was in the emergency state. The improved fuzzy controller was able to control a constant ethanol concentration under conditions of large initial error.The improved fuzzy control system was used in the GSH production phase of the optimal operation to indirectly control the specific growth rate mu to its critical value mu(c). In the GSH production phase of the fed-batch culture, the optimal solution was to control mu to mu(c) in order to maintain a maximum specific GSH production rate. The value of mu(c) also coincided with the critical specific growth rate at which no ethanol formation occurs. Therefore, the control of mu to mu(c) could be done indirectly by maintaining a constant ethanol concentration, that is, zero net ethanol formation, through proper manipulation of the glucose feed rate. Maximum production of GSH was realized using the developed FLC; maximum production was a consequence of the substrate feeding strategy and cysteine addition, and the FLC was a simple way to realize the strategy. (c) 1993 John Wiley & Sons, Inc.     

Production of shikonin derivatives by cell suspension cultures of Lithospermum erythrorhizon

An excellent new medium was developed for the production of shikonin derivatives by suspension cultures of Lithospermum erythrorhizon. We investigated the effects of all the components of White's medium on the production of these derivatives. Nitrate, phosphate, copper, sulfate and sucrose had especially marked effects. With the new, M-9, medium produced from these studies the yield of shikonin derivatives was 1400 mg/l and the yield for dried cells was about 12%, whereas it was 120 mg/l, or about 2% with White's medium.