ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue

Although trans-translation mediated by tmRNA-SmpB has long been known as the sole system to relieve bacterial stalled ribosomes, ArfA has recently been identified as an alternative factor for ribosome rescue in Escherichia coli. This process requires hydrolysis of nascent peptidyl-tRNA by RF2, which usually acts as a stop codon-specific peptide release factor. It poses a fascinating question of how ArfA and RF2 recognize and rescue the stalled ribosome. Here, we mapped the location of ArfA in the stalled ribosome by directed hydroxyl radical probing. It revealed an ArfA-binding site around the neck region of the 30S subunit in which the N- and C-terminal regions of ArfA are close to the decoding center and the mRNA entry channel, respectively. ArfA and RF2 sequentially enter the ribosome stalled in either the middle or 3′ end of mRNA, whereas RF2 induces a productive conformational change of ArfA only when ribosome is stalled at the 3′ end of mRNA. On the basis of these results, we propose that ArfA functions as the sensor to recognize the target ribosome after RF2 binding.     

Characterization of the reversible nature of the reaction catalyzed by sphingolipid ceramide N-deacylase. A novel form of reverse hydrolysis reaction.

Sphingolipid ceramide N-deacylase catalyzes a reversible reaction in which the amide linkages of the ceramides of various sphingolipids are cleaved or synthesized. Hydrolysis of sphingolipids by the enzyme proceeded efficiently at acidic pH in the presence of high concentrations of detergents, whereas the reverse reaction tended to be favored at neutral pH with a decrease in the detergent concentration. Although the catalytic efficiency (V(max)/K(m)) of the hydrolysis and reverse reactions was changed mainly by the concentration of detergents in the reaction mixture, V(max) and K(m) for the reverse reaction were relatively higher than those for the forward reaction, irrespective of the detergent concentration. The reverse reaction proceeded most efficiently when the molar ratio of lyso-sphingolipids and fatty acids was fixed at 1 : 1-2, the yield of the reaction exceeding 70-80%. The reverse and exchange (transacylation) reactions did not require ATP, CoA, metal ions or addition of organic solvents. Studies using inhibitors and chemical modifiers of the enzyme protein suggested that both the hydrolysis and condensation reactions are catalyzed at the same catalytic domain. These results indicate that the reverse hydrolysis reaction of the enzyme is unique, being completely different from those of lipases, proteases and glycosidases reported to date.     

Purification and characterization of a 7Fe ferredoxin from a thermophilic hydrogen-oxidizing bacterium, Bacillus schlegelii.

A ferredoxin (Fd) was purified from a thermophilic hydrogen-oxidizing bacterium, Bacillus schlegelii. This ferredoxin was a monomer with apparent molecular weight of 13,000 and contained 7 mol Fe/mol ferredoxin. The oxidized ferredoxin showed the characteristic EPR spectrum for [3Fe-4S]1+ (1.2 spin/mol Fd). This signal disappeared upon reduction with dithionite and new signals due to [3Fe-4S]0 and [4Fe-4S]1+ (0.7 spin/mol Fd) appeared. The quantitation of EPR signals and the iron content reveal that B. schlegelii ferredoxin contains one [3Fe-4S]1+/0 and one [4Fe-4S]2+/1+ cluster. The ferredoxin has the characteristic distribution of cysteines (-Cys8-X7-Cys16-X3-Cys20-Pro-) for 7Fe ferredoxins in the N-terminus.     

Resolution of racemic carboxylic acids via the lipasecatalyzed irreversible transesterification using vinyl esters; Effects of alcohols as nucleophiles and organic solvents on enantioselectivity

Summary The lipase-catalyzed irreversible transesterification procedure using vinyl esters has been applied to the resolution of racemic 2-phenoxypropanoic acids. The enantioselectivity was found to be affected profoundly by both the alcohol as a nucleophile and the organic solvent used.     

Rapid and Sensitive PCR Detection of Vibrio trachuri Pathogenic to Japanese Horse Mackerel (Trachurus japonicus)

A polymerase chain reaction (PCR) method was performed for rapid and sensitive detection of pathogenic Vibrio trachuri isolated from cultured Japanese horse mackerel. A set of primers was selected from the base sequence of the Pst I fragment of T9210 chromosomal DNA and used for PCR detection of T9210. This PCR specifically amplified the DNAs from V. trachuri T9210, T9213, and T9216 but not of those other bacterial strains. PCR using a Pst I-1 primer set made it possible to detect 100 fg of T9210 DNA. The PCR method reported here may be useful for detection and identification of V. trachuri pathogenic to Japanese horse mackerel.     

Negative Finding in Cross-Protective Activity of Japanese Borrelia Isolates against Infection with Three Species of Lyme Disease Borrelia in Outbred Mice

Outer surface protein A (OspA) is the most promising candidate for a component vaccine against Lyme disease caused by Borrelia burgdorferi sensu lato. Active cross-protection using a whole-cell vaccine prepared from strains belonging various OspA serotypes observed in Japan and worldwide was examined. No cross-protection was obtained by heterologous OspA-serotype vaccines. Since OspA is a highly variable protein expressed by Borrelia, this suggests that immunologically different OspA serotypes need to be combined for the development of an effective vaccine in Japan.     

Induction of the Acrosome Reaction of Hemicentrotus pulcherrimus Spermatozoa by the Egg Jelly Molecules, Fucose-Rich Glycoconjugate and Spem-Activating Peptide I

A fucose-rich glycoconjugate (FRG) was isolated from egg jelly of the sea urchin Hemicentrotus pulcherrimus by gel filtration. FRG induced the acrosome reaction in H. pulcherrimus spermatozoa in a concentration-dependent manner, although it showed about half the activity of the original unfractionated jelly. Synthetic sperm-activating peptide I (SAP-I: Gly-Phe-Asp-Leu-Asn-Gly-Gly-Gly-Val-Gly) increased the rate of the acrosome reaction induced by FRG; the maximal rate of the acrosome reaction with FRG and SAP-I being that of the unfractionated jelly. The half-maximal increase in induction of the acrosome reaction by SAP-I with FRG occurred at 4 × 10⁻¹⁰ M SAP-I, which was almost the same concentration inducing half-maximal stimulation of sperm respiration. Pronase digestion of FRG resulted in an 50% decrease in induction of the acrosome reaction and also in the elevation of cAMP in sperm. Some reagents (monensin and 3-isobutyl-1-methylxanthine) which increase intracellular pH, Ca²⁺ and cyclic nucleotides also increased the rates of the acrosome reaction induced by FRG or pronase-digested FRG. However, the rates did not reach those with FRG or pronase-digested FRG with SAP-I. These results indicate that SAP-I promotes induction of the acrosome reaction by acting as a specific co-factor of FRG.     

Molecular cloning and sequencing of cDNA encoding urinary stone protein, which is identical to osteopontin.

We have sequenced a cDNA of urinary stone protein. cDNA sequences show complete homology between urinary stone protein and human osteopontin (bone sialoprotein) (nucleotides 265-886 and 1183-1424). Osteopontin is a recently discovered bone matrix protein which has been implicated in mediating mineral formation within bone extracellular matrix. This result shows that osteopontin is presumably involved in stone formation as stone matrix.     

Stopped-flow X-ray scattering device with a slit-type mixer

A slit-type mixer specially designed for stopped-flow X-ray scattering was constructed. It mixes two solutions at a time, allowing a large-sized window to be used immediately after mixing. Dead time of the mixer was 13 ms with 3.5 kg/cm2 of pressure at the piston head. It has been successfully used for studying the tetramer-dimer interconversion of phosphorylase a. The applicability of this mixer to other detection methods, far-UV circular dichroism, light scattering, EXAFS and fluorescence is also indicated.