A deductive database system PACADE for analyzing 3-D and secondary structures of protein

We have developed a deductive database system PACADE for analyzing3-D and secondary structures of protein. The PA CADE systemconsists of a relational database created from Protein DataBank and a deductive engine DEE based on logic programming.It has the following features: (1) The system has an inferencemechanism. This means by which users can easily write and checkbiological hypotheses using logical and declarative rules insteadof procedural programs. (2) The relational database of the PACADE system stores data on bath 3-D and secondwy structuresof protein. The integration of this two level structure makesfeasible an abstract representation of the protein structure.We describe herein the design, functions, and implementationof this PACADE system.     

Characterization of the m7G(5')pppN-pyrophosphatase activity from HeLa cells.

The m7(G(5')pppN-pyrophosphatase activity previously detected in HeLa cells has been further characterized. Results from DEAE-cellulose column chromatography and polyacrylamide gel electrophoresis under nondenaturing conditions revealed only one enzyme activity in HeLa cell extracts which was capable of selectively hydrolyzing m7G(5')pppN to yield m7pG + ppN (where N = 2'-O-methylated or unmethylated ribonucleosides or oligonucleotides of up to 8 to 10 nucleosides in length). The majority (approximately 95%) of this activity was found in the cytoplasmic extract but appeared not to be associated with the lysosomal fraction. m7G(5')pppG was hydrolyzed by the partially purified enzyme in the absence of divalent cations at a pH optimum of 7.5 and a temperature optimum of 45 degrees, with a Michaelis constant (Km) of 1.7 micronM. Sedimentation analysis and gel filtration showed the molecular weight of the enzyme as approximately 81,000. Inhibition studies testing the effect of a number of prospective substrates on the rate of m7G(5')pppG hydrolysis have confirmed the importance of the methyl moiety at the N7 position of guanosine for enzyme-substrate interaction. Furthermore, the trimethylated guanosine-containing 5'-terminal structure derived from U-2 RNA was found not to serve as substrate, and 7-methylinosine, unlike 7-methylguanosine, was not an effective inhibitor of m7G(5')pppG hydrolysis. Thus, the 2-amino group of the 7-methylguanosine portion of m7G(5')pppN is also important for substrate interaction with this specific pyrophosphatase.     

Different stability of ligand-receptor complex formed with two endothelin receptor species, ETA and ETB.

There are at least two types of endothelin receptors, ETA and ETB, present in various tissues. We found that although biotinylated ET-1 could bind to both ETA and ETB receptors, the stability of the formed ligand-receptor complexes was different. When the preformed complexes of receptor (solubilized from canine brain and lung membranes) and biotinylated ET-1 were subjected to avidin agarose column chromatography, most of the ETA activity was recovered in the pass-through fraction and the remainder was recovered in the 0.5 M KSCN eluate as ligand-free forms. On the other hand, the ETB activity bound firmly to the avidin agarose column was eluted with 1.5 M KSCN. The detection of the complex of 125I-ET-1 and its receptor by SDS-PAGE run at a low temperature was only possible with the ETB fractions and the complex of 125I-ET-1 and ETA was unstable during the separation. These results suggest that the conformation of the ligand binding sites of canine ETA and ETB as well as the stability of their ligand-receptor complexes to SDS are significantly different. Similar observations were also obtained for human ETA and ETB receptors.     

The methylation of adenovirus-specific nuclear and cytoplasmic RNA.

Each poly(A) containing cytoplasmic AD-2 MRNA contains at its 5' terminus the general structure m7 GpppN1 pN2p or m7 GpppN1mpN2mpNp as well as an average of 4 m6A and 0.5-1 m5C residues per molecule. Almost all of the N1m residues are adenine derivatives including Am, m6Am and probably m26,6Am. The N2m is mostly Cm but small amounts of the other three methylated bases are also present. All the methylated constitutents of mRNA are distant from the 3' terminal poly(A). The amount of m6A appears to be greater in larger mRNA than in smaller mRNA. Nuclear Ad-2 specific RNA also contains caps, m6A, and m5C with about twice as much m6A relative to caps as cytoplasmic mRNA. The similarity of Ad-2 nuclear and mRNA to HeLa hnRNA and mRNA suggests that adenovirus mRNA production is a good model for eukaryotic mRNA production.     

Identification of two metabolites induced by a butyrolactone autoregulator IM-2 in Streptomyces sp. FRI-5

Abstract In order to determine whether non-elastase-producing strains of Pseudomonas aeruginosa such as N-10, PA103 and IFO3080 can express foreign elastase genes, we introduced elastase genes from P. aeruginosa IFO3455 (elastase-producing) as well as from PA103 and N-10 into non-elastase-producing P. aeruginosa strains. Results suggested that gene expression, secretion, and precursor processing systems of elastase were essentially normal in P. aeruginosa N-10 and IFO3080. Our studies using various elastase genes showed that both the elastase structural gene and 5'-upstream regions of P. aeruginosa PA103 were also normal. This was confirmed by the finding that P. aeruginosa N-10 and IFO3080 which carry the PA103 elastase gene produced elastase. Several deleted or chimeric genes were constructed using the 5'-upstream regions of elastase genes from P. aeruginosa N-10 or PA103 and studies of expression revealed that two individual DNA bases seem to be important in suppressing P. aeruginosa N-10 elastase gene expression. Possible reasons for the lack of elastase in these non-elastase-producing strains are discussed.     

Spatial variation in breeding phenology at small spatial scales: A stochastic effect of population size

Spatial variation in phenology can occur at small spatial scales over which individuals can disperse or forage within one generation. Previous studies have assumed that variations in phenological peaks are caused by differences in abiotic environmental characteristics. However, environments should generally be similar among local habitats over small spatial scales. When the local population size is small, the phenological peak of the local population should be strongly affected by the variation in timing expressed by individuals. If a regional population consists of small local subpopulations (e.g., a metapopulation), the stochastic processes regulated by population sizes may explain the spatial variation in phenology. In this study, we quantitatively evaluated the extent of the spatial and annual variations in the breeding phenology of the forest green tree frog, Rhacophorus arboreus habiting a small area (<10 km²). The spatial variation in phenological peaks among 25 breeding sites was large over 6 years. This spatial variation was not explained by differences in air temperature or water depth. Randomization tests revealed that a large portion of the spatial variation could be explained by differences in population size, without considering site-specific factors. Annual variations in phenological peaks tended to be greater for smaller populations. These results imply that the stochastic process might have caused the spatial and annual variations in the phenological peaks of R. arboreus observed in the study region. Understanding spatiotemporal variation in phenology determined by stochastic process would be important to better predict interspecific interactions and (meta)population dynamics at small spatial scales.     

Cooperation of the IFT-A complex with the IFT-B complex is required for ciliary retrograde protein trafficking and GPCR import

Cilia sense and transduce extracellular signals via specific receptors. The intraflagellar transport (IFT) machinery mediates not only bidirectional protein trafficking within cilia but also the import/export of ciliary proteins across the ciliary gate. The IFT machinery is known to comprise two multisubunit complexes, namely, IFT-A and IFT-B; however, little is known about how the two complexes cooperate to mediate ciliary protein trafficking. We here show that IFT144–IFT122 from IFT-A and IFT88–IFT52 from IFT-B make major contributions to the interface between the two complexes. Exogenous expression of the IFT88(Δα) mutant, which has decreased binding to IFT-A, partially restores the ciliogenesis defect of IFT88-knockout (KO) cells. However, IFT88(Δα)-expressing IFT88-KO cells demonstrate a defect in IFT-A entry into cilia, aberrant accumulation of IFT-B proteins at the bulged ciliary tips, and impaired import of ciliary G protein–coupled receptors (GPCRs). Furthermore, overaccumulated IFT proteins at the bulged tips appeared to be released as extracellular vesicles. These phenotypes of IFT88(Δα)-expressing IFT88-KO cells resembled those of IFT144-KO cells. These observations together indicate that the IFT-A complex cooperates with the IFT-B complex to mediate the ciliary entry of GPCRs as well as retrograde trafficking of the IFT machinery from the ciliary tip.