GNRA/receptor interacting modules: versatile modular units for natural and artificial RNA architectures

Interactions between GNRA tetraloops and their receptors are found frequently as modular units in various types of naturally occurring structured RNAs. Due to their functional importance, GNRA/receptor interactions have been studied extensively with regard to their 3D structures and biochemical and biophysical properties. Artificial non-natural GNRA/receptor modules have also been generated not only to obtain a better understanding of this class of motifs in natural RNA structures but also for application of these modular units to the design and construction of artificial RNA structures that can be used as platforms to generate functional RNAs applicable for nanobiotechnology. In this review, we present a survey of structures, functions, and analyses as well as artificial generation and application of GNRA/receptor interacting modules.     

NBS1 recruits RAD18 via a RAD6-like domain and regulates Pol η-dependent translesion DNA synthesis

Translesion DNA synthesis, a process orchestrated by monoubiquitinated PCNA, is critical for DNA damage tolerance. While the ubiquitin-conjugating enzyme RAD6 and ubiquitin ligase RAD18 are known to monoubiquitinate PCNA, how they are regulated by DNA damage is not fully understood. We show that NBS1 (mutated in Nijmegen breakage syndrome) binds to RAD18 after UV irradiation and mediates the recruitment of RAD18 to sites of DNA damage. Disruption of NBS1 abolished RAD18-dependent PCNA ubiquitination and Polη focus formation, leading to elevated UV sensitivity and mutation. Unexpectedly, the RAD18-interacting domain of NBS1, which was mapped to its C terminus, shares structural and functional similarity with the RAD18-interacting domain of RAD6. These domains of NBS1 and RAD6 allow the two proteins to interact with RAD18 homodimers simultaneously and are crucial for Polη-dependent UV tolerance. Thus, in addition to chromosomal break repair, NBS1 plays a key role in translesion DNA synthesis.     

The WD40 protein Morg1 facilitates Par6–aPKC binding to Crb3 for apical identity in epithelial cells

Formation of apico-basal polarity in epithelial cells is crucial for both morphogenesis (e.g., cyst formation) and function (e.g., tight junction development). Atypical protein kinase C (aPKC), complexed with Par6, is considered to translocate to the apical membrane and function in epithelial cell polarization. However, the mechanism for translocation of the Par6–aPKC complex has remained largely unknown. Here, we show that the WD40 protein Morg1 (mitogen-activated protein kinase organizer 1) directly binds to Par6 and thus facilitates apical targeting of Par6–aPKC in Madin-Darby canine kidney epithelial cells. Morg1 also interacts with the apical transmembrane protein Crumbs3 to promote Par6–aPKC binding to Crumbs3, which is reinforced with the apically localized small GTPase Cdc42. Depletion of Morg1 disrupted both tight junction development in monolayer culture and cyst formation in three-dimensional culture; apico-basal polarity was notably restored by forced targeting of aPKC to the apical surface. Thus, Par6–aPKC recruitment to the premature apical membrane appears to be required for definition of apical identity of epithelial cells.     

Studies on α-Alkyl-α-amino Acids

Effects of cytokinins were studied on rotenone-sensitive NADH dehydrogenase in mitochondria from fresh potato tubers (Solarium tuberosum), in consideration of the operation of external and rotenone-insensitive internal NADH dehydrogenases that has not been fully accounted for in previous studies. In submitochondrial particles (smp), zeatin was only weakly active, and zeatin riboside (ZR) was inactive. Inhibition rates at 400 μM of isopentenyladenine (iP) and isopentenyladenosine (iPA) were 45% and 30%, respectively, and that of BA (BA) was 64%. In intact mitochondria, the inhibition by iP and BA significantly increased, I₅₀ being 50 and 250 μM, respectively, but that by zeatin and iPA decreased. A structure–activity study showed that hydrophobic and steric factors are important for the activity. Cytokinins inhibited the electron flow via natural quinone more strongly than that via synthetic quinone. These results suggest that among the cytokinins the species that can regulate the electron transport is iP rather than its riboside or zeatin.     

Fungal Metabolism of trans-2-Octenoic Acid

Juvenile hormone esterases (JHEs) function in juvenile hormone (JH) degradation. In the silkworm, Bombyx mori, we have characterized authentic JHE (Bmjhe) and five other carboxyl/cholinesterase (CCE) genes (Bmcce-1 to -5) with GQSAG, a motif sequence of JHE. But none of the genes appeared to function in vivo as a JHE, except for Bmjhe. Recently it was reported that the GQSAG motif might be dispensable, and that the Thr-316 residue has functional significance for JHE activity. On the basis of these findings, we identified two novel JHE candidates, Bmcce-6 and Bmcce-7, that lack GQSAG but possess Thr-316. In the CCE phylogenetic tree, BmCCE-6 was close to the lepidopteran JHE cluster, while BmCCE-7 constituted the same cluster as pheromone-degrading esterases. The developmental expression profiles were different among Bmjhe, Bmcce-6, and Bmcce-7. None of the proteins hydrolyzed JH in vitro. Our results suggest that only one CCE (BmJHE) functions as JHE in the silkworm.     

Mass Spectra of Volatile Sulfur Compounds in Foods

The absolute configurations of twelve α-aryl and α,β-diarylalkylamines were studied as N-acyl derivatives by circular dichroism (CD) measurements and by gas chromatography (GC).

The signs of Cotton effects for the S-configuration around 260 nm were positive and those around 210 nm were negative, although some exceptions were found due to the substituents on the benzene nuclei. In contrast, the GC behavior was considered less sensitive to the substituents on the benzene nuclei, and the elution orders were an R-before S-configuration consistently on a chiral OA-300 column. The absolute configurations of some amines were estimated in this study. GC as well as CD measurements could be a promising method for the assignment of the absolute configuration.     

UV-Photolysis of S-(cis-l-Propenyl)-L-cysteine in Oxygen-free Aqueous Solution

From the comparisons of mass spectral fragmentations and gas chromatographic retention times with reference compounds, volatile flavor products from UV-photolysis of S-(cis-l-propenyl)-L-cysteine in oxygen-free aqueous solutions were identical with propanal, 2-methyl-2-pentenal, n-propyl mercaptan, allyl mercaptan, 1-propenyl mercaptan, 2-methylthiophene, 3-methylthiophene, 2,3-dimethylthiophene, 2,4-dimethylthiophene, 2,5-dimethylthiophene, 3,4-dimethylthiophene, n-propyl 1-propenyl sulfide and di- 1-propenyl sulfide. Moreover, from the comparison of two-dimentional thin-layer chromatograms with reference compounds, ninhydrin-positive products with interest in terms of the degradation mechanism were identical with alanine and cystine. It seems that above-mentioned thiophene derivatives are produced via 1-propenyl thiyl radicals.     

Determination of Caffeic Acid in the Digestive Juice of Silkworm Larvae and Its Antibacterial Activity against the Pathogenic Streptococcus faecalis AD–4

Caffeic acid (CA) was identified as an antibacterial substance in the digestive juice of silkworm larvae. Concentrations of CA in the digestive juice decreased from 460 ppm to 3 ppm as the starvation period of the larvae was prolonged from 1 hr to 12 hr. The specimens of digestive juice (ca. pH 10.0) containing 460 ppm and 222 ppm of CA had antibacterial activity against Streptococcus faecalis AD–4, a pathogenic intestinal bacterium affecting silkworm larvae, and an alkaline medium (pH 10.0) containing 500 ppm of authentic CA also exhibited antibacterial activity.

These findings suggest that CA plays an important role in the defense mechanism of silkworm larvae against the bacterial infection.     

Studies on the Degradation Mechanisms of Proteins and Their Derivatives in the Foods

Cysteine mercaptals and mercaptoles were prepared by the reactions of l-cystine with formaldehyde, acetaldehyde, n-butyraldehyde, benzaldehyde, furfural, pyruvic acid and levulinic acid in 6 n hydrochloric or sulfuric acid. Hydrogen sulfide released from cysteine mercaptals and mercaptoles in heated aqueous solutions (oil bath: 120°C) was determined. Although a small amount of hydrogen sulfide was liberated from l-cystine on one hour heating, its amount increased suddenly after three hours. Among these compounds l-cystine mercaptal of furfural was most unstable and a large amount of hydrogen sulfide was produced.