Structural basis for recruitment of human flap endonuclease 1 to PCNA

Flap endonuclease-1 (FEN1) is a key enzyme for maintaining genomic stability and replication. Proliferating cell nuclear antigen (PCNA) binds FEN1 and stimulates its endonuclease activity. The structural basis of the FEN1-PCNA interaction was revealed by the crystal structure of the complex between human FEN1 and PCNA. The main interface involves the C-terminal tail of FEN1, which forms two beta-strands connected by a short helix, the betaA-alphaA-betaB motif, participating in beta-beta and hydrophobic interactions with PCNA. These interactions are similar to those previously observed for the p21CIP1/WAF1 peptide. However, this structure involving the full-length enzyme has revealed additional interfaces that are involved in the core domain. The interactions at the interfaces maintain the enzyme in an inactive 'locked-down' orientation and might be utilized in rapid DNA-tracking by preserving the central hole of PCNA for sliding along the DNA. A hinge region present between the core domain and the C-terminal tail of FEN1 would play a role in switching the FEN1 orientation from an inactive to an active orientation.     

Facultative amphidromy involving estuaries in an annual amphidromous fish from a subtropical marginal range

Variation in the life cycle of diadromous fishes can be explained by differential food availability between marine and freshwater habitats, since migration is often interpreted as a mechanism for exploiting food resources. Theoretically, a migration pattern of mainly remaining in freshwater occurs in tropical and subtropical habitats where fluvial productivity possibly exceeds marine productivity. However, in Yakugachi River, Amami-Oshima Island, southern Japan, low nutrient concentrations in the river suggest that food availability is limited for the subtropical Ryukyu-ayu Plecoglossus altivelis ryukyuensis. Since Ryukyu-ayu is an amphidromous fish that mainly grows in rivers after spending 2 months in the sea, limited food availability in rivers would force this species to migrate to other habitats with better food availability. Otolith increment and Sr:Ca analyses of 48 adult Ryukyu-ayu collected from the Yakugachi River revealed that all individuals visited estuaries more than three times after moving upstream. Although the specific growth rates of this species in the river had no correlation with the salinity profile in the fluvial period, this movement may be an adaptive choice because the salinity profile significantly affected the body size at maturity. Our results highlighted individual-based variations in amphidromous migration for utilizing estuaries, which could be explained by relatively higher productivity in estuarine than in freshwater and marine habitats.     

Cell-wall Polysaccharides of Immature Barley Plants. II. Characterization of a Xyloglucan

A xyloglucan occurring in the hemicellulose II fraction of cell walls of immature barley plants was characterized by methylation and fragmentation analyses. The results indicated that the xyloglucan was mainly composed of the following repeating units:      

Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica

Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica.     

pH-responsive switching of near-infrared absorption of a diradical complex of Pt and 3,4-diaminobenzoate formed in aqueous solutions

In alkaline aqueous solutions, 3,4-diaminobenzoate (H₂(²L^PDA)⁻) reacts with Pt^II to form a 1:2 (Pt:L) complex that intensely absorbs near-infrared (NIR) light at 713 nm (ε = 8.0 × 10⁴ M⁻¹ cm⁻¹). The absorption disappeared at pH < 3 (in DMSO), showing pH-responsive switching of the NIR absorption. By comparing the NIR-absorbing behavior of this complex to that of a complex, [Pt^II(¹L^ISQ)₂]²⁻, containing the analogous phenylenediamine ligand [(¹L^ISQ)²⁻ = o-diiminobenzosemiquinonate radical], the complex can be formulated as [Pt^II(²L^ISQ)₂]²⁻. The assignment of the entity was consistent with the redox and spectroelectrochemical behaviors and electronic spin resonance (ESR) spectroscopy. First, one-electron oxidation of [Pt^II(²L^ISQ)₂]²⁻ formed an ESR-silent complex assignable to the dimeric complex [{Pt^II(²L^ISQ)(²L^IBQ)}₂]²⁻ [(²L^IBQ) = o-iminobenzoquinone form] in which the two radical centers at were antiferromagnetically coupled. Second, the one-electron reduced complex of [Pt^II(²L^ISQ)₂]²⁻ exhibited an ESR signal attributed to [Pt^II(²L^ISQ)(²L^PDA)]³⁻; 34% of the electronic spin was located at the Pt^II center rather than on the moiety. The pH-responsive switching-off of the NIR absorption was thus rationally explained by oxidation of [Pt^II(²L^ISQ)₂]²⁻ to [{Pt^II(²L^ISQ)(²L^IBQ)}₂]²⁻ by the increase of the rest potential of the solution in the lower pH region.     

Geographical cline and inter-seaside difference in cone characteristics related to climatic conditions of old planted Pinus thunbergii populations throughout Japan

Although cone morphology has been mainly utilized for taxonomy or forestry purposes, characterization of the environmental factors that influence its variation is still insufficient. Major conifers distributed over diverse climatic conditions like the Japanese archipelago could show cone morphology variation among populations related to large differences in key influential factors such as temperature, snow, irradiance and sunshine. Geographical variation in cone characteristics (cone size, seed production, seed productivity per cone and seed size) was examined across the species distribution in 24 old planted Pinus thunbergii populations (479 trees) along two major seasides in Japan (Pacific Ocean side and Japan Sea side). Variance components of cone characteristics explained by seaside were at similar levels to those for populations nested within seasides. Populations on the Japan Sea side produced cones that had larger size (length and width), higher seed production (number of filled seeds per cone and seed mass per cone) and seed productivity per cone (seed-to-ovule ratio). Analysis of covariance showed that significant latitudinal clines observed in cone size and seed productivity per cone were mostly a result of inter-seaside differences. Linear mixed model analysis detected that geographical variation in cone size, seed production and seed productivity per cone in the populations were affected significantly by low temperature, more snow, less solar irradiance and less sunshine time. Large cone sizes and high seed productivity per cone found in the populations on the Japan Sea side could be explained by a genetic or plastic response to maintain reproductive success.     

Rhizobial Factors Required for Stem Nodule Maturation and Maintenance in Sesbania rostrata-Azorhizobium caulinodans ORS571 Symbiosis

The molecular and physiological mechanisms behind the maturation and maintenance of N₂-fixing nodules during development of symbiosis between rhizobia and legumes still remain unclear, although the early events of symbiosis are relatively well understood. Azorhizobium caulinodans ORS571 is a microsymbiont of the tropical legume Sesbania rostrata, forming N₂-fixing nodules not only on the roots but also on the stems. In this study, 10,080 transposon-inserted mutants of A. caulinodans ORS571 were individually inoculated onto the stems of S. rostrata, and those mutants that induced ineffective stem nodules, as displayed by halted development at various stages, were selected. From repeated observations on stem nodulation, 108 Tn5 mutants were selected and categorized into seven nodulation types based on size and N₂ fixation activity. Tn5 insertions of some mutants were found in the well-known nodulation, nitrogen fixation, and symbiosis-related genes, such as nod, nif, and fix, respectively, lipopolysaccharide synthesis-related genes, C₄ metabolism-related genes, and so on. However, other genes have not been reported to have roles in legume-rhizobium symbiosis. The list of newly identified symbiosis-related genes will present clues to aid in understanding the maturation and maintenance mechanisms of nodules.     

Increase of β-Fructofuranosidase Content in Tomato Fruit during the Ripening Process

β-Chloro-l-alanine was catalytically converted to pyruvate, ammonia and chloride by α-aminoisobutyrate (AIB) decomposing enzyme (α, β elimination), which was synchronously inactivated. There was a linear relationship between α, β elimination and inactivation. With apoenzyme, neither α, β elimination nor inactivation occurred. These facts suggest that α, β elimination is dependent on pyridoxal 5′-phosphate, and inactivation cooperates with α, β elimination (syncatalytic inactivation). But it seemed that d-form of β-chloroalanine was not a substrate for AIB decomposing enzyme, because just half amount of β-chloro-dl-alanine was decomposed to pyruvate by the enzyme.

An identical active site for each of following three reactions were shown by the fact that AIB decomposing activity, transamination activity and α, β elimination activity were lost in parallel. From a kinetic study, the affinity of the enzyme toward β-chloro-l-alanine was shown to be higher than that toward AIB or l-alanine. The turnover number, about 8,000, of α, β elimination during the inactivation of one mol of the enzyme was much larger than that of d-amino acid transaminase or alanine racemase.     

Kinetic properties and substrate inhibition of α-galactosidase from Aspergillus niger

The recombinant AglB produced by Pichia pastoris exhibited substrate inhibition behavior for the hydrolysis of p-nitrophenyl α-galactoside, whereas it hydrolyzed the natural substrates, including galactomanno-oligosaccharides and raffinose family oligosaccharides, according to the Michaelian kinetics. These contrasting kinetic behaviors can be attributed to the difference in the dissociation constant of second substrate from the enzyme and/or to the ability of the leaving group of the substrates. The enzyme displays the grater k_cat/K_m values for hydrolysis of the branched α-galactoside in galactomanno-oligosaccharides than that of raffinose and stachyose. A sequence comparison suggested that AglB had a shallow active-site pocket, and it can allow to hydrolyze the branched α-galactosides, but not linear raffinose family oligosaccharides.