Crystal structure of the sweet-tasting protein thaumatin II at 1.27 Å

Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 Å. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the Cα atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.     

Akhirin regulates the proliferation and differentiation of neural stem cells/progenitor cells at neurogenic niches in mouse brain

Specialized microenvironment, or neurogenic niche, in embryonic and postnatal mouse brain plays critical roles during neurogenesis throughout adulthood. The subventricular zone (SVZ) and the dentate gyrus (DG) of hippocampus in the mouse brain are two major neurogenic niches where neurogenesis is directed by numerous regulatory factors. Now, we report Akhirin (AKH), a stem cell maintenance factor in mouse spinal cord, plays a pivotal regulatory role in the SVZ and in the DG. AKH showed specific distribution during development in embryonic and postnatal neurogenic niches. Loss of AKH led to abnormal development of the ventricular zone and the DG along with reduction of cellular proliferation in both regions. In AKH knockout mice (AKH^−/−), quiescent neural stem cells (NSCs) increased, while proliferative NSCs or neural progenitor cells decreased at both neurogenic niches. In vitro NSC culture assay showed increased number of neurospheres and reduced neurogenesis in AKH^−/−. These results indicate that AKH, at the neurogenic niche, exerts dynamic regulatory role on NSC self-renewal, proliferation and differentiation during SVZ and hippocampal neurogenesis.     

Development and characterisation of microsatellite loci in Farfugium japonicum (Asteraceae)

Eight microsatellite loci for the perennial herb Farfugium japonicum, including the rheophytic variety luchuense endemic to riparian areas of the Ryukyu Islands, Japan, were isolated and characterised. The number of alleles ranged from 5 to 14. The expected (H _E) and observed (H _O) heterozygosities were 0.344–0.885 and 0.121–0.754, respectively, from 69 individuals in one population. Six loci exhibited significantly fewer heterozygotes than expected under Hardy–Weinberg equilibrium (P < 0.05). The primers amplifying microsatellite sequences in F. japonicum may provide a population genetics tool useful in the establishment of a conservation strategy.     

Cleavage of a model DNA replication fork by a Type I restriction endonuclease

Cleavage of a DNA replication fork leads to fork restoration by recombination repair. In prokaryote cells carrying restriction–modification systems, fork passage reduces genome methylation by the modification enzyme and exposes the chromosome to attack by the restriction enzyme. Various observations have suggested a relationship between the fork and Type I restriction enzymes, which cleave DNA at a distance from a recognition sequence. Here, we demonstrate that a Type I restriction enzyme preparation cleaves a model replication fork at its branch. The enzyme probably tracks along the DNA from an unmethylated recognition site on the daughter DNA and cuts the fork upon encountering the branch point. Our finding suggests that these restriction–modification systems contribute to genome maintenance through cell death and indicates that DNA replication fork cleavage represents a critical point in genome maintenance to choose between the restoration pathway and the destruction pathway.     

Inhibition of hepatic damage and liver fibrosis by brain natriuretic peptide

Anti-fibrotic and organ protective effects of brain natriuretic peptide (BNP) have been reported. In this study, effects of BNP on liver fibrosis were examined in the carbon tetrachloride (CCl₄)-induced liver fibrosis model using BNP-transgenic (Tg) and wild-type (WT) mice. Twice-a-week intraperitoneal injections of CCl₄ for 8 weeks resulted in massive liver fibrosis, augmented transforming growth factor (TGF)-β₁ and type I procollagen α₁ chain (Col1a1) mRNA expression, and the hepatic stellate cell (HSC) activation in WT mice, all of which were significantly suppressed in Tg mice. These observations indicate that BNP inhibits liver fibrosis by attenuating the activation of HSCs.     

Computational chemical analysis of Ru(II)‐Pheox–catalyzed highly enantioselective intramolecular cyclopropanation reactions

Computational chemical analysis of Ru(II)‐Pheox–catalyzed highly enantioselective intramolecular cyclopropanation reactions was performed using density functional theory (DFT). In this study, cyclopropane ring–fused γ‐lactones, which are 5.8 kcal/mol more stable than the corresponding minor enantiomer, are obtained as the major product. The results of the calculations suggest that the enantioselectivity of the Ru(II)‐Pheox–catalyzed intramolecular cyclopropanation reaction is affected by the energy differences between the starting structures 5l and 5i . The reaction pathway was found to be a stepwise mechanism that proceeds through the formation of a metallacyclobutane intermediate. This is the first example of a computational chemical analysis of enantioselective control in an intramolecular carbene‐transfer reaction using C₁‐symmetric catalysts.     

Successful expression of a novel bacterial gene for pinoresinol reductase and its effect on lignan biosynthesis in transgenic Arabidopsis thaliana

Pinoresinol reductase and pinoresinol/lariciresinol reductase play important roles in an early step of lignan biosynthesis in plants. The activities of both enzymes have also been detected in bacteria. In this study, pinZ, which was first isolated as a gene for bacterial pinoresinol reductase, was constitutively expressed in Arabidopsis thaliana under the control of the cauliflower mosaic virus 35S promoter. Higher reductive activity toward pinoresinol was detected in the resultant transgenic plants but not in wild-type plant. Principal component analysis of data from untargeted metabolome analyses of stem, root, and leaf extracts of the wild-type and two independent transgenic lines indicate that pinZ expression caused dynamic metabolic changes in stems, but not in roots and leaves. The metabolome data also suggest that expression of pinZ influenced the metabolisms of lignan and glucosinolates but not so much of neolignans such as guaiacylglycerol-8-O-4′-feruloyl ethers. In-depth quantitative analysis by liquid chromatography–tandem mass spectrometry (LC-MS/MS) indicated that amounts of pinoresinol and its glucoside form were markedly reduced in the transgenic plant, whereas the amounts of glucoside form of secoisolariciresinol in transgenic roots, leaves, and stems increased. The detected levels of lariciresinol in the transgenic plant following β-glucosidase treatment also tended to be higher than those in the wild-type plant. Our findings indicate that overexpression of pinZ induces change in lignan compositions and has a major effect not only on lignan biosynthesis but also on biosynthesis of other primary and secondary metabolites.     

Characterization of the catabolic pathway for a phenylcoumaran-type lignin-derived biaryl in Sphingobium sp. strain SYK-6

Sphingobium sp. strain SYK-6 is capable of degrading various lignin-derived biaryls. We determined the catabolic pathway of a phenylcoumaran-type compound, dehydrodiconiferyl alcohol (DCA) in SYK-6, and identified some of the DCA catabolism genes. In SYK-6 cells, the alcohol group of DCA was oxidized to the carboxyl group, first at the B-ring side chain and then at the A-ring side chain. The resultant metabolite was degraded to 5-formylferulate and vanillin through the decarboxylation and the Cα–Cβ cleavage of the A-ring side chain. Based on the DCA catabolic pathway, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) genes are thought to be involved in the conversion of DCA into an aldehyde intermediate (DCA-L) and the conversion of DCA-L into a carboxylic acid intermediate (DCA-C), respectively. SLG_05620 and SLG_24930, which belong to quinohemoprotein ADH and aryl ADH, respectively, were isolated as the genes responsible for the oxidation of DCA. In addition to these genes, multiple genes similar to SLG_05620 and SLG_24930 were found to confer DCA oxidation activities on Escherichia coli cells. In order to identify the DCA-L dehydrogenase genes, the DCA-L oxidation activities of the SYK-6 gene products of putative twenty-one ALDH genes were examined. Significant activities were observed in the four ALDH gene products, including the SLG_27910 product, which showed the highest activity. The disruption of SLG_27910 caused a decreased conversion of DCA-L, suggesting that SLG_27910 plays an important role in the DCA-L oxidation. In conclusion, no specific gene seems to be solely responsible for the conversion of DCA and DCA-L, however, the multiple genes encoding quinohemoprotein ADH and aryl ADH genes, and four ALDH genes are probably involved in the conversion processes.     

A Dominant Mutation in the Light-Oxygen and Voltage2 Domain Vicinity Impairs Phototropin1 Signaling in Tomato

In higher plants, blue light (BL) phototropism is primarily controlled by the phototropins, which are also involved in stomatal movement and chloroplast relocation. These photoresponses are mediated by two phototropins, phot1 and phot2. Phot1 mediates responses with higher sensitivity than phot2, and phot2 specifically mediates chloroplast avoidance and dark positioning responses. Here, we report the isolation and characterization of a Nonphototropic seedling1 (Nps1) mutant of tomato (Solanum lycopersicum). The mutant is impaired in low-fluence BL responses, including chloroplast accumulation and stomatal opening. Genetic analyses show that the mutant locus is dominant negative in nature. In dark-grown seedlings of the Nps1 mutant, phot1 protein accumulates at a highly reduced level relative to the wild type and lacks BL-induced autophosphorylation. The mutant harbors a single glycine-1484-to-alanine transition in the Hinge1 region of a phot1 homolog, resulting in an arginine-to-histidine substitution (R495H) in a highly conserved A′α helix proximal to the light-oxygen and voltage2 domain of the translated gene product. Significantly, the R495H substitution occurring in the Hinge1 region of PHOT1 abolishes its regulatory activity in Nps1 seedlings, thereby highlighting the functional significance of the A′α helix region in phototropic signaling of tomato.Being sessile in nature, plants have developed diverse sets of sensory mechanisms, integrating external cues such as light, water, and temperature to adapt their growth and development to the ambient environment. Plants have evolved a cohort of photoreceptors such as red/far-red light-sensing phytochromes (Chen and Chory, 2011), UV-A/blue light (BL)-sensing phototropins (Christie, 2007; Holland et al., 2009; Suetsugu and Wada, 2013), cryptochromes (Yu et al., 2010; Liu et al., 2011), Zeitlupe (ZTL)/Flavin-binding, Kelch repeat, F-box protein1/light-oxygen and voltage (LOV)-kelch protein2 members of the ZTL/ADAGIO putative family of photoreceptors (Suetsugu and Wada, 2013), and UV-B light-sensing UV-B resistance8 (Heijde and Ulm, 2012), enabling them to sense nearly the full range of the solar spectrum. One of the most visually obvious photoresponses of flowering plants involves the growth and orientation of organs toward or away from light, particularly during the early stages of growth and the establishment of seedlings (Iino, 1990) and during gap-filling situations in dense canopy conditions (Ballaré, 1999) for optimizing photosynthesis and interspecies/intraspecies competition. Several studies involving the relative effectiveness of different wavelengths of the solar spectrum as well as monitoring of lateral differences in light intensity revealed that the directional growth of plants is specifically mediated by the UV-A/blue region of the visible spectrum. Molecular genetic analysis of Arabidopsis (Arabidopsis thaliana) mutants inhibited in hypocotyl curvature toward BL revealed that, among the UV-A light-/BL-specific photoreceptors, the phototropins perceive ambient light as a cue for directional growth (Liscum and Briggs, 1995; Kagawa et al., 2001).Phototropins have been identified in several plant species, ranging from the green alga Chlamydomonas reinhardtii to higher plants (Briggs et al., 2001). To date, two members of the phototropins have been reported from higher plants, phot1 and phot2, which share sequence homology (Sakai et al., 2001). Physiological analyses with Arabidopsis mutants lacking phot1 and phot2 have revealed that, in addition to regulating the hypocotyl curvature of seedlings toward BL (Huala et al., 1997; Christie et al., 1998), phototropins also regulate a diverse range of responses in flowering plants (Christie and Murphy, 2013; Hohm et al., 2013). These responses include chloroplast movements (Sakai et al., 2001), nuclear positioning (Iwabuchi et al., 2007), stomatal opening (Kinoshita et al., 2001), sun tracking (Inoue et al., 2008b), leaf expansion (Ohgishi et al., 2004), leaf movements (Inoue et al., 2005), leaf photomorphogenesis (Kozuka et al., 2011), leaf flattening (Sakamoto and Briggs, 2002), and the rapid inhibition of the growth of etiolated hypocotyls (Folta and Spalding, 2001).While both phot1 and phot2 overlap in function in regulating phototropism, chloroplast accumulation, leaf expansion, and stomatal opening, they also exhibit differential photosensitivity to BL, where phot1 is more sensitive to low-fluence BL than phot2. Both phot1 and phot2 redundantly regulate the chloroplast accumulation toward low-fluence BL, and phot2 exclusively regulates the chloroplast avoidance from high-fluence BL (Jarillo et al., 2001; Kagawa et al., 2001), while phot1 solely mediates the rapid inhibition of the elongation of etiolated hypocotyls (Folta and Spalding, 2001). Analysis of mutants downstream of blue light perception by phototropins revealed that the phototropin signaling branches out at an early step, and phot1 and phot2 trigger distinct photoresponses recruiting multiple signaling partners (Christie and Murphy, 2013; Hohm et al., 2013).Molecular characterizations have shown that phototropins are plasma membrane-associated Ser/Thr kinases containing a photosensory domain (Briggs and Christie, 2002) in the N-terminal region composed of two LOV domains (LOV1 and LOV2) and the kinase domain at the C-terminal end. The LOV1 and LOV2 domains bind the FMN as chromophore and are responsible for BL sensing by phototropin. Although phototropins characteristically possess two LOV domains, the photoregulation of phototropin activity is predominantly mediated by LOV2 (Christie, 2007). The exposure to BL also causes adduct formation between the FMN and the Cys residue in LOV domains and leads to the phosphorylation of phototropin, which is believed to be the primary step in the transmission of phototropic signals (Christie et al., 1998; Sakai et al., 2000). To decipher the functions of different domains of phototropins, many different substitution mutants of phototropins have been generated, which have enabled the elucidation of the functional significance of the different domains (Matsuoka and Tokutomi, 2005; Jones et al., 2007; Kong et al., 2007; Inoue et al., 2008a). Inoue et al. (2008a) showed that the BL-induced autophosphorylation of Ser-851 in the C-terminal kinase domain of phototropin is the primary step for initiating stomatal opening, phototropism, chloroplast accumulation, and leaf flattening. Mutational studies also revealed that the photosensory N-terminal domain of phototropin acts as a kinase inhibitor, where the LOV2 domain inhibits the activity of kinase domain by binding to it, and BL exposure is required for the dissociation of the LOV2 domain, enabling phosphorylation of the kinase domain (Matsuoka and Tokutomi, 2005; Jones et al., 2007).While our current understanding of phototropism has been greatly facilitated by the isolation of phototropins and their signaling mutants, the phot mutants identified to date are loss-of-function alleles. The lack of dominant-negative alleles or alleles with increased sensitivity to phototropic stimulus has hindered exploration into the roles of different domains of phot proteins in regulating phototropic signaling. In addition, the dearth of mutants defective in phototropin or phototropin-mediated responses has been a major bottleneck in furthering our understanding of the function of phototropins in crop species. Although phototropin homologs have been identified from a variety of crop species, including oat (Avena sativa; Zacherl et al., 1998), rice (Oryza sativa; Kanegae et al., 2000), and tomato (Solanum lycopersicum; Sharma et al., 2007; Sharma and Sharma, 2007), only the coleoptile phototropism1 mutant of rice has been isolated, which is defective in BL phototropism (Haga et al., 2005).Here, we report that in a mutant screen for nonphototropic seedlings under continuous BL, we recovered a strong dominant-negative mutation of phot1. The dominant-negative mutations are useful to elucidate redundant functions, as mutant protein in addition to suppressing its own functions can also suppress the function of its partners. The characterization of this new phot1 mutant revealed that the dominant activity is caused by the substitution of an Arg residue located in the A′α helix in the Hinge1 region between the LOV1 and LOV2 domains. Our study shows the functional importance of the A′α helix (Halavaty and Moffat, 2007) in regulating phot1-mediated signaling in tomato.