In vivo and in vitro characterization of site-specific recombination of actinophage R4 integrase

The site-specific integrase of actinophage R4 belongs to the serine recombinase family. During the lysogenization process, it catalyzes site-specific recombination between the phage genome and the chromosome of Streptomyces parvulus 2297. An in vivo assay using Escherichia coli cells revealed that the minimum lengths of the recombination sites attB and attP are 50-bp and 49-bp, respectively, for efficient intramolecular recombination. The in vitro assay using overproduced R4 integrases as a hexahistidine (His(6))-glutathione-S-transferase (GST)-R4 integrase fusion protein, showed that the purified protein preparation retains the site-specific recombination activity which catalyzes the site-specific recombination between attP and attB in the intermolecular reaction. It also revealed that the inverted repeat within attP is essential for efficient in vitro intermolecular recombination. In addition, a gel shift assay showed that His(6)-GST-R4 integrase bound to the 50-bp attB and 49-bp attP specifically. Moreover, based on a detailed comparison analysis of amino acid sequences of serine integrases, we found the DNA binding region that is conserved in the serine recombinase containing the large C-terminal domain. Based on the results presented on this report, attachment sites needed in vitro and in vivo for site-specific recombination by the R4 integrase have been defined more precisely. This knowledge is useful for developing new genetic manipulation tools in the future.     

DNA methylation imprints on the IG-DMR of the Dlk1-Gtl2 domain in mouse male germline

Mouse genomes show a large cluster of imprinted genes at the Dlk1-Gtl2 domain in the distal region of chromosome 12. An intergenic-differentially methylated region (IG-DMR) located between Dlk1 and Gtl2 is specifically methylated in the male germline; IG-DMR regulates the parental allele-specific expression of imprinted genes. Here, we show the resetting of IG-DMR methylation marks during male germ-cell differentiation. For parental allele-specific methylation analysis, polymorphisms were detected in a 2.6-kb IG-DMR in three mouse strains. Bisulfite methylation analysis showed erasure of the marks by E14 and re-establishment before birth. The IG-DMR methylation status was maintained in spermatogonia and spermatocytes of mature testes. The IG-DMR methylation status established before birth is thus maintained throughout the lifetime in the male germline.     

Suppression of endoplasmic reticulum stress-induced caspase activation and cell death by the overexpression of Bcl-xL or Bcl-2

Continuous endoplasmic reticulum (ER) stress, such as the accumulation of unfolded proteins, results in cell death and relates to the pathogenesis of some neurodegenerative diseases. Treatment of brefeldin A, an inhibitor of transport between the ER and Golgi complex, induced cell death during 24 h, which accompanied activation of caspase-2, caspase-3 and caspase-9, starting at 12 h and increasing time-dependently up to 28 h. Caspase-2 was expressed and activated in not only mitochondria and cytosol, but also in the microsomal fraction containing ER and Golgi. Of note is that overexpression of Bcl-x(L) or Bcl-2 in PC12 cells markedly suppressed brefeldin A-induced activation of caspases and resulting cell death. Delivery of anti-Bcl-2 antibody into the Bcl-2-overexpressed cells again recovered apoptosis. While the brefeldin A-treatment induced the phosphorylation of both c-Jun N-terminal kinase (JNK) and p38 MAPK, overexpression of Bcl-x(L) or Bcl-2 reduced the prolonged phosphorylation of JNK, but not of p38 MAPK. Pretreatment with a JNK inhibitor, SP600125, suppressed the brefeldin A-induced caspase-2 activation and cell death significantly. Thus, our results suggest that protective effects of Bcl-x(L) and Bcl-2 against brefeldin A-induced cell death appear to be dependent on the regulation of JNK activation.     

Increased internalization of p120-uncoupled E-cadherin and a requirement for a dileucine motif in the cytoplasmic domain for endocytosis of the protein

E-cadherin is a member of the cadherin family of Ca2+-dependent cell-cell adhesion molecules. E-cadherin associates with beta-catenin at the membrane-distal region of its cytosolic domain and with p120 at the membrane-proximal region of its cytoplasmic domain. It has been shown that a pool of cell surface E-cadherin is constitutively internalized and recycled back to the surface. Further, p120 knockdown by small interference RNA resulted in dose-dependent elimination of cell surface E-cadherin. Consistent with these observations, we found that selective uncoupling of p120 from E-cadherin by introduction of amino acid substitutions in the p120-binding site increased the level of E-cadherin endocytosis. The increased endocytosis was clathrin-dependent, because it was blocked by expression of a dominant-negative form of dynamin or by hypertonic shock. A dileucine motif in the juxtamembrane cytoplasmic domain is required for E-cadherin endocytosis, because substitution of these residues to alanine resulted in impaired internalization of the protein. The alanine substitutions in the p120-uncoupled construct reduced endocytosis of the protein, indicating that this motif was dominant to p120 binding in the control of E-cadherin endocytosis. Therefore, these results are consistent with the idea that p120 regulates E-cadherin endocytosis by masking the dileucine motif and preventing interactions with adaptor proteins required for internalization.     

Mitochondria are targets for geranylgeranylacetone-induced cardioprotection against ischemia-reperfusion in the rat heart

It has been shown that orally administered geranylgeranylacetone (GGA), an anti-ulcer drug, induces expression of heat shock protein 72 (HSP72) and provides protection against ischemia-reperfusion in rat hearts. The underlying protective mechanisms, however, remain unknown. Mitochondria have been shown to be a selective target for heat stress-induced cardioprotection. Therefore, we hypothesized that preservation of mitochondrial function, owing to an opening of a putative channel in the inner mitochondrial membrane, the mitochondrial ATP-sensitive potassium (mitoK(ATP)) channel, could be involved in GGA- or heat stress-induced cardioprotection against ischemia-reperfusion. Rats were treated with oral GGA or vehicle. Twenty-four hours later, each heart was isolated and perfused with a Langendorff apparatus. GGA-treated hearts showed better functional recovery, and less creatine kinase was released during a 30-min reperfusion period, after 20 min of no-flow ischemia. Concomitant perfusion with 5-hydroxydecanoate (5-HD, 100 microM) or glibenclamide (10 microM) abolished the GGA-induced cardioprotective effect. GGA also showed preserved mitochondrial respiratory function, isolated at the end of the reperfusion period, which was abolished with 5-HD treatment. GGA prevented destruction of the mitochondrial structure by ischemia-reperfusion, as shown by electron microscopy. In cultured cardiomyocytes, GGA induced HSP72 expression and resulted in less damage to cells, including less apoptosis in response to hypoxia-reoxygenation. Treatment with 5-HD abolished the GGA-induced cardioprotective effects but did not affect HSP72 expression. Our results indicate that preserved mitochondrial respiratory function, owing to GGA-induced HSP72 expression, may, at least in part, have a role in cardioprotection against ischemia-reperfusion. These processes may involve opening of the mitoK(ATP) channel.     

A murine model of esophageal candidiasis with local characteristic symptoms

A simple method to establish a murine esophageal candidiasis model that displayed characteristic symptoms of the condition was developed using the sedative agent, chlorpromazine. Mice were immunosuppressed with prednisolone and were given tetracycline hydrochloride. One day later, the mice received chlorpromazine to keep them in a sedated state for about 3 hr. Under the sedated condition, they were infected with 4 x 10(7) viable cells of Candida albicans by intra-esophageal injection with a round-head needle on syringe. From day 3 to day 6 post inoculation, 10(5)-10(6) colony forming units of C. albicans were recovered from the esophageal tube of each mouse and whitish, curd-like patches were observed on most of the inner surface of the tube. Histological examination showed that C. albicans in esophageal lesions grew mainly in mycelial form. In this experimental model, intragastric administration of an itraconazole oral solution (20 mg/kg/day) was clearly effective. This model would provide a useful tool to investigate the pathogenesis of C. albicans esophageal infection and the efficacy of various antifungal agents microbiologically and symptomatically.     

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.     

Intrafamilial transmission of Helicobacter pylori among the population of endemic areas in Japan

BACKGROUND: Helicobacter pylori (H. pylori) infection is a worldwide phenomenon related to several gastrointestinal diseases. However, because many aspects concerning the route of transmission remain unclear, we performed this epidemiologic study to clarify the route of intrafamilial transmission of H. pylori. MATERIALS AND METHODS: A retrospective study was performed in three widely separate areas in Japan to investigate the prevalence of H. pylori infection. In 1993, 613 residents were tested as were 4136 in 2002, including 1447 family members of 625 families. Antibody to H. pylori (anti-H. pylori) was determined by enzyme-linked immunosorbent assay. RESULTS: In 2002, the age-adjusted anti-H. pylori prevalence in Hoshino Village (67.5%) was significantly higher than in Kasuya Town (55.0%) and in Ishigaki City (54.7%) (p < .0001, p = .0039, respectively). The age-adjusted anti-H. pylori prevalence of Ishigaki City significantly decreased from 1993 (68.4%) to 2002 (52.5%), showing an age cohort effect. However, the prevalence did not significantly differ in children aged 0-6 years of Ishigaki City between 1993 (9.6%) and 2002 (10.3%). A familial analysis in 2002 demonstrated that the prevalence of anti-H. pylori was significantly higher in children with anti-H. pylori-positive (21.6%, 22 of 102) than with -negative mothers (3.2%, 3 of 95) (p < .0001, by Mantel-Haenszel test), whereas there was no significant difference between children with anti-H. pylori-positive and -negative fathers. Moreover, the prevalence was significantly higher in wives with anti-H. pylori-positive (64.0%, 208 of 325) than with -negative husbands (46.5%, 80 of 172) (p = .0071, by Mantel-Haenszel test) and in husbands with anti-H. pylori-positive (72.2%, 208 of 288) than with -negative wives (56.0%, 117 of 209) (p = .0106, by Mantel-Haenszel test). CONCLUSIONS: In the last decade, H. pylori infection decreased in the general population of Japan by improvement of general hygiene conditions, but did not differ in young children, most likely because of mother-to-child transmission.     

Focus on Metabolism: Glutathionylation and Reduction of Methacrolein in Tomato Plants Account for Its Absorption from the Vapor Phase

A large portion of the volatile organic compounds emitted by plants are oxygenated to yield reactive carbonyl species, which have a big impact on atmospheric chemistry. Deposition to vegetation driven by the absorption of reactive carbonyl species into plants plays a major role in cleansing the atmosphere, but the mechanisms supporting this absorption have been little examined. Here, we performed model experiments using methacrolein (MACR), one of the major reactive carbonyl species formed from isoprene, and tomato (Solanum lycopersicum) plants. Tomato shoots enclosed in a jar with MACR vapor efficiently absorbed MACR. The absorption efficiency was much higher than expected from the gas/liquid partition coefficient of MACR, indicating that MACR was likely metabolized in leaf tissues. Isobutyraldehyde, isobutyl alcohol, and methallyl alcohol (MAA) were detected in the headspace and inside tomato tissues treated with MACR vapor, suggesting that MACR was enzymatically reduced. Glutathione (GSH) conjugates of MACR (MACR-GSH) and MAA (MAA-GSH) were also detected. MACR-GSH was essentially formed through spontaneous conjugation between endogenous GSH and exogenous MACR, and reduction of MACR-GSH to MAA-GSH was likely catalyzed by an NADPH-dependent enzyme in tomato leaves. Glutathionylation was the metabolic pathway most responsible for the absorption of MACR, but when the amount of MACR exceeded the available GSH, MACR that accumulated reduced photosynthetic capacity. In an experiment simulating the natural environment using gas flow, MACR-GSH and MAA-GSH accumulation accounted for 30% to 40% of the MACR supplied. These results suggest that MACR metabolism, especially spontaneous glutathionylation, is an essential factor supporting MACR absorption from the atmosphere by tomato plants.Plants emit vast amounts of volatile organic chemicals (VOCs) into the atmosphere. The annual emission of VOCs other than methane is estimated to be approximately 1,300 Tg of carbon (Goldstein and Galbally, 2007), with approximately 90% originating from biogenic sources, of which one-third (approximately 500 Tg of carbon/year) is isoprene (Guenther et al., 1995). In the atmosphere, VOCs undergo the chemical processes of photolysis and reaction with hydroxyl and nitrate radicals (Atkinson and Arey, 2003). Isoprene, for example, is converted into a series of isomeric hydroxyl-substituted alkyl peroxyl radicals, which are further converted into methyl vinyl ketone (MVK; but-3-en-2-one) and methacrolein (MACR; 2-methylprop-2-enal; Liu et al., 2013). These VOCs and their oxygenated products (oVOCs) are important components for the production of ozone and aerosols, and thus have a big impact on atmospheric chemistry and even on the climate system (Goldstein and Galbally, 2007). VOCs and oVOCs are removed from the atmosphere through oxidation to carbon monoxide or dioxide, dry or wet deposition, or secondary aerosol formation (Goldstein and Galbally, 2007). Among these, deposition to vegetation plays a major role in the removal of VOCs and oVOCs from the atmosphere (Karl et al., 2010).A significant portion of the deposition to vegetation is attributable to the uptake of VOCs and oVOCs by plants, and a field study showed that MVK and MACR were immediately lost once they entered a leaf through stomata (Karl et al., 2010). Under growth conditions where stomatal conductance is high enough, the partitioning of VOCs between air and leaf water phases in equilibrium and the capacity of the plant to metabolize, translocate, and store VOCs determine their uptake rate (Tani et al., 2013). The immediate loss in leaves observed with MVK and MACR is indicative of efficient enzymatic reactions metabolizing them; however, the details of the metabolism of these oVOCs have been little investigated so far.The absorption and metabolism of several VOCs by plants have been reported. Airborne ent-kaurene was absorbed by Arabidopsis (Arabidopsis thaliana), Japanese cypress (Chamaecyparis obtusa), and Japanese cedar (Cryptomeria japonica) plants and converted into GAs (Otsuka et al., 2004). Arabidopsis absorbed (Z)-3-hexenal and converted it into (Z)-3-hexen-1-ol or further into (Z)-3-hexen-1-yl acetate using NADPH and acetyl-CoA, probably inside the plant tissues (Matsui et al., 2012). Nicotiana attenuata plants absorbed dimethyl disulfide formed by rhizobacteria (Meldau et al., 2013). The sulfur atom derived from volatile dimethyl disulfide was assimilated into plant proteins. Karl et al. (2010) assumed that aldehyde dehydrogenase, which is involved in detoxification that limits aldehyde accumulation and oxidative stress (Kirch et al., 2004), is involved in the uptake of oVOCs containing an aldehyde moiety; however, they did not provide direct evidence supporting their assumption.Conjugation of VOCs and oVOCs with sugar or glutathione (GSH) is another way to metabolize them. (Z)-3-Hexen-1-ol in the vapor phase was taken up by tomato (Solanum lycopersicum) plants and converted into its glycoside (Sugimoto et al., 2014). (E)-2-Hexenal reacts with GSH spontaneously and/or via glutathione S-transferase (GST) to form hexanal-GSH, which is subsequently reduced to hexanol-GSH (Davoine et al., 2006), although it is uncertain whether airborne (E)-2-hexenal is converted into its corresponding GSH adduct. Glutathionylation of (E)-2-hexenal is common and has been confirmed in grapevine (Vitis vinifera) and passion fruit (Passiflora edulis; Kobayashi et al., 2011; Fedrizzi et al., 2012). The catabolites formed from the GSH adduct in these crops are precursors for important flavor components.Although it is clear that oVOCs are absorbed by vegetation and that their efficient uptake is probably supported by metabolism in plant tissues, the metabolic fates of oVOCs taken up from the vapor phase into plants have been little studied. Here, we performed a series of model experiments using tomato seedlings and MACR to dissect the fates of oVOCs once they entered into plant tissues. To clearly see absorption of MACR and its fates in plant tissues, a model experiment under enclosed conditions with a high concentration of MACR was first carried out. Subsequently, an airflow system with a realistically low concentration of MACR was used. Tomato plants efficiently absorbed MACR. Reduction of the carbonyl moiety and the double bond conjugated to the carbonyl and conjugation with GSH were the major methods of metabolism of exogenous MACR. The metabolism seemed to be involved in the detoxification of reactive carbonyl species, which, in turn, accounted for the oVOC deposition to vegetation.