Expression,purification, and crystallization of glutamyl-tRNA(Gln) specific amidotransferase from Bacillus stearothermophilus

Although the genes that encode the glutamyl-tRNA(Gln) (Glu-tRNA(Gln)) specific amidotransferase (Glu-AdTase) from various bacteria and eukaryotic organelles are known, the precise mechanism of the enzyme is still unclear. One of the reasons is that there is no information on the three-dimensional structure of the complex, the Glu-AdTase:Glu-tRNA(Gln):ATP:amino group donor. To obtain the crystals of Glu-AdTase, the Glu-AdTase of Bacillus stearothermophilus was overexpressed and purified after cloning of the gene that encodes the enzyme. The cloned DNA contained the full-length gene cluster that represented the Glu-AdTase of B. stearothermophilus, and was organized as an operon that consisted of three open-reading frames (ORFs). The order of the genes was gatCAB, as shown in Bacillus subtilis. The ORFs showed a high amino-acid homology to those of B. subtilis (A subunit, 73.2%; B subunit, 81.6%; C subunit, 69.5%) and Staphylococcus aureus (A subunit, 61.9%; B subunit, 71.8%; C subunit, 45.9%). The ORFs were re-cloned on the overexpression vector, pTrc99a, and a recombinant pTrcgatCABBST was obtained. The Glu-AdTase that was overexpressed with pTrcgatCABBST in Escherichia coli retained transamidation activity on the mischarged glutamic acid on the tRNA(Gln). It also produced correctly-charged Gln-tRNA(Gln) at 37, 42, and 50 degrees C. Although Glu-AdTases from both B. subtilis and B. stearothermophilus were subjected to crystallization, the micro-crystals were only obtained from the B. stearothermophilus enzyme.     

Differential diagnosis of Taenia asiatica using multiplex PCR

Taenia asiatica and T. saginata are frequently confused tapeworms due to their morphological similarities and sympatric distribution in Asian regions. To resolve this problem, a high-resolution multiplex PCR assay was developed to distinguish T. asiatica infections from infection with other human Taenia tapeworms. For molecular characterization, the species specificity of all materials used was confirmed by sequencing of the cox1 gene. Fifty-two samples were analyzed in this study, comprising 20 samples of T. asiatica genomic DNA from China, Korea, and the Philippines; 24 samples of T. saginata from Belgium, Chile, China, Ethiopia, France, Indonesia, Korea, Laos, the Philippines, Poland, Taiwan, Thailand, and Switzerland; and 10 samples of T. solium from Cape Verde, China, Honduras, and Korea. The diagnostic quality of the results obtained using PCR and species-specific primers designed from valine tRNA and NADH genes was equal to that based on the nucleotide sequencing of the cox1 gene. Using oligonucleotide primers Ta4978F, Ts5058F, Tso7421F, and Rev7915, the multiplex PCR assay was useful for the differentially diagnosing T. asiatica, T. saginata, and T. solium based on 706-, 629-, and 474-bp bands.     

Occurrence of a Hybrid Between Taenia saginata and Taenia asiatica Tapeworms in Cambodia

Human infection with Taenia asiatica or a hybrid between Taenia saginata and T. asiatica has not been reported in Cambodia. We detected for the first time a hybrid form between T. saginata and T. asiatica in Preah Vihear Province, Cambodia. An adult tapeworm specimen, i.e., 75 cm long strobila without scolex, was expelled from a 27-year-old man after praziquantel medication and purging. It was morphologically indistinguishable between T. saginata and T. asiatica. Several proglottids were molecularly analyzed to confirm the tapeworm species. The mitochondrial gene encoding cytochrome c oxidase subunit 1 (cox1) and nuclear genes encoding elongation factor-1α (ef1) and ezrin-radixin-moesin (ERM)-like protein (elp) were sequenced, and a single-allele analysis was performed to confirm the haploid genotype. The results revealed that our sample showed a discrepancy between the mitochondrial and 2 nuclear genes. It possessed homozygous sequences typical of T. saginata at cox1 and ef1 loci. However, it was heterozygous at the elp locus, with 1 allele in T. asiatica (elpA) and 1 in T. saginata (elpC), which indicates that it is a hybrid between T. saginata and T. asiatica. The present results confirmed the presence of a hybrid between T. saginata and T. asiatica in Cambodia and strongly suggest the existence of also ‘pure’ T. asiatica in Cambodia.     

Mitochondrial Genome of Spirometra theileri Compared with Other Spirometra Species

This study was carried out to provide information on the taxonomic classification and analysis of mitochondrial genomes of Spirometra theileri. One strobila of S. theileri was collected from the intestine of an African leopard (Panthera pardus) in the Maswa Game Reserve, Tanzania. The complete mtDNA sequence of S. theileri was 13,685 bp encoding 36 genes including 12 protein genes, 22 tRNAs and 2 rRNAs with absence of atp8. Divergences of 12 protein-coding genes were as follow: 14.9% between S. theileri and S. erinaceieuropaei, 14.7% between S. theileri and S. decipiens, and 14.5% between S. theileri with S. ranarum. Divergences of 12 proteins of S. theileri and S. erinaceieuropaei ranged from 2.3% in cox1 to 15.7% in nad5, while S. theileri varied from S. decipiens and S. ranarum by 1.3% in cox1 to 15.7% in nad3. Phylogenetic relationship of S. theileri with eucestodes inferred using the maximum likelihood and Bayesian inferences exhibited identical tree topologies. A clade composed of S. decipiens and S. ranarum formed a sister species to S. erinaceieuropaei, and S. theileri formed a sister species to all species in this clade. Within the diphyllobothridean clade, Dibothriocephalus, Diphyllobothrium and Spirometra formed a monophyletic group, and sister genera were well supported.     

Complete Mitochondrial Genome of Haplorchis taichui and Comparative Analysis with Other Trematodes

Mitochondrial genomes have been extensively studied for phylogenetic purposes and to investigate intra- and interspecific genetic variations. In recent years, numerous groups have undertaken sequencing of platyhelminth mitochondrial genomes. Haplorchis taichui (family Heterophyidae) is a trematode that infects humans and animals mainly in Asia, including the Mekong River basin. We sequenced and determined the organization of the complete mitochondrial genome of H. taichui. The mitochondrial genome is 15,130 bp long, containing 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Like other trematodes, it does not encode the atp8 gene. All genes are transcribed from the same strand. The ATG initiation codon is used for 9 protein-coding genes, and GTG for the remaining 3 (nad1, nad4, and nad5). The mitochondrial genome of H. taichui has a single long non-coding region between trnE and trnG. H. taichui has evolved as being more closely related to Opisthorchiidae than other trematode groups with maximal support in the phylogenetic analysis. Our results could provide a resource for the comparative mitochondrial genome analysis of trematodes, and may yield genetic markers for molecular epidemiological investigations into intestinal flukes.     

Characterization of primary thermal degradation features of lignocellulosic biomass after removal of inorganic metals by diverse solvents

Poplar wood powders were treated with distilled water, tap water, HCl and HF, respectively, to remove inorganics from the biomass and to investigate effect of demineralization processes on pyrolysis behavior of the biomass. TG and DTG revealed that maximum degradation temperatures rose slightly from 362°C for control to 372°C, 366°C and 368°C after demineralization with distilled water, HCl and HF, respectively. Maximum degradation rates also increased from 0.96%/°C for control to 1.15%/°C for HF-biomass, 1.23%/°C for DI-H(2)O-biomass, and 1.55%/°C for HCl-biomass. Analytical pyrolysis-GC/MS of demineralized biomasses produced approximately 45 pyrolysis compounds. Total amount of low molecular weight compounds, such as acetic acid, acetol, and 3-hydroxypropanal, was significantly lowered in the demineralized biomasses. But levoglucosan increased 2-10-folds in the demineralized biomasses. One of the features regarding lignin derivatives was the reduction of the amount of C6-type phenols, such as phenol, guaiacol, and syringol after demineralization.     

Hydrophobic interface between two regulators of K+ conductance domains critical for calcium-dependent activation of large conductance Ca2+-activated K+ channels

It has been suggested that the large conductance Ca(2)+-activated K(+) channel contains one or more domains known as regulators of K(+) conductance (RCK) in its cytosolic C terminus. Here, we show that the second RCK domain (RCK2) is functionally important and that it forms a heterodimer with RCK1 via a hydrophobic interface. Mutant channels lacking RCK2 are nonfunctional despite their tetramerization and surface expression. The hydrophobic residues that are expected to form an interface between RCK1 and RCK2, based on the crystal structure of the bacterial MthK channel, are well conserved, and the interactions of these residues were confirmed by mutant cycle analysis. The hydrophobic interaction appears to be critical for the Ca(2+)-dependent gating of the large conductance Ca(2+)-activated K(+) channel.     

Role of the Rice Hexokinases OsHXK5 and OsHXK6 as Glucose Sensors

The Arabidopsis (Arabidopsis thaliana) hexokinase 1 (AtHXK1) is recognized as an important glucose (Glc) sensor. However, the function of hexokinases as Glc sensors has not been clearly demonstrated in other plant species, including rice (Oryza sativa). To investigate the functions of rice hexokinase isoforms, we characterized OsHXK5 and OsHXK6, which are evolutionarily related to AtHXK1. Transient expression analyses using GFP fusion constructs revealed that OsHXK5 and OsHXK6 are associated with mitochondria. Interestingly, the OsHXK5ΔmTP-GFP and OsHXK6ΔmTP-GFP fusion proteins, which lack N-terminal mitochondrial targeting peptides, were present mainly in the nucleus with a small amount of the proteins seen in the cytosol. In addition, the OsHXK5NLS-GFP and OsHXK6NLS-GFP fusion proteins harboring nuclear localization signals were targeted predominantly in the nucleus, suggesting that these OsHXKs retain a dual-targeting ability to mitochondria and nuclei. In transient expression assays using promoter∷luciferase fusion constructs, these two OsHXKs and their catalytically inactive alleles dramatically enhanced the Glc-dependent repression of the maize (Zea mays) Rubisco small subunit (RbcS) and rice α-amylase genes in mesophyll protoplasts of maize and rice. Notably, the expression of OsHXK5, OsHXK6, or their mutant alleles complemented the Arabidopsis glucose insensitive2-1 mutant, thereby resulting in wild-type characteristics in seedling development, Glc-dependent gene expression, and plant growth. Furthermore, transgenic rice plants overexpressing OsHXK5 or OsHXK6 exhibited hypersensitive plant growth retardation and enhanced repression of the photosynthetic gene RbcS in response to Glc treatment. These results provide evidence that rice OsHXK5 and OsHXK6 can function as Glc sensors.In higher plants, sugars are known to function as signaling molecules in addition to being a fundamental source of fuel for carbon and energy metabolism. Indeed, sugars have been shown to regulate physiological processes during the entire plant life cycle, from germination to flowering and senescence, and to function during defense responses to biotic and abiotic stresses (Jang and Sheen, 1994; Jang et al., 1997; Perata et al., 1997; Smeekens and Rook, 1997; Smeekens, 1998; Wingler et al., 1998; Rolland et al., 2001, 2006; Leon and Sheen, 2003; Gibson, 2005; Biemelt and Sonnewald, 2006; Seo et al., 2007). Therefore, to sustain normal plant growth and development, rigorous sugar sensing and signaling systems are important for coordinating and modulating many essential metabolic pathways.Glc, one of the main products of photosynthesis, is the most widely recognized sugar molecule that regulates plant signaling pathways (Koch, 1996; Yu et al., 1996; Ho et al., 2001; Chen, 2007). Yeast (Saccharomyces cerevisiae) has several Glc sensors, including the hexokinase ScHXK2, Glc transporter-like proteins Sucrose nonfermenting 3 (Snf3) and Restores glucose transport 2 (Rgt2), and G protein-coupled receptor Gpr1. These sensors have been reported to sense the internal and external Glc status as part of mechanisms controlling cell growth and gene expression (Rolland et al., 2001; Lemaire et al., 2004; Santangelo, 2006). Similarly, recent studies in plants have unveiled sugar sensing and signaling systems mediated by hexokinase as a Glc sensor or G protein-coupled receptors in a hexokinase-independent way (Rolland et al., 2001, 2002, 2006; Chen et al., 2003; Moore et al., 2003; Holsbeeks et al., 2004; Cho et al., 2006b; Huang et al., 2006). In addition, plant Snf1-related protein kinase 1 (SnRK1), which is an ortholog of the yeast Snf1, plays important roles linking sugar signal, as well as stress and developmental signals, for the global regulation of plant metabolism, energy balance, growth, and survival (Baena-González et al., 2007; Lu et al., 2007; Baena-González and Sheen, 2008).In addition to the catalytic role of hexokinase in plants, which is to facilitate hexose phosphorylation to form hexose-6-P, the role of hexokinase as an evolutionarily conserved Glc sensor was first recognized from biochemical, genetic, and molecular studies of Arabidopsis (Arabidopsis thaliana) hexokinase 1 (AtHXK1) transgenic plants and glucose insensitive2 (gin2) mutants (Jang et al., 1997; Rolland et al., 2002; Harrington and Bush, 2003; Moore et al., 2003; Cho et al., 2006b). Transgenic plants expressing catalytically inactive AtHXK1 mutant alleles in the gin2 mutant background have provided compelling evidence that the catalytic and sensory functions of AtHXK1 are uncoupled in the Arabidopsis plant (Moore et al., 2003). Furthermore, proteomics and yeast two-hybrid interaction experiments have revealed that in the nucleus, AtHXK1 interacts with two partners, the vacuolar H⁺-ATPase B1 and the 19S regulatory particle of proteasome subunit, to directly control the expression of specific photosynthetic genes (Cho et al., 2006b; Chen, 2007). In these studies, the interactions between AtHXK1 and vacuolar H⁺-ATPase B1 or 19S regulatory particle of proteasome subunit appeared not to require the enzymatic activity of AtHXK1. In the tomato (Solanum lycopersicum) plant, AtHXK1 expression causes a reduction in photosynthesis, growth inhibition, and the induction of rapid senescence (Dai et al., 1999), which are all characteristics of sugar sensing and signaling in photosynthetic tissues. With the exception of Arabidopsis HXK1, the role of hexokinases as Glc sensors has yet to be demonstrated in other plant species (Halford et al., 1999; Veramendi et al., 2002; Rolland et al., 2006).Hexokinases have been shown to associate with various subcellular compartments, including mitochondria, chloroplasts, Golgi complexes, endoplasmic reticula, plasma membranes, and cytosols, suggesting numerous distinct intracellular functions (Schleucher et al., 1998; Wiese et al., 1999; Frommer et al., 2003; Olsson et al., 2003; Giese et al., 2005; Cho et al., 2006a; Kandel-Kfir et al., 2006; Rezende et al., 2006; Damari-Weissler et al., 2007). In yeast, the Glc sensor ScHXK2 has a nuclear localization signal (NLS) within its N-terminal domain and resides partly in the nucleus in addition to the cytosol (Herrero et al., 1998; Randez-Gil et al., 1998). Furthermore, the nuclear localization of ScHXK2 is required for Glc repression of several genes, such as SUC2, HXK1, and GLK1 (Herrero et al., 1998; Rodríguez et al., 2001). A portion of cellular AtHXK1, which is predominantly associated with mitochondria, was also found to reside in the nucleus (Yanagisawa et al., 2003; Cho et al., 2006b). Under conditions of Glc excess, it has thus been hypothesized that nuclear AtHXK1 binds its substrate Glc, resulting in the suppression of target gene expression (Cho et al., 2006b; Chen, 2007).We have previously isolated 10 rice (Oryza sativa) hexokinases, OsHXK1 through OsHXK10, and demonstrated that all of these subtypes possess hexokinase activity (Cho et al., 2006a). The results of this previous study showed that OsHXK4 and OsHXK7 reside in the chloroplast stroma and cytosol, respectively. Based on sequence similarity and subcellular localization, we have identified two rice hexokinases homologous to AtHXK1, OsHXK5 and OsHXK6. The subcellular localization of OsHXK5 and OsHXK6, observed with GFP fusion constructs, suggested that OsHXK5 and OsHXK6 retain a dual-targeting ability to mitochondria and nuclei. This finding prompted us to examine whether these homologues play a role in Glc sensing and signaling in rice. To address this question, we observed the function of OsHXK5 and OsHXK6 in mesophyll protoplasts of maize (Zea mays) and rice and in transgenic rice plants. In addition, we transformed the Arabidopsis gin2-1 mutant with either wild-type or catalytically inactive alleles of OsHXK5 and OsHXK6 and analyzed their sugar sensing and signaling characteristics. Finally, the conserved role of hexokinase as a Glc sensor in Arabidopsis and rice plants is discussed.