Characterization of truncated endo-ß-1,4-glucanases from a compost metagenomic library and their saccharification potentials.

A gene encoding an endo-ß-1,4-glucanase (Cel6H-f481) was cloned from a compost metagenomic library. The gene, cel6H-f481, was composed of 1446 bp to encode a fused protein of 481 amino acid residues (50,429 Da), i.e., 445 residues (Cel6H-445) from the metagenome, and 36 residues from the pUC19 vector at N-terminus. Cel6H-445 belonged to glycosyl hydrolase (GH) family 6 and showed 71% identity with Actinotalea fermentans endoglucanase with low coverage. Several active bands of truncated forms were observed by activity staining of the crude extract. Major truncated enzymes of 35 (Cel6H-p35) and 23 kDa (Cel6H-p23) were separated by HiTrap Q chromatography. The two enzymes had the same optimum temperature (50 °C) and pH (5.5), but Cel6H-p35 was more thermostable than Cel6H-p23 and other GH6 endoglucanases reported. Both enzymes efficiently hydrolyzed carboxymethyl-cellulose (CMC) and barley ß-glucan, but hardly hydrolyzed other substrates tested. The Vmax of Cel6H-p35 for CMC was 1.4 times greater than that of Cel6H-p23. The addition of the crude enzymes to a commercial enzyme set increased the saccharification of pretreated rice straw powder by up to 30.9%. These results suggest the N-terminal region of Cel6H-p35 contributes to thermostability and specific activity, and that the enzymes might be a useful additive for saccharification.

Learning, memory and exploratory similarities in genetically identical cloned dogs.

Somatic cell nuclear transfer allows generation of genetically identical animals using donor cells derived from animals with particular traits. To date, few studies have investigated whether or not these cloned dogs will show identical behavior patterns. To address this question, learning, memory and exploratory patterns were examined using six cloned dogs with identical nuclear genomes. The variance of total incorrect choice number in the Y-maze test among cloned dogs was significantly lower than that of the control dogs. There was also a significant decrease in variance in the level of exploratory activity in the open fields test compared to age-matched control dogs. These results indicate that cloned dogs show similar cognitive and exploratory patterns, suggesting that these behavioral phenotypes are related to the genotypes of the individuals.

Characterization of a Functional Role of the Bradyrhizobium japonicum Isocitrate Lyase in Desiccation Tolerance.

Bradyrhizobium japonicum is a nitrogen-fixing symbiont of soybean. In previous studies, transcriptomic profiling of B. japonicum USDA110, grown under various environmental conditions, revealed the highly induced gene aceA, encoding isocitrate lyase (ICL). The ICL catalyzes the conversion of isocitrate to succinate and glyoxylate in the glyoxylate bypass of the TCA cycle. Here, we evaluated the functional role of B. japonicum ICL under desiccation-induced stress conditions. We purified AceA (molecular mass = 65 kDa) from B. japonicum USDA110, using a His-tag and Ni-NTA column approach, and confirmed its ICL enzyme activity. The aceA mutant showed higher sensitivity to desiccation stress (27% relative humidity (RH)), compared to the wild type. ICL activity of the wild type strain increased approximately 2.5-fold upon exposure to 27% RH for 24 h. The aceA mutant also showed an increased susceptibility to salt stress. Gene expression analysis of aceA using qRT-PCR revealed a 148-fold induction by desiccation, while other genes involved in the glyoxylate pathway were not differentially expressed in this condition. Transcriptome analyses revealed that stress-related genes, such as chaperones, were upregulated in the wild-type under desiccating conditions, even though fold induction was not dramatic (ca. 1.5-2.5-fold).

The mechanism of antibacterial activity of phlorofucofuroeckol-A against methicillin-resistant Staphylococcus aureus.

To find more effective ways of overcoming methicillin-resistant Staphylococcus aureus (MRSA), there has been considerable interest in the use of marine-derived constituents as alternatives to control pathogenic microorganisms. In this study, we investigated whether phlorofucofuroeckol-A (PFF) isolated from the edible brown alga Eisenia bicyclis suppressed production or function of penicillin-binding protein 2a (PBP2a). The antimicrobial mode of action of PFF in MRSA was identified by measuring cell membrane integrity and using the time-kill curve method. We attempted to determine the antimicrobial effects of PFF on the expression level of the resistance determinants mecA and its regulatory genes mecI and mecR1 in MRSA by reverse transcriptase polymerase chain reaction. PFF suppressed mecI, mecR1, and mecA gene expression in a dose-dependent manner. In addition, we revealed PFF mediates the suppressive effect of PBP2a expression in MRSA by Western blot analysis. PFF suppressed production of the PBP2a protein, suggesting that PFF probably acts by controlling the methicillin resistance-associated genes involved in the cell wall and production of PBP2a. These results demonstrate that PFF isolated from E. bicyclis significantly suppressed the expression of the methicillin resistance-associated genes and production of PBP2a, which is considered the primary cause of methicillin resistance.

Removal of off-flavors from sea tangle (Laminaria japonica) extract by fermentation with Aspergillus oryzae.

This study was conducted to reduce off-flavors from sea tangle (Laminaria japonica) extract since the typical odor of seaweed is an impediment to consumption of seaweed products. Fifty-six odor compounds emitted from the extract were identified using a thermal desorbor and gas chromatography-mass spectrometry. On the basis of expected odor intensity (EOI), isovaleric acid (41.2%), allyl isothiocyanate (22.6%), octanal (11.1%) and acetaldehyde (10.6%) were responsible for about 85.5% of total odor strength in the extract, suggesting that the odor of the extract might mainly be attributed to these compounds. The EOIs of odor compounds were dramatically reduced or disappeared during fermentation by Aspergillus oryzae. Total EOI of the odor compounds decreased about four-fold, compared with that of the raw extract (control) after the four days of fermentation at 30°C with agitation at 120 rpm. These results indicate that microbial fermentation may be a good strategy to reduce off-flavors of seaweeds.

Molecular characterization of three crustin genes in the morotoge shrimp, Pandalopsis japonica.

Crustins are among the most important antimicrobial peptides (AMPs) found in decapod crustaceans. They are small cationic AMPs (5-7 kDa) characterized by a proline-rich amino-terminal domain and a cysteine-rich carboxyl-terminal domain. Here, the first 3 crustin-like cDNAs (Pj-crus Ia, Ib, and II) were identified from the morotoge shrimp, Pandalopsis japonica. The full-length cDNAs of Pj-crus Ia, Ib, and II consisted of 1135, 580, and 700 nucleotides and encoded putative proteins containing 109, 119, and 186 amino acids residues, respectively. All 3 identified Pj-crus sequences exhibited the conserved domain organization for crustins, including a signal sequence, a cysteine-containing region, a glycine-rich region, and a whey-acidic protein (WAP) domain. Amino acid sequence comparisons and phylogenetic analysis revealed that the Pj-crus Ia and Ib belong to type I crustins (e.g., carcinin), which have been mostly identified from Brachyura and Astacidea, whereas Pj-crus II was classified as belonging to the type II crustins, which are mainly found in Dendrobranchiata. An analysis of the organization of these 3 Pj-crus genes revealed that the splicing site within the WAP domain may be an important key for classifying types I and II crustin family members. The tissue distribution profile results showed that the Pj-crus I genes were expressed in a tissue-specific manner but that the Pj-crus II gene was expressed ubiquitously, suggesting that these crustins may play different roles in various tissues or under different physiological conditions. The bacterial challenge results suggested that the Pj-crus genes may be transcriptionally influenced by different bacterial types. This comparative study of various crustin family members will help extend the knowledge on the crustacean innate immune response, which will provide important basic information for controlling shrimp immunity against various pathogens.

Two type I crustacean hyperglycemic hormone (CHH) genes in Morotoge shrimp (Pandalopsis japonica): cloning and expression of eyestalk and pericardial organ isoforms produced by alternative splicing and a novel type I CHH with predicted structure shared with type II CHH peptides.

Crustacean hyperglycemic hormone (CHH) peptide family members play critical roles in growth and reproduction in decapods. Three cDNAs encoding CHH family members (Pj-CHH1ES, Pj-CHH1PO, and Pj-CHH2) were isolated by a combination of bioinformatic analysis and conventional cloning strategies. Pj-CHH1ES and Pj-CHH1PO were products of the same gene that were generated by alternative mRNA splicing, whereas Pj-CHH2 was the product of a second gene. The Pj-CHH1 and Pj-CHH2 genes had four exons and three introns, suggesting the two genes arose from gene duplication. The three cDNAs were classified in the type I CHH subfamily, as the deduced amino acid sequences had a CHH precursor-related peptide sequence positioned between the N-terminal signal sequence and C-terminal mature peptide sequence. The Pj-CHH1ES isoform was expressed at a higher level in the eyestalk X-organ/sinus gland (XO/SG) complex and at a lower level in the gill. The Pj-CHH1PO isoform was expressed at higher levels in the XO/SG complex, brain, abdominal ganglion, and thoracic ganglion and at a lower level in the epidermis. Pj-CHH2 was expressed at a higher level in the thoracic ganglion and at a lower level in the gill. Real-time polymerase chain reaction was used to quantify the effects of eyestalk ablation on the mRNA levels of the three Pj-CHHs in the brain, thoracic ganglion, and gill. Eyestalk ablation reduced expression of Pj-CHH1ES in the brain and Pj-CHH1PO and Pj-CHH2 in the thoracic ganglion. Sequence alignment of the Pj-CHHs with CHHs from other species indicated that Pj-CHH2 had an additional alanine at position #9 of the mature peptide. Molecular modeling showed that the Pj-CHH2 mature peptide had a short alpha helix (α1) in the N-terminal region, which is characteristic of type II CHHs. This suggests that Pj-CHH2 differs in function from other type I CHHs.

Whole-genome expression profiling of Bradyrhizobium japonicum in response to hydrogen peroxide.

Bradyrhizobium japonicum, a nitrogen-fixing bacterium in soil, establishes a symbiotic relationship with the leguminous soybean plant. Despite a mutualistic association between the two partners, the host plant produces an oxidative burst to protect itself from the invasion of rhizobial cells. We investigated the effects of H(2)O(2)-mediated oxidative stress on B. japonicum gene expression in both prolonged exposure (PE) and fulminant shock (FS) conditions. In total, 439 and 650 genes were differentially expressed for the PE and FS conditions, respectively, at a twofold cut-off with q < 0.05. A number of genes within the transport and binding proteins category were upregulated during PE and a majority of those genes are involved in ABC transporter systems. Many genes encoding ? factors, global stress response proteins, the FixK(2) transcription factor, and its regulatory targets were found to be upregulated in the FS condition. Surprisingly, catalase and peroxidase genes which are typically expressed in other bacteria under oxidative stress were not differentially expressed in either condition. The isocitrate lyase gene (aceA) was induced by fulminant H(2)O(2) shock, as was evident at both the transcriptional and translational levels. Interestingly, there was no significant effect of H(2)O(2) on exopolysaccharide production at the given experimental conditions.

Two juvenile hormone esterase-like carboxylesterase cDNAs from a Pandalus shrimp (Pandalopsis japonica): cloning, tissue expression, and effects of eyestalk ablation.

Methyl farnesoate (MF), a crustacean juvenile hormone (JH) analog, plays important roles in the regulation of a number of physiological processes such as molting, metamorphosis, and reproduction. Understanding its metabolic pathway is a key for various potential applications in crustacean aquaculture, including artificial seed production and enhancement of growth. Although the synthetic pathway of MF is well established, little is known about its degradation and recycling in crustaceans. In insects, juvenile hormone esterase (JHE), a carboxylesterase, is responsible for JH inactivation. Two cDNAs, encoding JHE-like carboxylesterases (CXEs) from the hepatopancreas and ovary of Pandalopsis japonica, were isolated by using a combination of in-silico data mining from an expressed sequence tag (EST) database and traditional PCR-based cloning. The full length Pj-CXE1 (2084bp) and Pj-CXE2 (1985bp) cDNAs encoded proteins composed of 584 and 581 amino acids, respectively. The active site sequence and domain organization of the Pj-CXEs were highly conserved, including the catalytic triad and other motifs, which suggested that both Pj-CXEs are biologically active carboxylesterases. Phylogenetic analysis of the deduced sequences of Pj-CXEs showed that both were most closely related to the JHEs from non-lepidopteran insects. End-point RT-PCR showed that Pj-CXE1 was expressed primarily in the gonad, whereas Pj-CXE2 was expressed in both the hepatopancreas and hindgut. Quantitative PCR showed that Pj-CXE1 was upregulated in the gonads by eyestalk ablation (ESA). In contrast, ESA had no significant effect on Pj-CXE2 expression in hepatopancreas or gonad. This is the first report of the cloning of two JHE-like CXE cDNAs in decapods and the upregulation of Pj-CXE1 by acute withdrawal of eyestalk neuropeptides. Further study is needed to understand the function of CXEs in MF metabolism and its regulation by eyestalk neuropeptides.

Genome-wide transcriptional and physiological responses of Bradyrhizobium japonicum to paraquat-mediated oxidative stress.

The rhizobial bacterium Bradyrhizobium japonicum functions as a nitrogen-fixing symbiont of the soybean plant (Glycine max). Plants are capable of producing an oxidative burst, a rapid proliferation of reactive oxygen species (ROS), as a defense mechanism against pathogenic and symbiotic bacteria. Therefore, B. japonicum must be able to resist such a defense mechanism to initiate nodulation. In this study, paraquat, a known superoxide radical-inducing agent, was used to investigate this response. Genome-wide transcriptional profiles were created for both prolonged exposure (PE) and fulminant shock (FS) conditions. These profiles revealed that 190 and 86 genes were up- and downregulated for the former condition, and that 299 and 105 genes were up- and downregulated for the latter condition, respectively (>2.0-fold; P < 0.05). Many genes within putative operons for F(0)F(1)-ATP synthase, chemotaxis, transport, and ribosomal proteins were upregulated during PE. The transcriptional profile for the FS condition strangely resembled that of a bacteroid condition, including the FixK(2) transcription factor and most of its response elements. However, genes encoding canonical ROS scavenging enzymes, such as superoxide dismutase and catalase, were not detected, suggesting constitutive expression of those genes by endogenous ROS. Various physiological tests, including exopolysaccharide (EPS), cellular protein, and motility characterization, were performed to corroborate the gene expression data. The results suggest that B. japonicum responds to tolerable oxidative stress during PE through enhanced motility, increased translational activity, and EPS production, in addition to the expression of genes involved in global stress responses, such as chaperones and sigma factors.

Characterization of two vitellogenin cDNAs from a Pandalus shrimp (Pandalopsis japonica): expression in hepatopancreas is down-regulated by endosulfan exposure.

Endosulfan is a neurotoxic organochlorine insecticide of the cyclodiene family of pesticides that inhibits molting and reproduction in aquatic crustaceans. In order to determine the molecular mechanism of endosulfan as an endocrine disrupting chemical (EDC), differential display RT-PCR (DDRT-PCR) was used to isolate genes in the shrimp, Pandalopsis japonica, affected by endosulfan exposure. PCR screening of cDNA from the hepatopancreas from control and endosulfan-exposed animals, using 120 sets of random primers, yielded partial cDNAs encoding two vitellogenin-like proteins (Pj-Vg1 and -Vg2). Complete sequences were obtained using a combination of RT-PCR and RACE-PCR. Pj-Vg1 (7883bp) encoded a protein composed of 2533 amino acid residues (283.27 kDa estimated mass), whereas Pj-Vg2 (7792 bp) encoded a protein composed of 2537 amino acids residues (284.87 kDa estimated mass). Alignment of the Pj-Vgs with those of other vitellogenins identified a conserved subtilisin cleavage site (RQKR) and the lipoprotein N-terminal (vitellin), DUF1081, and von Willebrand factor type D domains, indicating both genes encoded functional proteins. Phylogenetic analysis showed that Pj-Vg1 and -Vg2 were most similar to Pandalus hypsinotus Vg. Both Pj-Vg1 and -Vg2 were expressed primarily in the hepatopancreas, although the Pj-Vg2 transcript was also detected in the ovary. The effects of the 3-day endosulfan exposure (2.5 microg/L and 25 microg/L) on Vg expression in the hepatopancreas were determined by quantitative RT-PCR. Expression of both transcripts was significantly inhibited at 25 microg/L suggesting that Pj-Vgs can be used as indicator for endosulfan exposure.

Partial purification and characterization of glutaminase from Lactobacillus reuteri KCTC3594.

In this study, we attempted to purify and characterize glutaminase (EC. 3.5.1.2) from Lactobacillus reuteri KCTC3594. The glutaminase was purified approximately 21-fold from the cell-free extract of L. reuteri KCTC3594 by protamine sulfate treatment and chromatography methods including anion exchange and gel filtration. The sizes of two major bands of the enzyme were presumed to be 70 and 50 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The glutaminase activity of L. reuteri KCTC3594 was assayed in various ranges of pH, temperature, and salt concentrations. The enzyme activity was optimal at 40 degrees C and pH of 7.5. It was shown that the glutaminase was salt-tolerant because the enzyme activity was maintained 50% at 15% (w/v) salt concentrations. On the other hand, the enzyme was strongly inhibited up to 80% by 6-diazo-5-oxo-L-norleucine (10 mM) and iodoacetate (50 mM) indicating that the purified enzyme represents typical characteristics of glutaminase.