Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field.

A Gram-stain-negative oval-rod-shaped, spore-forming anaerobic bacterium, designated as strain MCWD5T, was isolated from sediment of a salt pond in the Republic of Korea (35° 7' 18″ N 126° 19' 4″ E). The 16S rRNA gene sequence analysis revealed that strain MCWD5T had low similarity values to members in the family Lachnospiraceae, such as Robinsoniella peoriensis PPC31T (94.8 %), Ruminococcusgauvreauii CCRI-16110T (94.2 %) and Lachnotalea glycerini DLD10T (94.0 %), and its phylogenetic position is unstable. The strain could grow at 20-42 °C (optimum, 38-42 °C), pH 5.5-10.0 (pH 7.0) and with 0-6 % (2.0 %) NaCl. Strain MCWD5T could not use nitrate, nitrite, sulfate or sulfite as electron acceptors. The strain could utilize various carbohydrates, such as arabinose, cellobiose, glucose, etc., and polymers such as pectin and starch. The major fatty acids of strain MCWD5T were C14 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7c DMA and summed feature 8 (C17 : 1ω8c and/or C17 : 2), which was clearly different from those of related genera. The major polar lipids were diphosphatidyglycerol, phosphatidyglycerol and an unknown phospholipid. Based on the results of phylogenetic, physiologic and chemotaxonomic studies, Anaerosacchariphilus polymeriproducens gen. nov., sp. nov. with the type strain MCWD5T (=KCTC 15595T=DSM 105757T) is proposed in the family Lachnospiraceae.

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions.

Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment.

A Gram-staining-negative, thin rod-shaped, anaerobic bacterium designated MCWD3(T) was isolated from sediment of the deep sea in Ulleung Basin, East Sea, Korea. The ranges of temperature, pH and NaCl for growth of this strain were 15-40°C (optimum 29°C), 5.0-10.0 (optimum pH 6.5), and 1-5%, respectively. The major fatty acids were iso-C(15:0) (30%) and iso-C(15:0) dimethyl acetal (17%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipids, phospholipids, and aminolipids. The fermentation product from yeast extract was acetate. Phylogenetic analysis based on 16S rRNA genes indicated that the isolate was related to Sporosalibacterium faouarense (92.8% sequence identity), Clostridiisalibacter paucivorans (92.6%), and Brassicibacter mesophilus (92.4%). However, the isolate was differentiated from these genera by both physiological and chemotaxonomical properties. On the basis of a polyphasic taxonomic analysis, we propose that MCWD3(T) represents a novel taxon with the name Abyssisolibacter fermentans gen. nov. sp. nov.

Construction of target-specific virus-like particles for the delivery of algicidal compounds to harmful algae.

Harmful algal blooms (HABs) can lead to substantial socio-economic losses and extensive damage to aquatic ecosystems, drinking water sources and human health. Common algicidal techniques, including ozonation, ultrasonic treatment and dispersion of algae-killing chemicals, are unsatisfactory both economically and ecologically. This study therefore presents a novel alternative strategy for the efficient control of deleterious algae via the use of host-specific virus-like particles (VLPs) combined with chemically synthesized algicidal compounds. The capsid protein of HcRNAV34, a single-stranded RNA virus that infects the toxic dinoflagellate, Heterocapsa circularisquama, was expressed in and purified from Escherichia coli and then self-assembled into VLPs in vitro. Next, the algicidal compound, thiazolidinedione 49 (TD49), was encapsidated into HcRNAV34 VLPs for specific delivery to H. circularisquama. Consequently, HcRNAV34 VLPs demonstrated the same host selectivity as naturally occurring HcRNAV34 virions, while TD49-encapsidated VLPs showed a more potent target-specific algicidal effect than TD49 alone. These results indicate that target-specific VLPs for the delivery of cytotoxic compounds to nuisance algae might provide a safe, environmentally friendly approach for the management of HABs in aquatic ecosystems.

Minke whale genome and aquatic adaptation in cetaceans.

The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.

Enhanced indirubin production in recombinant Escherichia coli harboring a flavin-containing monooxygenase gene by cysteine supplementation.

In our previous study, a batch fermentation of recombinant Escherichia coli DH5α cells harboring the fmo gene from Methylophaga aminisulfidivorans MP(T) produced indirubin (5.0mg/L) and indigo (920mg/L) in a 5L fermenter containing tryptophan medium (2g/L tryptophan, 5g/L yeast extract, 10g/L NaCl). In this study, it was found that indirubin production greatly increased when 0.36g/L cysteine was added to the tryptophan medium, although cysteine inhibited the growth of the recombinant E. coli harboring the fmo gene. However, the addition of cysteine did not inhibit the expression level and activity of FMO in the cell. Indigo was synthesized by the dimerization of two 3-hydroxyindole molecules under the non-enzymatic reaction. Cysteine influenced the regioselectivity of FMO and enhanced the synthesis of 2-hydroxyindole instead of 3-hydroxyindole, which might function to increase indirubin production. The optimal culture conditions for indirubin production in tryptophan medium were determined from the response surface methodology analysis: 2g/L tryptophan, 5g/L yeast extract, 10g/L NaCl, 0.36g/L (3mM) cysteine, pH 8.0 at 35°C. Under these conditions, the recombinant E. coli cells were capable of producing 223.6mg/L of indirubin from 2g/L of tryptophan. The intracellular accumulation of the indirubin crystals might stress the cell, which may be a main reason for the poor growth of the recombinant E. coli pBlue 1.7.

Expression and bioconversion of recombinant m- and p-hydroxybenzoate hydroxylases from a novel moderate halophile, Chromohalobacter sp.

p-Hydroxybenzoate hydroxylase (pobA) and m-hydroxybenzoate hydroxylase (mobA) genes, from the moderate halophile Chromohalobacter sp. HS-2, were expressed and characterized. Solubilities of overexpressed recombinant MobA and PobA were enhanced by the induction of the heat-shock proteins DnaJ and DnaK. Each MobA and PobA maintained stable activity under high NaCl concentrations. V (max) and K (m) values for MobA with m-hydroxybenzoate were 70 µmol min(-1) mg(-1) protein and 81 µM, respectively. Similarly, those of PobA with p-hydroxybenzoate as substrate were 5 µmol min(-1) mg(-1) protein and 129 µM, respectively. The Escherichia coli expression system, including induction of heat shock proteins, was used to convert hydroxybenzoates into protocatechuate (3,4-dihydroxybenzoate) and revealed that resting cells harboring mobA converted 15 mM m-hydroxybenzoate to 15 mM protocatechuate while those harboring pobA converted 50 mM p-hydroxybenzoate to 35 mM protocatechuate at 30 °C, respectively.

Optimization of culture conditions and comparison of biomass productivity of three green algae.

Culture conditions for the mass production of three green algae, Chlorella sp., Dunaliella salina DCCBC2 and Dunaliella sp., were optimized using a response surface methodology (RSM). A central composite design was applied to investigate the effects of initial pH, nitrogen and phosphate concentrations on the cultivation of microalgae. The optimal growth conditions estimated from the design are as follows: Chlorella sp. (initial pH 7.2, ammonium 17 mM, phosphate 1.2 mM), D. salina DCCBC2 (initial pH 8.0, nitrate 3.3 mM, phosphate 0.0375 mM) and Dunaliella sp. (initial pH 8.0, nitrate 3.7 mM, phosphate 0.17 mM). Culturing the microalgae with the optimized conditions confirmed that the maximum growth rates were attained for these parameters. The optimum CO(2) concentrations of Chlorella sp., D. salina DCCBC2 and Dunaliella sp. were 1.0, 3.0 and 1.0% (v/v), respectively. The specific growth rates (µ) of Chlorella sp., D. salina DCCBC2 and Dunaliella sp. were 0.58, 0.78 and 0.56 day(-1), respectively, and the biomass productivities were 0.28, 0.54 and 0.30 g dry cell wt l(-1) day(-1), respectively. The CO(2) fixation rates of Chlorella sp., D. salina DCCBC2 and Dunaliella sp. were 42.8, 90.9 and 45.5 mg l(-1) day(-1), respectively. Mixotrophic cultivation of Chlorella sp. with glucose increased biomass productivity from 0.28 to 0.51 g dry cell wt l(-1) day(-1). However, D. salina DCCBC2 and Dunaliella sp. were not stimulated by several organic compounds tested.

Draft genome sequence of Methylophaga aminisulfidivorans MP T.

Methylophaga aminisulfidivorans MP(T) is a restricted facultatively marine methylotrophic bacterium that grows on methanol, methylated amines, dimethyl sulfide, and dimethyl sulfoxide. Here we present the high-quality draft genome sequence of M. aminisulfidivorans MP(T) (KCTC 12909(T) = JCM 14647(T)), consisting of a chromosome (3,092,085 bp) and a plasmid (16,875 bp).

Molecular characterization of enteroviruses detected in Gyeong-Ju and Po-Hang provinces of Korea in 2003.

We identified and characterized enteroviruses by amplifying the partial VP1 gene from pediatric patients with aseptic meningitis and other enterovirus-related diseases from the Gyeong-Ju and Po-Hang provinces of Korea in 2003. We identified two strains each of coxsackievirus A (CA) 6, CA9, and CA10; three enterovirus 71 (EV71) strains; and six echovirus 30 (E30) strains. The three EV71 strains were characterized as genogroup C4. These results are the first documentation reporting the occurrence of CA10 and EV71 genogroup C4.

Both subunits of ATP-citrate lyase from Chlorobium tepidum contribute to catalytic activity.

ATP-citrate lyase (ACL) is an essential enzyme of the reductive tricarboxylic acid (RTCA) pathway of CO(2) assimilation. The RTCA pathway occurs in several groups of autotrophic prokaryotes, including the green sulfur bacteria. ACL catalyzes the coenzyme A (CoA)-dependent and MgATP-dependent cleavage of citrate into oxaloacetate and acetyl-CoA, representing a key step in the RTCA pathway. To characterize this enzyme from the green sulfur bacterium Chlorobium tepidum and determine the role of its two distinct polypeptide chains, recombinant holo-ACL as well as its two individual subunit polypeptides were synthesized in Escherichia coli. The recombinant holoenzyme, prepared from coexpressed large and small ACL genes, and the individual large and small subunit polypeptides, prepared from singly expressed genes, were all purified to homogeneity to high yield. Purified recombinant holo-ACL was isolated at high specific activity, and its k(cat) was comparable to that of previously prepared native C. tepidum ACL. Moreover, the purified recombinant large and small subunit polypeptides were able to reconstitute the holo-ACL in vitro, with activity levels approaching that of recombinant holo-ACL prepared from coexpressed genes. Stoichiometric amounts of each subunit protein were required to maximize the activity and form the most stable structure of reconstituted holo-ACL. These results suggested that this reconstitution system could be used to discern the catalytic role of specific amino acid residues on each subunit. Reconstitution and mutagenesis studies together indicated that residues of each subunit contributed to different aspects of the catalytic mechanism, suggesting that both subunit proteins contribute to the active site of C. tepidum ACL.

Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis.

Methanococcus maripaludis is a mesophilic archaeon that reduces CO2 to methane with H2 or formate as an energy source. It contains two membrane-bound energy-conserving hydrogenases, Eha and Ehb. To determine the role of Ehb, a deletion in the ehb operon was constructed to yield the mutant, strain S40. Growth of S40 was severely impaired in minimal medium. Both acetate and yeast extract were necessary to restore growth to nearly wild-type levels, suggesting that Ehb was involved in multiple steps in carbon assimilation. However, no differences in the total hydrogenase specific activities were found between the wild type and mutant in either cell extracts or membrane-purified fractions. Methanogenesis by resting cells with pyruvate as the electron donor was also reduced by 30% in S40, suggesting a defect in pyruvate oxidation. CO dehydrogenase/acetyl coenzyme A (CoA) synthase and pyruvate oxidoreductase had higher specific activities in the mutant, and genes encoding these enzymes, as well as AMP-forming acetyl-CoA synthetase, were expressed at increased levels. These observations support a role for Ehb in anabolic CO2 assimilation in methanococci.

Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis.

In Methanococcus maripaludis strain JJ, deletion of the homolog to cbiJ, which encodes the corrin biosynthetic enzyme precorrin 6-X reductase, yielded an auxotroph that required either cobamide or acetate for good growth. This phenotype closely resembled that of JJ117, a mutant in which tandem repeats were introduced into the region immediately downstream of the homolog of cbiJ. Mutant JJ117 also produced low quantities of cobamides, about 15 nmol g(-1) protein or 1-2% of the amount found in wild-type cells. These results confirm the role of the cbiJ homolog in cobamide biosynthesis in the Archaea and suggest the presence of low amounts of a bypass activity in these organisms.

Two novel mutations in the C7 gene in a Korean patient with complement C7 deficiency.

Complement C7 deficiency is an autosomal recessive disorder well known to be associated with increased susceptibility to meningococcal infection and has mostly been reported in Caucasians. In the Korean population, no case of C7 deficiency has been reported to date. Recently we experienced an 11-yr-old girl with meningococcal meningitis who was diagnosed as having C7 deficiency based upon the undetectable serum C7 protein on radial immunodiffusion and the undetectable serum total and C7 hemolytic activities. To identify the genetic basis of the C7 deficiency of the patient, we performed a mutation analysis for the C7 gene and found two novel mutations; a point mutation at the 3' splice acceptor site of intron 4 (c.281-1G>T) and a large deletion mutation encompassing almost the whole C7 gene from exon 1 to exon 17 (c.1-?_2350+?del). A haplotype analysis showed that the large deletion mutation was inherited from the patient's father. To the best of our knowledge, this is the first confirmed case of C7 deficiency in Korea.

Inactive caspase 3 activates Akt in human leukemia cells susceptible or resistant to apoptosis induced by phorbol ester.

Phorbol 12-myristate 13-acetate (PMA) is a protein kinase C (PKC) activator and tumor promoter that induces terminal differentiation in human myeloid leukemia cells. We undertook to characterize phorbol ester-activated PKC-mediated cell cycle arrest and apoptosis. In the present studies, we determined the effect of high intracellular levels of the anti-apoptosis Bcl-2 protein on caspase 3 activation and cyctochrome c release during phorbol ester 12-myristate 13-acetate (PMA)-induced apoptosis. For this, we used the U937 cells, Bcl-2 overexpressed U937 cells (U937/Bcl-2) and the PMA-resistant derivative cell line R-U937. The G1 arrest of U937 cells and U937/Bcl-2 cells induced by treatment with 20 nM PMA is associated with cyclin A down-regulation and accumulation of p21, cdks inhibitor. However, PMA had no effect on the levels of cyclin A expression and p21 expression under the same conditions of time and concentration of PMA in the R-U937 cells. Treatment with 20 nM PMA for 24 h produced morphological features of apoptosis and DNA fragmentation in U937 and U937/Bcl-2 cells, but not in R-U937 cells. This was associated with the caspase 3 activation and cyctochrome c release. R-U937 cells exhibited less cytochrome c release and sustained phosphorylation level of Akt during PMA-induced apoptosis. These findings indicate that R-U937 cells are resistant to PMA-induced apoptosis by a mechanism of the signaling defect in the activation of the caspase 3 that is involved in the execution of apoptosis.