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ABSTRACT: High-throughput growth phenotyping is receiving great attention for establishing the genotype-phenotype map of sequenced organisms owing to the ready availability of complete genome sequences. To date, microbial growth phenotypes have been investigated mostly by the conventional method of batch cultivation using test tubes, Erlenmeyer flasks, or the recently available microwell plates. However, the current batch cultivation methods are time- and labor-intensive, and often fail to consider sophisticated environmental changes. The implementation of batch cultures at the nanoliter scale has been difficult because of the quick evaporation of the culture medium inside the reactors. Here, we report a microfluidic system that allows independent cell cultures in evaporation-free multiplex nanoliter reactors under different culture conditions to assess the behavior of cells. The design allows three experimental replicates for each of eight culture environments in a single run. We demonstrate the versatility of the device by performing growth curve experiments with Escherichia coli and microbiological assays of antibiotics against the opportunistic pathogen Pseudomonas aeruginosa. Our study highlights that the microfluidic system can effectively replace the traditional batch culture methods with nanoliter volumes of bacterial cultivations, and it may be therefore promising for high-throughput growth phenotyping as well as for single-cell analyses.
Analytical Chemistry 04/2013; · 5.86 Impact Factor
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ABSTRACT: Rhodopsin-containing marine microbes such as those in the class Flavobacteria play a pivotal role in the biogeochemical cycle of the euphotic zone . Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins is important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in marine oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of cytophaga, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.
Genome Biology and Evolution 01/2013; · 4.62 Impact Factor
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ABSTRACT: Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.
Journal of bacteriology 09/2012; 194(17):4757-8. · 3.94 Impact Factor
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Kevin F Brulois,
Heesoon Chang,
Amy Si-Ying Lee,
Armin Ensser,
Lai-Yee Wong,
Zsolt Toth,
Sun Hwa Lee,
Hye-Ra Lee,
Jinjong Myoung,
Don Ganem, Tae-Kwang Oh,
Jihyun F Kim,
Shou-Jiang Gao,
Jae U Jung
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ABSTRACT: Efficient genetic modification of herpesviruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) has come to rely on bacterial artificial chromosome (BAC) technology. In order to facilitate this approach, we generated a new KSHV BAC clone, called BAC16, derived from the rKSHV.219 virus, which stems from KSHV and Epstein-Barr virus-coinfected JSC1 primary effusion lymphoma (PEL) cells. Restriction enzyme and complete sequencing data demonstrate that the KSHV of JSC1 PEL cells showed a minimal level of sequence variation across the entire viral genome compared to the complete genomic sequence of other KSHV strains. BAC16 not only stably propagated in both Escherichia coli and mammalian cells without apparent genetic rearrangements, but also was capable of robustly producing infectious virions (∼5 × 10(7)/ml). We also demonstrated the utility of BAC16 by generating deletion mutants of either the K3 or K5 genes, whose products are E3 ligases of the membrane-associated RING-CH (MARCH) family. While previous studies have shown that individual expression of either K3 or K5 results in efficient downregulation of the surface expression of major histocompatibility complex class I (MHC-I) molecules, we found that K5, but not K3, was the primary factor critical for the downregulation of MHC-I surface expression during KSHV lytic reactivation or following de novo infection. The data presented here demonstrate the utility of BAC16 for the generation and characterization of KSHV knockout and mutant recombinants and further emphasize the importance of functional analysis of viral genes in the context of the KSHV genome besides the study of individual gene expression.
Journal of Virology 06/2012; 86(18):9708-20. · 5.40 Impact Factor
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ABSTRACT: A Gram-staining-negative, aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, D1-y4T, was isolated from a tidal flat sediment of the South Sea in South Korea and subjected to a polyphasic study. Strain D1-y4T grew optimally at 25°C, pH 7.0-7.5 and in the presence of 2-3 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain D1-y4T belonged to the genus Geatbulibacter, joining the type strain of Geatbulibacter marinus, with which it exhibited 97.8 % 16S rRNA gene sequence similarity. Sequence similarities to Gaetbulibacter saemankumensis SMK-12T and Gaetbulibacter aestuarii KYW382T were 96.5 and 96.2 %, respectively. Strain D1-y4T contained MK-6 as the predominant menaquionone and iso-C15:0, iso-C15:1 G and anteiso-C15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain D1-y4T was 34.6 mol% and its mean DNA-DNA relatedness value with G. marinus KCTC 23046T was 7 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain D1-y4T is distinguishable from the three recognized Gaetbulibacter species. On the basis of the data presented here, strain D1-y4T is considered to represent a novel species of the genus Geatbulibacter, for which the name Geatbulibacter lutimaris sp. nov. is proposed. The type strain is D1-y4T (= KCTC 23716T = CCUG 61504T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 06/2012; · 2.11 Impact Factor
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ABSTRACT: A Gram-staining-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, BB-Mw22T, was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30-37 °, pH 7.0-7.5 and in the presence of 2-3 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22T belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22T was clearly separated from other taxa. Strain BB-Mw22T exhibited 95.3-97.7 % 16S rRNA gene sequence similarity to the type strains of the five recognized Kangiella species. Strain BB-Mw22T contained Q-8 as the predominant ubiquionone and iso-C15:0 and iso-C11:0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22T was 48.9 mol% and its mean DNA-DNA hybridization values with K. geojedonensis YCS-5T, K. japonica JCM 16211T and 'K. taiwanensis' JCM 17727T were 14-28 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22T is distinguishable from the five recognized Kangiella species and 'K. taiwanensis'. On the basis of the data presented, strain BB-Mw22T is considered to represent a novel species of the genus Kangiella, for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22T (= KCTC 23892T = CCUG 62217T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 06/2012; · 2.11 Impact Factor
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ABSTRACT: Elucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced.
We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. A genome-scale metabolic network of E. coli B was reconstructed and used to identify genetic bases of the phenotypes unique to B compared with K-12 through in silico complementation testing. This systems analysis revealed that E. coli B is well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella. Furthermore, E. coli B has an additional type II secretion system and a different cell wall and outer membrane composition predicted to be more favorable for protein secretion. In contrast, E. coli K-12 showed a higher expression of heat shock genes and was less susceptible to certain stress conditions.
This integrative systems approach provides a high-resolution system-wide view and insights into why two closely related strains of E. coli, B and K-12, manifest distinct phenotypes. Therefore, systematic understanding of cellular physiology and metabolism of the strains is essential not only to determine culture conditions but also to design recombinant hosts.
Genome biology 05/2012; 13(5):R37. · 6.63 Impact Factor
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ABSTRACT: A novel lipolytic enzyme was isolated from a metagenomic library obtained from tidal flat sediments on the Korean west coast. Its putative functional domain, designated MPlaG, showed the highest similarity to phospholipase A from Grimontia hollisae CIP 101886, though it was screened from an emulsified tricaprylin plate. Phylogenetic analysis showed that MPlaG is far from family I.6 lipases, including Staphylococcus hyicus lipase, a unique lipase which can hydrolyze phospholipids, and is more evolutionarily related to the bacterial phospholipase A(1) family. The specific activities of MPlaG against olive oil and phosphatidylcholine were determined to be 2,957 ± 144 and 1,735 ± 147 U mg(-1), respectively, which means that MPlaG is a lipid-preferred phospholipase. Among different synthetic esters, triglycerides, and phosphatidylcholine, purified MPlaG exhibited the highest activity toward p-nitrophenyl palmitate (C(16)), tributyrin (C(4)), and 1,2-dihexanoyl-phosphatidylcholine (C(8)). Finally, MPlaG was identified as a phospholipase A(1) with lipase activity by cleavage of the sn-1 position of OPPC, interfacial activity, and triolein hydrolysis. These findings suggest that MPlaG is the first experimentally characterized phospholipase A(1) with lipase activity obtained from a metagenomic library. Our study provides an opportunity to improve our insight into the evolution of lipases and phospholipases.
Applied and environmental microbiology 04/2012; 78(14):4959-66. · 3.69 Impact Factor
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ABSTRACT: In our previous study, Bacillus subtilis strain BSK3S, containing a polymyxin biosynthetic gene cluster from Paenibacillus polymyxa, could produce polymyxin only in the presence of exogenously added L-2,4-diaminobutyric acid (Dab). The dependence of polymyxin production on exogenous Dab was removed by introducing an ectB gene encoding the diaminobutyrate synthase of P. polymyxa into BSK3S (resulting in strain BSK4). We found, by observing the complete inhibition of polymyxin synthesis when the spo0A gene was knocked out (strain BSK4-0A), that Spo0A is indispensable for the production of polymyxin. Interestingly, the abrB-spo0A double-knockout mutant, BSK4-0A-rB, and the single abrB mutant, BSK4-rB, showed 1.7- and 2.3-fold increases, respectively, in polymyxin production over that of BSK4. These results coincided with the transcription levels of pmxA in the strains observed by quantitative real-time PCR (qRT-PCR). The AbrB protein was shown to bind directly to the upstream region of pmxA, indicating that AbrB directly inhibits the transcription of polymyxin biosynthetic genes. The BSK4-rB strain, producing high levels of polymyxin, will be useful for the development and production of novel polymyxin derivatives.
Applied and environmental microbiology 03/2012; 78(12):4194-9. · 3.69 Impact Factor
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ABSTRACT: A Gram-staining-negative, non-spore-forming, facultatively anaerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, BR-18T, was isolated from marine sand on the western coast of South Korea, and subjected to a polyphasic study. Strain BR-18T grew optimally at 25 °C, at pH 6.5-7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BR-18T fell within the clade comprising Mucilaginibacter species, joining the type strains of Mucilaginibacter rigui and 'Mucilaginibacter lutimaris', with which it exhibited 16S rRNA gene sequence similarity values of 95.9 and 96.6 %, respectively. Sequence similarity to the type strains of the other Mucilaginibacter species was 93.4-95.5 % and less than 91.6 % to the other species used in the phylogenetic analysis. Strain BR-18T contained MK-7 as the predominant menaquinone, summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and iso-C15:0 as the major fatty acids and sphingolipids. The major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The DNA G+C content was 42.4 mol%. The phylogenetic distinctiveness and differential phenotypic properties revealed that strain BR-18T is separate from other Mucilaginibacter species. On the basis of the data presented, strain BR-18T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter litoreus sp. nov. is proposed. The type strain is BR-18T (= KCTC 23697T = CCUG 61484T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 01/2012; · 2.11 Impact Factor
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Hye-Ra Lee,
Won-Chan Choi,
Stacy Lee,
Jungwon Hwang,
Eunha Hwang,
Koushik Guchhait,
Juergen Haas,
Zsolt Toth,
Young Ho Jeon, Tae-Kwang Oh,
Myung Hee Kim,
Jae U Jung
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ABSTRACT: Herpesvirus-associated ubiquitin-specific protease (HAUSP) regulates the stability of p53 and the p53-binding protein MDM2, implicating HAUSP as a therapeutic target for tuning p53-mediated antitumor activity. Here we report the structural analysis of HAUSP with Kaposi's sarcoma-associated herpesvirus viral interferon (IFN) regulatory factor 4 (vIRF4) and the discovery of two vIRF4-derived peptides, vif1 and vif2, as potent and selective HAUSP antagonists. This analysis reveals a bilateral belt-type interaction that results in inhibition of HAUSP. The vif1 peptide binds the HAUSP TRAF domain, competitively blocking substrate binding, whereas the vif2 peptide binds both the HAUSP TRAF and catalytic domains, robustly suppressing its deubiquitination activity. Peptide treatments comprehensively blocked HAUSP, leading to p53-dependent cell-cycle arrest and apoptosis in culture and to tumor regression in xenograft mouse model. Thus, the virus has developed a unique strategy to target the HAUSP-MDM2-p53 pathway, and these virus-derived short peptides represent biologically active HAUSP antagonists.
Nature Structural & Molecular Biology 11/2011; 18(12):1336-44. · 12.71 Impact Factor
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ABSTRACT: A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25(T), was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25(T) grew optimally at 25 °C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25(T) formed a cluster with the type strains of Actibacter sediminis, Aestuariicola saemankumensis and Lutimonas vermicola. Strain DPG-25(T) exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis, Aestuariicola saemankumensis and L. vermicola, respectively. Strain DPG-25(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0) and iso-C(17 : 0) 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25(T) were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25(T) demonstrated that this strain is distinguishable from Actibacter sediminis, Aestuariicola saemankumensis and L. vermicola. On the basis of the data presented here, strain DPG-25(T) represents a novel species in a novel genus of the family Flavobacteriaceae, for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25(T) ( = KCTC 23702(T) = CCUG 61485(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 11/2011; 62(Pt 9):2163-8. · 2.11 Impact Factor
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ABSTRACT: A Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated strain HWDM-33(T), was isolated from seawater of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HWDM-33(T) grew optimally at pH 7-8, at 25 °C and in the presence of 2-3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HWDM-33(T) clustered with Erythrobacter gangjinensis K7-2(T), with which it shared 96.9 % sequence similarity. Strain HWDM-33(T) exhibited 94.2-95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized species of the genus Erythrobacter. Strain HWDM-33(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c, C(17 : 1)ω6c, and C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HWDM-33(T) was 66.1 mol%. Differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain HWDM-33(T) was separate from E. gangjinensis and other recognized species of the genus Erythrobacter. On the basis of the data presented here, strain HWDM-33(T) represents a novel species of the genus Erythrobacter, for which the name Erythrobacter marinus sp. nov. is proposed. The type strain is HWDM-33(T) ( = KCTC 23554(T) = CCUG 60528(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 10/2011; 62(Pt 9):2050-5. · 2.11 Impact Factor
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ABSTRACT: A Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated HDW-32(T), was isolated from seawater of the Yellow Sea, Korea. Strain HDW-32(T) grew optimally at pH 7-8, at 30 °C and with 2-3 % (w/v) NaCl. Strain HDW-32(T) exhibited 95.1 % 16S rRNA gene sequence similarity with Nitratireductor basaltis J3(T), 94.8 % sequence similarity with Ahrensia kielensis IAM 12618(T) and <94.5 % with other members of the family Phyllobacteriaceae. In the neighbour-joining, maximum-likelihood and maximum-parsimony trees based on 16S rRNA gene sequences, strain HDW-32(T) clustered with A. kielensis IAM 12618(T). Strain HDW-32(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c as the major fatty acid. Differences in polar lipids, DNA G+C content and other phenotypic properties distinguished strain HDW-32(T) from A. kielensis JCM 20689(T). Strain HDW-32(T) could also be distinguished from representatives of the genera Nitratireductor and Hoeflea by differences in fatty acids and polar lipids. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain HDW-32(T) represents a novel species belonging to a novel genus of the family Phyllobacteriaceae of the class Alphaproteobacteria, for which the name Pseudahrensia aquimaris gen. nov., sp. nov. is proposed. The type strain of the type species is HDW-32(T) ( = KCTC 23345(T) = CCUG 60023(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 10/2011; 62(Pt 9):2056-61. · 2.11 Impact Factor
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ABSTRACT: A Gram-negative, motile, rod-shaped bacterial strain, designated HDW-15(T), was isolated from seawater of the Yellow Sea, Korea, and subjected to a polyphasic taxonomic study. Strain HDW-15(T) grew optimally at pH 7.0-8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain HDW-15(T) fell within the clade comprising Marinomonas species, joining the type strain of Marinomonas arctica, with which it exhibited highest 16S rRNA gene sequence similarity (97.7 %). The 16S rRNA gene sequence similarity values between strain HDW-15(T) and the type strains of other Marinomonas species were in the range 93.7-97.2 %. Mean DNA-DNA relatedness values between strain HDW-15(T) and the type strains of M. arctica, Marinomonas polaris and Marinomonas pontica were 5.0-9.9 %. The DNA G+C content of the isolate was 48.7 mol%. Strain HDW-15(T) contained Q-8 as the predominant ubiquinone and C(18 : 1)ω7c, summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) and C(16 : 0) as the major fatty acids. The major polar lipids found in strain HDW-15(T) were phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, showed that strain HDW-15(T) can be differentiated from other Marinomonas species. On the basis of the data presented, strain HDW-15(T) is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas hwangdonensis sp. nov. is proposed. The type strain is HDW-15(T) ( = KCTC 23661(T) = CCUG 61321(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 10/2011; 62(Pt 9):2062-7. · 2.11 Impact Factor
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ABSTRACT: The signal transducer and activator of transcription 3 (STAT3) is constitutively activated in cancer cells. Therefore, blocking the aberrant activity of STAT3 in tumor cells is a validated therapeutic strategy. To discover novel inhibitors of STAT3 activity, we screened against microbial natural products using a dual-luciferase assay. Using the microbial metabolome library, we identified cosmomycin C (CosC), which was isolated from the mycelium extract of Streptomyces sp. KCTC19769, as a STAT3 pathway inhibitor. CosC inhibited STAT3 (Tyr705) phosphorylation and subsequent nuclear translocation in MDA-MB-468 breast cancer cells. CosC-mediated inhibition of STAT3 signaling pathway was confirmed by suppressed expression of STAT3 downstream target proteins including cyclin D1, Bcl-xL, survivin, Mcl-1, and VEGF in CosC-treated MDA-MB-468 cells. Flow cytometry showed that CosC caused accumulation in the G(0)-G(1) phase of the cell cycle and induced apoptosis via PARP cleavage and caspase-3 activation. Based on these findings, CosC may be a potential candidate for modulation of STAT3 pathway.
Bioorganic & medicinal chemistry 10/2011; 19(24):7582-9. · 2.82 Impact Factor
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ABSTRACT: A Gram-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MA1-1(T), was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain MA1-1(T) is phylogenetically closely related to Litoreibacter species and to Thalassobacter arenae. It exhibited 16S rRNA gene sequence similarities of 97.3, 97.1 and 97.3% to the type strains of Litoreibacter albidus, Litoreibacter janthinus and T. arenae, respectively. Strain MA1-1(T) contained Q-10 as the predominant ubiquinone and C(18:1)ω7c as the predominant fatty acid. The polar lipid profile of strain MA1-1(T) was similar to those of the type strains of L. albidus and L. janthinus. T. arenae was found to be phylogenetically and chemotaxonomically more closely related to Litoreibacter species and strain MA1-1(T) than to Thalassobacter stenotrophicus, the type species of the genus Thalassobacter. The DNA G+C content of strain MA1-1(T) was 57.9 mol%, and DNA-DNA relatedness to the type strains of the two Litoreibacter species and T. arenae was 9-14%. Differential phenotypic properties, together with the observed phylogenetic and genetic distinctiveness, distinguished strain MA1-1(T) from the two Litoreibacter species and T. arenae. On the basis of the data presented, strain MA1-1(T) is considered to represent a novel species of the genus Litoreibacter, for which the name Litoreibacter meonggei sp. nov. is proposed. The type strain is MA1-1(T) ( = KCTC 23699(T) = CCUG 61486(T)). In this study, it is also proposed that Thalassobacter arenae is reclassified as a member of the genus Litoreibacter, Litoreibacter arenae comb. nov. (type strain GA2-M15(T) = DSM 19593(T) = KACC 12675(T)). An emended description of the genus Litoreibacter is also presented.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 10/2011; 62(Pt 8):1825-31. · 2.11 Impact Factor
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ABSTRACT: A Gram-negative, non-flagellated, motile by gliding, aerobic rod, designated DPG-24(T), was isolated from seawater of Geoje Island in the South Sea, Korea. Strain DPG-24(T) grew optimally at 30-37 °C, at pH 7.0-7.5 and with 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DPG-24(T) belonged to the genus Winogradskyella and clustered with Winogradskyella poriferorum UST030701-295(T) and Winogradskyella exilis 022-2-26(T). Strain DPG-24(T) exhibited 97.6 and 95.8% 16S rRNA gene sequence similarities with W. poriferorum UST030701-295(T) and W. exilis 022-2-26(T), respectively, and 92.4-95.7% with other members of the genus Winogradskyella. Strain DPG-24(T) contained MK-6 as the predominant menaquinone and iso-C(15:1) G, iso-C(15:0) and iso-C(17:0) 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The DNA G+C content was 36.7 mol%. DNA-DNA relatedness between the isolate and W. poriferorum JCM 12885(T) was 10.8%. The differential phenotypic properties and phylogenetic and genetic distinctiveness enabled strain DPG-24(T) to be differentiated from recognized members of the genus Winogradskyella. On the basis of the data presented, strain DPG-24(T) is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella aquimaris sp. nov. is proposed; the type strain is DPG-24(T) ( = KCTC 23502(T) = CCUG 60798(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 10/2011; 62(Pt 8):1814-8. · 2.11 Impact Factor
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ABSTRACT: The genera Dokdonia and Krokinobacter, members of the family Flavobacteriaceae in the phylum Bacteroidetes, were found to be phylogenetically closely related from the result of 16S rRNA gene sequence analysis. Dokdonia donghaensis DSW-1(T) exhibited 16S rRNA gene sequence similarity values of 99.3, 98.1 and 98.1% to Krokinobacter genikus Cos-13(T), Krokinobacter diaphorus MSKK-32(T) and Krokinobacter eikastus PMA-26(T), respectively. A taxonomic study of D. donghaensis DSW-1(T), K. genikus CIP 108744(T), K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T) was conducted using a polyphasic approach. The major fatty acids (>10% of the total fatty acids) in the four strains were iso-C(15:0), iso-C(15:1) G and iso-C(17:0) 3-OH, and their overall fatty acid profiles were essentially similar. The predominant menaquinone found in the type strains of the three species of the genus Krokinobacter was MK-6, in line with the genus Dokdonia. The polar lipid profiles of the type strains of the three species of the genus Krokinobacter were similar to that of D. donghaensis DSW-1(T) in that phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid were the major polar lipids. In addition, one unidentified aminophospholipid was also present as a major polar lipid in K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T). D. donghaensis DSW-1(T) was distinguishable from K. genikus CIP 108744(T), K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T) by genetic relatedness and differential phenotypic properties. On the basis of these data, it is proposed that K. genikus, K. diaphorus and K. eikastus be reclassified into the genus Dokdonia as Dokdonia genika comb. nov. (type strain is Cos-13(T) = NBRC 100811(T) = CIP 108744(T)), Dokdonia diaphoros comb. nov. (type strain is MSKK-32(T) = NBRC 100817(T) = CIP 108745(T)), and Dokdonia eikasta comb. nov. (type strain is PMA-26(T) = NBRC 100814(T) = CIP 108743(T)), respectively. An emended description of the genus Dokdonia is also presented.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 10/2011; 62(Pt 8):1896-901. · 2.11 Impact Factor
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ABSTRACT: Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.
Journal of bacteriology 10/2011; 193(19):5539-40. · 3.94 Impact Factor
