References (28)

Title : Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere - Kwak_2014_PLoS.One_9_e106704
Author(s) : Kwak MJ , Jeong H , Madhaiyan M , Lee Y , Sa TM , Oh TK , Kim JF
Ref : PLoS ONE , 9 :e106704 , 2014
Abstract : Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.
ESTHER : Kwak_2014_PLoS.One_9_e106704
PubMedSearch : Kwak_2014_PLoS.One_9_e106704
PubMedID: 25211235
Gene_locus related to this paper: metrj-b1lyj4 , 9rhiz-a0a089nx06 , 9rhiz-a0a089ntx8 , 9rhiz-a0a089nl64

Title : Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins - Kwon_2013_Genome.Biol.Evol_5_187
Author(s) : Kwon SK , Kim BK , Song JY , Kwak MJ , Lee CH , Yoon JH , Oh TK , Kim JF
Ref : Genome Biol Evol , 5 :187 , 2013
Abstract : Rhodopsin-containing marine microbes such as those in the class Flavobacteriia play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488-494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are 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 the 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 Cytophagia, 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.
ESTHER : Kwon_2013_Genome.Biol.Evol_5_187
PubMedSearch : Kwon_2013_Genome.Biol.Evol_5_187
PubMedID: 23292138

Title : Novel metagenome-derived, cold-adapted alkaline phospholipase with superior lipase activity as an intermediate between phospholipase and lipase - Lee_2012_Appl.Environ.Microbiol_78_4959
Author(s) : Lee MH , Oh KH , Kang CH , Kim JH , Oh TK , Ryu CM , Yoon JH
Ref : Applied Environmental Microbiology , 78 :4959 , 2012
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.
ESTHER : Lee_2012_Appl.Environ.Microbiol_78_4959
PubMedSearch : Lee_2012_Appl.Environ.Microbiol_78_4959
PubMedID: 22544255
Gene_locus related to this paper: 9bact-b0fb14

Title : Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4 - Yu_2012_J.Bacteriol_194_4757
Author(s) : Yu DS , Jeong H , Lee DH , Kwon SK , Song JY , Kim BK , Park MS , Ji GE , Oh TK , Kim JF
Ref : Journal of Bacteriology , 194 :4757 , 2012
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.
ESTHER : Yu_2012_J.Bacteriol_194_4757
PubMedSearch : Yu_2012_J.Bacteriol_194_4757
PubMedID: 22887663
Gene_locus related to this paper: bifbp-e4nxi9

Title : Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor - Hwang_2011_J.Biol.Chem_286_12450
Author(s) : Hwang J , Kim Y , Kang HB , Jaroszewski L , Deacon AM , Lee H , Choi WC , Kim KJ , Kim CH , Kang BS , Lee JO , Oh TK , Kim JW , Wilson IA , Kim MH
Ref : Journal of Biological Chemistry , 286 :12450 , 2011
Abstract : Considerable attention has recently been paid to the N-Myc downstream-regulated gene (NDRG) family because of its potential as a tumor suppressor in many human cancers. Primary amino acid sequence information suggests that the NDRG family proteins may belong to the alpha/beta-hydrolase (ABH) superfamily; however, their functional role has not yet been determined. Here, we present the crystal structures of the human and mouse NDRG2 proteins determined at 2.0 and 1.7 A resolution, respectively. Both NDRG2 proteins show remarkable structural similarity to the ABH superfamily, despite limited sequence similarity. Structural analysis suggests that NDRG2 is a nonenzymatic member of the ABH superfamily, because it lacks the catalytic signature residues and has an occluded substrate-binding site. Several conserved structural features suggest NDRG may be involved in molecular interactions. Mutagenesis data based on the structural analysis support a crucial role for helix alpha6 in the suppression of TCF/beta-catenin signaling in the tumorigenesis of human colorectal cancer, via a molecular interaction.
ESTHER : Hwang_2011_J.Biol.Chem_286_12450
PubMedSearch : Hwang_2011_J.Biol.Chem_286_12450
PubMedID: 21247902
Gene_locus related to this paper: human-NDRG2

Title : A novel family VII esterase with industrial potential from compost metagenomic library - Kang_2011_Microb.Cell.Fact_10_41
Author(s) : Kang CH , Oh KH , Lee MH , Oh TK , Kim BH , Yoon J
Ref : Microb Cell Fact , 10 :41 , 2011
Abstract : BACKGROUND: Among the vast microbial genomic resources now available, most microbes are unculturable in the laboratory. A culture-independent metagenomic approach is a novel technique that circumvents this culture limitation. For the screening of novel lipolytic enzymes, a metagenomic library was constructed from compost, and the clone of estCS2 was selected for lipolytic properties on a tributyrin-containing medium. RESULTS: The estCS2 sequence encodes a protein of 570 amino acid residues, with a predicted molecular mass of 63 kDa, and based on amino acid identity it most closely matches (45%) the carboxylesterase from Haliangium ochraceum DSM 14365. EstCS2 belong to family VII, according to the lipolytic enzyme classification proposed by Arpigny and Jaeger, and it retains the catalytic triad Ser245-Glu363-His466 that is typical of an alpha/beta hydrolase. The Ser245 residue in the catalytic triad of EstCS2 is located in the consensus active site motif GXSXG. The EstCS2 exhibits strong activity toward p-nitrophenyl caproate (C6), and it is stable up to 60 degrees C with an optimal enzymatic activity at 55 degrees C. The maximal activity is observed at pH 9, and it remains active between pH 6-10. EstCS2 shows remarkable stability in up to 50% (v/v) dimethyl sulfoxide (DMSO) or dimethylformamide (DMF). The enzyme has the ability to cleave sterically hindered esters of tertiary alcohol, as well as to degrade polyurethanes, which are widely used in various industries. CONCLUSIONS: The high stability of EstCS2 in organic solvents and its activity towards esters of ketoprofen and tertiary alcohols, and in polyurethane suggests that it has potential uses for many applications in biotransformation and bioremediation.
ESTHER : Kang_2011_Microb.Cell.Fact_10_41
PubMedSearch : Kang_2011_Microb.Cell.Fact_10_41
PubMedID: 21619698

Title : Complete genome sequence of the polycyclic aromatic hydrocarbon-degrading bacterium Alteromonas sp. strain SN2 - Jin_2011_J.Bacteriol_193_4292
Author(s) : Jin HM , Jeong H , Moon EJ , Math RK , Lee K , Kim HJ , Jeon CO , Oh TK , Kim JF
Ref : Journal of Bacteriology , 193 :4292 , 2011
Abstract : Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.
ESTHER : Jin_2011_J.Bacteriol_193_4292
PubMedSearch : Jin_2011_J.Bacteriol_193_4292
PubMedID: 21705606
Gene_locus related to this paper: altss-f5zcy5 , altss-f5z698

Title : Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681 - Kim_2010_J.Bacteriol_192_6103
Author(s) : Kim JF , Jeong H , Park SY , Kim SB , Park YK , Choi SK , Ryu CM , Hur CG , Ghim SY , Oh TK , Kim JJ , Park CS , Park SH
Ref : Journal of Bacteriology , 192 :6103 , 2010
Abstract : Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.
ESTHER : Kim_2010_J.Bacteriol_192_6103
PubMedSearch : Kim_2010_J.Bacteriol_192_6103
PubMedID: 20851896
Gene_locus related to this paper: paep6-e0ra24 , paep6-e0rkv6 , paep6-e0rmc7 , paep6-e0rmu8 , paeps-e3ebx3

Title : Genome sequences of Escherichia coli B strains REL606 and BL21(DE3) - Jeong_2009_J.Mol.Biol_394_644
Author(s) : Jeong H , Barbe V , Lee CH , Vallenet D , Yu DS , Choi SH , Couloux A , Lee SW , Yoon SH , Cattolico L , Hur CG , Park HS , Segurens B , Kim SC , Oh TK , Lenski RE , Studier FW , Daegelen P , Kim JF
Ref : Journal of Molecular Biology , 394 :644 , 2009
Abstract : Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
ESTHER : Jeong_2009_J.Mol.Biol_394_644
PubMedSearch : Jeong_2009_J.Mol.Biol_394_644
PubMedID: 19786035
Gene_locus related to this paper: eco57-b3a913 , ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-YfhR

Title : Novel cold-adapted alkaline lipase from an intertidal flat metagenome and proposal for a new family of bacterial lipases - Kim_2009_Appl.Environ.Microbiol_75_257
Author(s) : Kim EY , Oh KH , Lee MH , Kang CH , Oh TK , Yoon JH
Ref : Applied Environmental Microbiology , 75 :257 , 2009
Abstract : A new lipase, LipEH166, isolated from an intertidal flat metagenome, showed no amino acid similarity to any known lipolytic enzyme except in the consensus region. This suggested that LipEH166 and its homologues belong to a new family of lipolytic enzymes. Partial characterization indicated that LipEH166 is a novel cold-adapted alkaline lipase.
ESTHER : Kim_2009_Appl.Environ.Microbiol_75_257
PubMedSearch : Kim_2009_Appl.Environ.Microbiol_75_257
PubMedID: 18931297
Gene_locus related to this paper: 9bact-b1pz93

Title : Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011 - Kim_2009_J.Bacteriol_191_678
Author(s) : Kim JF , Jeong H , Yu DS , Choi SH , Hur CG , Park MS , Yoon SH , Kim DW , Ji GE , Park HS , Oh TK
Ref : Journal of Bacteriology , 191 :678 , 2009
Abstract : Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report the complete genome sequence of B. animalis subsp. lactis AD011 that was isolated from an infant fecal sample. Biological functions encoded in a single circular chromosome of 1,933,695 bp, smallest among the completely sequenced bifidobacterial genomes, are suggestive of their probiotic functions, such as utilization of bifidogenic factors and a variety of glycosidic enzymes and biosynthesis of polysaccharides.
ESTHER : Kim_2009_J.Bacteriol_191_678
PubMedSearch : Kim_2009_J.Bacteriol_191_678
PubMedID: 19011029
Gene_locus related to this paper: bifan-b2ea73 , bifan-b2eam2 , bifan-b2eck9 , bifas-c6ahs7 , biflb-c6a5u1 , bifa0-b8dw94 , bifan-b2e8c8

Title : Complete genome sequence of Leuconostoc citreum KM20 - Kim_2008_J.Bacteriol_190_3093
Author(s) : Kim JF , Jeong H , Lee JS , Choi SH , Ha M , Hur CG , Kim JS , Lee S , Park HS , Park YH , Oh TK
Ref : Journal of Bacteriology , 190 :3093 , 2008
Abstract : Leuconostoc citreum is one of the most prevalent lactic acid bacteria during the manufacturing process of kimchi, the best-known Korean traditional dish. We have determined the complete genome sequence of L. citreum KM20. It consists of a 1.80-Mb chromosome and four circular plasmids and reveals genes likely involved in kimchi fermentation and its probiotic effects.
ESTHER : Kim_2008_J.Bacteriol_190_3093
PubMedSearch : Kim_2008_J.Bacteriol_190_3093
PubMedID: 18281406
Gene_locus related to this paper: leuck-b1mwg5 , leuck-b1mwm3 , leuck-b1mxa8 , leuck-b1mxk9 , leuck-b1my46 , leuck-b1mz26 , leuck-b1mwr2

Title : The crystal structure of the estA protein, a virulence factor from Streptococcus pneumoniae -
Author(s) : Kim MH , Kang BS , Kim S , Kim KJ , Lee CH , Oh BC , Park SC , Oh TK
Ref : Proteins , 70 :578 , 2008
PubMedID: 17932928
Gene_locus related to this paper: strpn-SP0614

Title : Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases - Lee_2006_Appl.Environ.Microbiol_72_7406
Author(s) : Lee MH , Lee CH , Oh TK , Song JK , Yoon JH
Ref : Applied Environmental Microbiology , 72 :7406 , 2006
Abstract : We cloned lipG, which encoded a lipolytic enzyme, from a Korean tidal flat metagenomic library. LipG was related to six putative lipases previously identified only in bacterial genome sequences. These enzymes comprise a new family. We partially characterized LipG, providing the first experimental data for a member of this family.
ESTHER : Lee_2006_Appl.Environ.Microbiol_72_7406
PubMedSearch : Lee_2006_Appl.Environ.Microbiol_72_7406
PubMedID: 16950897
Gene_locus related to this paper: 9bact-q1paf1

Title : New cold-adapted lipase from Photobacterium lipolyticum sp. nov. that is closely related to filamentous fungal lipases - Ryu_2006_Appl.Microbiol.Biotechnol_70_321
Author(s) : Ryu HS , Kim HK , Choi WC , Kim MH , Park SY , Han NS , Oh TK , Lee JK
Ref : Applied Microbiology & Biotechnology , 70 :321 , 2006
Abstract : A Photobacterium strain, M37, showing lipolytic activity, was previously isolated from an intertidal flat of the Yellow Sea in Korea and identified as Photobacterium lipolyticum sp. nov. In the present study, the corresponding gene was cloned using the shotgun method. The amino acid sequence deduced from the nucleotide sequence (1,023 bp) corresponded to a protein of 340 amino acid residues with a molecular weight of 38,026. No sequence similarity was found with any known bacterial lipases/esterases; instead, the most similar enzymes were several filamentous fungal lipases. Although the similarity was very low (less than 16%), there were many conserved regions over the entire sequence and N-terminal oxyanion hole (RG) region, a signature sequence of filamentous fungal lipases. The novel protein M37 was produced in both a soluble and insoluble form when the Escherichia coli cells harboring the gene were cultured at 18 degrees C. The soluble protein exhibited lipase activity in a pH-stat assay using an olive oil emulsion. The M37 lipase also displayed a maximum activity at 25 degrees C and maintained its activity at a low temperature range (5-25 degrees C) with an activation energy (E(a)) of 2.07 kcal/mol. Accordingly, these results indicate that the M37 lipase from P. lipolyticum sp. nov. is a new cold-adapted enzyme.
ESTHER : Ryu_2006_Appl.Microbiol.Biotechnol_70_321
PubMedSearch : Ryu_2006_Appl.Microbiol.Biotechnol_70_321
PubMedID: 16088345
Gene_locus related to this paper: 9gamm-q5drn8

Title : MELDB: a database for microbial esterases and lipases - Kang_2006_FEBS.Lett_580_2736
Author(s) : Kang HY , Kim JF , Kim MH , Park SH , Oh TK , Hur CG
Ref : FEBS Letters , 580 :2736 , 2006
Abstract : MELDB is a comprehensive protein database of microbial esterases and lipases which are hydrolytic enzymes important in the modern industry. Proteins in MELDB are clustered into groups according to their sequence similarities based on a local pairwise alignment algorithm and a graph clustering algorithm (TribeMCL). This differs from traditional approaches that use global pairwise alignment and joining methods. Our procedure was able to reduce the noise caused by dubious alignment in the distantly related or unrelated regions in the sequences. In the database, 883 esterase and lipase sequences derived from microbial sources are deposited and conserved parts of each protein are identified. HMM profiles of each cluster were generated to classify unknown sequences. Contents of the database can be keyword-searched and query sequences can be aligned to sequence profiles and sequences themselves.
ESTHER : Kang_2006_FEBS.Lett_580_2736
PubMedSearch : Kang_2006_FEBS.Lett_580_2736
PubMedID: 16647704

Title : Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood - Yoon_2005_Int.J.Syst.Evol.Microbiol_55_733
Author(s) : Yoon JH , Lee CH , Oh TK
Ref : Int J Syst Evol Microbiol , 55 :733 , 2005
Abstract : A Gram-variable, motile, endospore-forming, halotolerant bacillus, strain JG-30(T), was isolated from the traditional Korean fermented seafood jeotgal, and was subjected to a polyphasic taxonomic study. This organism grew optimally at 37 degrees C and in the presence of 0-1 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain JG-30(T) forms a distinct phylogenetic lineage within the evolutionary radiation encompassed by the genus Bacillus. Strain JG-30(T) was characterized chemotaxonomically as having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C(15 : 0) and iso-C(14 : 0) as the major fatty acids. The DNA G+C content was 45 mol%. Strain JG-30(T) exhibited levels of 16S rRNA gene sequence similarity of less than 95.7 % to Bacillus species with validly published names. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JG-30(T) (=KCTC 3880(T)=DSM 16189(T)) was classified within the genus Bacillus as a novel species, for which the name Bacillus cibi sp. nov. is proposed.
ESTHER : Yoon_2005_Int.J.Syst.Evol.Microbiol_55_733
PubMedSearch : Yoon_2005_Int.J.Syst.Evol.Microbiol_55_733
PubMedID: 15774653
Gene_locus related to this paper: 9baci-a0a084gmw3 , 9baci-a0a084gjz2 , 9baci-a0a084h1w6 , metid-a0a084gkg9

Title : Zinc in lipase L1 from Geobacillus stearothermophilus L1 and structural implications on thermal stability - Choi_2005_FEBS.Lett_579_3461
Author(s) : Choi WC , Kim MH , Ro HS , Ryu SR , Oh TK , Lee JK
Ref : FEBS Letters , 579 :3461 , 2005
Abstract : Lipase L1 from Geobacillus stearothermophilus L1 contains an unusual extra domain, making a tight intramolecular interaction with the main catalytic domain through a Zn2+-binding coordination. To elucidate the role of the Zn2+, we disrupted the Zn2+-binding site by mutating the zinc-ligand residues (H87A, D61A/H87A, and D61A/H81A/H87A/D238A). The activity vs. temperature profiles of the mutant enzymes showed that the disruption of the Zn2+-binding site resulted in a notable decrease in the optimal temperature for maximal activity from 60 to 45-50 degrees C. The mutations also abolished the Zn2+-induced thermal stabilization. The wild-type enzyme revealed a 34.6-fold increase in stabilization with the addition of Zn2+ at 60 degrees C, whereas the mutant enzymes exhibited no response to Zn2+. Additional circular dichroism spectroscopy studies also confirmed the structural stabilizing role of Zn2+ on lipase L1 at elevated temperatures.
ESTHER : Choi_2005_FEBS.Lett_579_3461
PubMedSearch : Choi_2005_FEBS.Lett_579_3461
PubMedID: 15949807
Gene_locus related to this paper: geost-lipas

Title : High-level heterologous expression and properties of a novel lipase from Ralstonia sp. M1 - Quyen_2005_Protein.Expr.Purif_39_97
Author(s) : Quyen DT , Giang Le TT , Nguyen TT , Oh TK , Lee JK
Ref : Protein Expr Purif , 39 :97 , 2005
Abstract : The mature lipase LipA and its 56aa-truncated chaperone DeltaLipBhis (with 6xhis-tag) from Ralstonia sp. M1 were over-expressed in Escherichia coli BL21 under the control of T7 promoter with a high level of 70 and 12mg protein per gram of wet cells, respectively. The simply purified lipase LipA was effectively refolded by Ni-NTA purified chaperone DeltaLipBhis in molar ratio 1:1 at 4 degrees C for 24 hours in H2O. The in vitro refolded lipase LipA had an optimal activity in the temperature range of 50-55 degrees C and was stable up to 45 degrees C with more than 84% activity retention. The maximal activity was observed at pH 10.75 for hydrolysis of olive oil and found to be stable over alkaline pH range 8.0-10.5 with more than 52% activity retention. The enzyme was found to be highly resistant to many organic solvents especially induced by ethanolamine (remaining activity 137-334%), but inhibited by 1-butanol and acetonitrile (40-86%). Metal ions Cu2+, Sn2+, Mn2+, Mg2+, and Ca2+ stimulated the lipase slightly with increase in activity by up to 22%, whereas Zn2+ significantly inhibited the enzyme with the residual activity of 30-65% and Fe3+ to a lesser degree (activity retention of 77-86%). Tween 80, Tween 60, and Tween 40 induced the activation of the lipase LipA (222-330%) and 0.2-1% (w/v) of Triton X-100, X-45, and SDS increased the lipase activity by up to 52%. However, 5% (w/v) of Triton X-100, X-45, and SDS inhibited strongly the activity by 31-89%. The inhibitors including DEPC, EDTA, PMSF, and 2-mercaptoethanol (0.1-10mM) inhibited moderately the lipase with remaining activity of 57-105%. The lipase LipA hydrolyzed a wide range of triglycerides, but preferentially short length acyl chains (C4 and C6). In contrast to the triglycerides, medium length acyl chains (C8 and C14) of p-nitrophenyl (p-NP) esters were preferential substrates of this lipase. The enzyme preferentially catalyzed the hydrolysis of cottonseed oil (317%), cornoil (227%), palm oil (222%), and wheatgerm oil (210%) in comparison to olive oil (100%).
ESTHER : Quyen_2005_Protein.Expr.Purif_39_97
PubMedSearch : Quyen_2005_Protein.Expr.Purif_39_97
PubMedID: 15596365

Title : Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent - Jeong_2005_Nucleic.Acids.Res_33_7066
Author(s) : Jeong H , Yim JH , Lee C , Choi SH , Park YK , Yoon SH , Hur CG , Kang HY , Kim D , Lee HH , Park KH , Park SH , Park HS , Lee HK , Oh TK , Kim JF
Ref : Nucleic Acids Research , 33 :7066 , 2005
Abstract : Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we present the 7.2-megabase genome of the marine bacterium Hahella chejuensis including genes responsible for the biosynthesis of a pigment which has the lytic activity against a red-tide dinoflagellate. H.chejuensis is the first sequenced species in the Oceanospiralles clade, and sequence analysis revealed its distant relationship to the Pseudomonas group. The genome was well equipped with genes for basic metabolic capabilities and contained a large number of genes involved in regulation or transport as well as with characteristics as a marine heterotroph. Sequence analysis also revealed a multitude of genes of functional equivalence or of possible foreign origin. Functions encoded in the genomic islands include biosynthesis of exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigmentation. Molecular structure of the algicidal pigment, which was determined through LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In conclusion, our work provides new insights into mitigating algal blooms in addition to genetic make-up, physiology, biotic interactions and biological roles in the community of a marine bacterium.
ESTHER : Jeong_2005_Nucleic.Acids.Res_33_7066
PubMedSearch : Jeong_2005_Nucleic.Acids.Res_33_7066
PubMedID: 16352867
Gene_locus related to this paper: hahch-q2s6v8 , hahch-q2s7u4 , hahch-q2s8m0 , hahch-q2s9b5 , hahch-q2s9n3 , hahch-q2s796 , hahch-q2s803 , hahch-q2s809 , hahch-q2s829 , hahch-q2sae5 , hahch-q2sav4 , hahch-q2sbd6 , hahch-q2sc65 , hahch-q2scc5 , hahch-q2sci6 , hahch-q2sct6 , hahch-q2scw7 , hahch-q2sdy2 , hahch-q2seh8 , hahch-q2seq6 , hahch-q2sfm2 , hahch-q2sfm4 , hahch-q2sfm9 , hahch-q2sfx3 , hahch-q2sgj4 , hahch-q2sgn6 , hahch-q2sgt0 , hahch-q2sgz8 , hahch-q2shj8 , hahch-q2shp0 , hahch-q2shq5 , hahch-q2shv0 , hahch-q2shv4 , hahch-q2shz6 , hahch-q2sic0 , hahch-q2sil6 , hahch-q2sj56 , hahch-q2sje1 , hahch-q2sje8 , hahch-q2skf9 , hahch-q2skg3 , hahch-q2skl5 , hahch-q2skv5 , hahch-q2sl80 , hahch-q2sll2 , hahch-q2slq4 , hahch-q2sls7 , hahch-q2sm17 , hahch-q2sn09 , hahch-q2sn54 , hahch-q2snn5 , hahch-q2snq6 , hahch-q2snw9 , hahch-q2spi5 , hahch-q2spk1 , hahch-q2spm8 , hahch-q2sq02 , hahch-q2sqg8 , hahch-q2sqn4 , hahch-q2sqx6 , hahch-q2sjs2

Title : Occurrence of ofloxacin ester-hydrolyzing esterase from Bacillus niacini EM001. - Kim_2004_J.Mol.Catal.B.Enzym_27_237
Author(s) : Kim HK , Na HS , Park MS , Oh TK , Lee TS
Ref : J Mol Catal B Enzym , 27 :237 , 2004
Abstract : A Bacillus niacini strain (EM001) producing an ofloxacin ester-enantioselective esterase was isolated from the soil samples collected near Taejon, Korea. The cloned gene showed that the esterase EM001 composed of 495 amino acids corresponding to a relative molecular weight (Mr) of 54,098 kDa. Based on the Mr and the protein sequence, the esterase EM001 was similar to p-nitrobenzyl esterase from Bacillus subtilis with an identity of 41.8%. The optimum temperature and pH of the purified His-tagged enzyme were 45 degC and 9.0, respectively. The purified esterase EM001 hydrolyzed preferably (R)-ofloxacin propyl ester than (S)-form ester at the initial reaction phase with an eeP of 67% until the conversion rate become up to 35%.
ESTHER : Kim_2004_J.Mol.Catal.B.Enzym_27_237
PubMedSearch : Kim_2004_J.Mol.Catal.B.Enzym_27_237
Gene_locus related to this paper: bacni-Q6KG48

Title : A novel lipase\/chaperone pair from Ralstonia sp. M1: analysis of the folding interaction and evidence for gene loss in R. solanacearum - Quyen_2004_Mol.Genet.Genomics_272_538
Author(s) : Quyen DT , Nguyen TT , Le TT , Kim HK , Oh TK , Lee JK
Ref : Mol Genet Genomics , 272 :538 , 2004
Abstract : A microbial strain (referred to as M1) that produces an extracellular lipase was isolated from a soil sample in Vietnam, and identified as a Ralstonia species by partial sequencing of its 16S rDNA. A genomic library was constructed from Pst I fragments, and a colony showing lipase activity was selected for further analysis. Sequencing of the 4.7-kb insert in this clone (named M1-72) revealed one incomplete and three complete ORFs, predicted to encode a partial hypothetical glutaminyl tRNA synthetase (304 aa), a hypothetical transmembrane protein (500 aa), a lipase (328 aa) and a lipase chaperone (352 aa), respectively. Alignment of the insert sequence with the corresponding region of the genome of R. solanacearum GMI1000 (GenBank Accession No. AL646081) confirmed the presence in the latter of the genes for the hypothetical transmembrane protein and glutaminyl tRNA synthetase, which exhibited 89-91% identity to their counterparts in M1. However, R. solanacearum GMI1000 lacks the complete lipase-encoding gene and the major part of the chaperone-encoding gene, creating a so-called "black hole". The deduced amino acid sequences of the products of the lipase gene lipA and chaperone gene lipB from strain M1 shared 49.3-60.3% and 23.9-32.7% identity, respectively, with those of the Burkholderia lipase/chaperone subfamily I.2. lipB is located downstream of lipA, and separated from it by only 9 bp, and each gene has a putative ribosome binding site. The mature lipase LipA, a His-tagged derivative (LipAhis), the tagged full-length chaperone LipBhis and a truncated form (DeltaLipBhis) lacking the 56 N-terminal residues were expressed in Escherichia coli BL21. LipA, LipAhis and DeltaLipBhis could be expressed at high levels (70, 15 and 12 mg/g wet cells, respectively) and were easily purified. However, LipBhis was expressed at a much lower level which precluded purification. The specific activity of purified LipAhis, expressed on its own, was very low (<52 U/mg). However, after co-incubation with the purified DeltaLipBhis in vitro, the specific activity of the enzyme was markedly enhanced, indicating that the chaperone facilitated correct folding of the enzyme. A lipase:chaperone ratio of 1:10 was found to be optimal, yielding an enzyme preparation with a specific activity of 650 U/mg.
ESTHER : Quyen_2004_Mol.Genet.Genomics_272_538
PubMedSearch : Quyen_2004_Mol.Genet.Genomics_272_538
PubMedID: 15668771
Gene_locus related to this paper: 9rals-q67dx2

Title : Sequence-based approach to finding functional lipases from microbial genome databases - Kwoun_2004_FEMS.Microbiol.Lett_235_349
Author(s) : Kwoun Kim H , Jung YJ , Choi WC , Ryu HS , Oh TK , Lee JK
Ref : FEMS Microbiology Letters , 235 :349 , 2004
Abstract : A sequence-based approach was used to retrieve functional lipases from microbial genome databases. Many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (Ser, Asp, His) and oxyanion hole sequence (HG). To obtain the lipase genes satisfying the sequence rule, PCR cloning was performed, while the lipase activities were tested using a tributyrin/tricaprylin plate and p-nitrophenyl caproate. Among nine putative lipases from four strains, five functional lipolytic proteins were obtained from Archaeoglobus fulgidus, Deinococcus radiodurans, and Agrobacterium tumefaciens. All five lipases exhibited a relatively low sequence similarity (less than 26.7%) with known lipases and turned out to belong to different lipase families. Accordingly, the current results indicate that the proposed strategic approach based on the microbial genome is an efficient and rapid method for finding novel and functional lipases.
ESTHER : Kwoun_2004_FEMS.Microbiol.Lett_235_349
PubMedSearch : Kwoun_2004_FEMS.Microbiol.Lett_235_349
PubMedID: 15183884

Title : Expression and characterization of Ca(2+)-independent lipase from Bacillus pumilus B26 - Kim_2002_Biochim.Biophys.Acta_1583_205
Author(s) : Kim HK , Choi HJ , Kim MH , Sohn CB , Oh TK
Ref : Biochimica & Biophysica Acta , 1583 :205 , 2002
Abstract : A lipase-producing Bacillus pumilus strain (B26) was isolated from a soil sample collected in Korea. The cloned gene showed that the lipase B26 composed of a 34-amino-acid signal sequence and a 181-amino-acid mature part corresponding to a molecular mass (M(r)) of 19,225. Based on the M(r) and the protein sequence, the lipase B26 belongs to the lipase family I.4. The optimum temperature and pH of the purified enzyme were 35 degrees C and 8.5, respectively. The lipase B26 showed a 'Ca(2+)-independent thermostability and catalytic activity'. These are novel properties observed for the first time in lipase B26 among all bacterial lipases and correspond with the suggestion that this enzyme had no Ca(2+)-binding motif around the catalytic His156 residue. This enzyme seems to be a true lipase based on the experimental results that it could hydrolyze various long-chain triglycerides (C(14)-C(18)) and triolein (C(18:1)) and that it showed a typical interfacial activation mechanism toward both tripropionin and p-nitrophenyl butyrate.
ESTHER : Kim_2002_Biochim.Biophys.Acta_1583_205
PubMedSearch : Kim_2002_Biochim.Biophys.Acta_1583_205
PubMedID: 12117564

Title : Novel zinc-binding center and a temperature switch in the Bacillus stearothermophilus L1 lipase - Jeong_2002_J.Biol.Chem_277_17041
Author(s) : Jeong ST , Kim HK , Kim SJ , Chi SW , Pan JG , Oh TK , Ryu SE
Ref : Journal of Biological Chemistry , 277 :17041 , 2002
Abstract : The bacterial thermoalkalophilic lipases optimally hydrolyze saturated fatty acids at elevated temperatures. They also have significant sequence homology with staphylococcal lipases, and both the thermoalkalophilic and staphylococcal lipases are grouped as the lipase family I.5. We report here the first crystal structure of the lipase family I.5, the structure of a thermoalkalophilic lipase from Bacillus stearothermophilus L1 (L1 lipase) determined at 2.0-A resolution. The structure is in a closed conformation, and the active site is buried under a long lid helix. Unexpectedly, the structure exhibits a zinc-binding site in an extra domain that accounts for the larger molecular size of the family I.5 enzymes in comparison to other microbial lipases. The zinc-coordinated extra domain makes tight interactions with the loop extended from the C terminus of the lid helix, suggesting that the activation of the family I.5 lipases may be regulated by the strength of the interactions. The unusually long lid helix makes strong hydrophobic interactions with its neighbors. The structural information together with previous biochemical observations indicate that the temperature-mediated lid opening is triggered by the thermal dissociation of the hydrophobic interactions.
ESTHER : Jeong_2002_J.Biol.Chem_277_17041
PubMedSearch : Jeong_2002_J.Biol.Chem_277_17041
PubMedID: 11859083
Gene_locus related to this paper: geost-lipas

Title : Crystallization and preliminary X-ray analysis of a thermoalkalophilic lipase from Bacillus stearothermophilus L1 - Jeong_2001_Acta.Crystallogr.D.Biol.Crystallogr_57_1300
Author(s) : Jeong ST , Kim HK , Kim SJ , Pan JG , Oh TK , Ryu SE
Ref : Acta Crystallographica D Biol Crystallogr , 57 :1300 , 2001
Abstract : A thermoalkalophilic lipase from Bacillus stearothermophilus L1 (L1 lipase) was crystallized in two different crystal forms using a low concentration of the enzyme and a calcium-exchange process. The first, needle-like, crystal form, which diffracts to about 3.5 A, belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 67.84, b = 72.96, c = 104.41 A. The second, monoclinic, crystal form, which behaves better than the first form for crystallographic analyses, belongs to the monoclinic space group C2 and has unit-cell parameters a = 119.62, b = 85.05, c = 98.36 A, beta = 99.73 degrees. From the monoclinic crystals, a native data set and a samarium-derivative data set were collected to 2.0 and 2.3 A resolution, respectively. The difference Patterson map between the two data sets shows strong heavy-atom peaks, indicating that the crystals are suitable for a high-resolution structure determination.
ESTHER : Jeong_2001_Acta.Crystallogr.D.Biol.Crystallogr_57_1300
PubMedSearch : Jeong_2001_Acta.Crystallogr.D.Biol.Crystallogr_57_1300
PubMedID: 11526325

Title : Gene cloning and characterization of thermostable lipase from Bacillus stearothermophilus L1 - Kim_1998_Biosci.Biotechnol.Biochem_62_66
Author(s) : Kim HK , Park SY , Lee JK , Oh TK
Ref : Biosci Biotechnol Biochem , 62 :66 , 1998
Abstract : The gene coding for an extracellular lipase of Bacillus stearothermophilus L1 was cloned in Escherichia coli. Sequence analysis showed an open reading frame of 1254 bp, which encodes a polypeptide of 417 amino acid residues. The polypeptide was composed of a signal sequence (29 amino acids) and a mature protein of 388 amino acids. An alanine replaces the first glycine in the conserved pentapeptide (Gly-X-Ser-X-Gly) around the active site serine. The expressed lipase was purified by hydrophobic interaction and ion exchange chromatography using buffers containing 0.02% (v/v) Triton X-100. The lipase was most active at 60-65 degrees C and in alkaline conditions around pH 9-10. The lipase had highest activity toward p-nitrophenyl caprylate among the synthetic substrates and tripropionin among the triglycerides. It hydrolyzed beef tallow and palm oil more rapidly than olive oil at 50 degrees C.
ESTHER : Kim_1998_Biosci.Biotechnol.Biochem_62_66
PubMedSearch : Kim_1998_Biosci.Biotechnol.Biochem_62_66
PubMedID: 9501519
Gene_locus related to this paper: geost-lipas

Title : Characterization of an alkaline lipase from Proteus vulgaris K80 and the DNA sequence of the encoding gene - Kim_1996_FEMS.Microbiol.Lett_135_117
Author(s) : Kim HK , Lee JK , Kim H , Oh TK
Ref : FEMS Microbiology Letters , 135 :117 , 1996
Abstract : A facultatively anaerobic bacterium producing an extracellular alkaline lipase was isolated from the soil collected near a sewage disposal plant in Korea and identified to be a strain of Proteus vulgaris. The molecular mass of the purified lipase K80 was estimated to be 31 kDa by SDS-PAGE. It was found to be an alkaline enzyme having maximum hydrolytic activity at pH 10, while fairly stable in a wide pH range from 5 to 11. The gene for lipase K80 was cloned in Escherichia coli. Sequence analysis showed an open reading frame of 861 bp coding for a polypeptide of 287 amino acid residues. The deduced amino acid sequence of the lipase gene had 46.3% identity to the lipase from Pseudomonas fragi.
ESTHER : Kim_1996_FEMS.Microbiol.Lett_135_117
PubMedSearch : Kim_1996_FEMS.Microbiol.Lett_135_117
PubMedID: 8598267
Gene_locus related to this paper: provu-lipas