• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.421-429
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• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• Microbiology and Biotechnology Letters
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• v.35 no.4
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• pp.352-356
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• 2007

A Lactobacillus sp. has been isolated from infant feces and characterized according to its physiological properties and identified as Lactobacillus acidophilus KLA1012. A gene coding surface layer protein (SLP) has been cloned and the sequence has been determined. The nucleotide sequence of slpA was 1,338 bp in size and was identical to that of L. acidophilus ATCC 4356 (100%). Amino acid sequence of SLP-A was deduced from the nucleotide sequence and it had signal sequence at N-terminal, consisting of positively charged amino acid mainly lysine. slpA was cloned and heterologously expressed in E. coli M15 and the 45.2 kDa surface-layer protein band was examined by SDS-PAGE and confirmed by Western blotting using polyclonal antibody against L. acidophilus KLA 1012 SLP-A protein.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.749-756
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• 2010

In many conditions, bacterial surface properties are changed as a result of variation in the growth medium and conditions. This study examined the influence of bile salt concentrations (0-0.1%) on colony morphotype, hydrophobicity, $H_2O_2$ concentration, S-layer protein production, and slpA gene expression in Lactobacillus acidophilus ATCC 4356. It was observed that two types of colonies (R and S) were in the control group and the stress condition. When the bile level increased in the medium, the amount of S type was more than the R type. A stepwise increment in the bile concentration resulted in a stepwise decline in the maximum growth rate. The results showed that hydrophobicity was increased in 0.01%-0.02% bile, but it was decreased in 0.1% bile. Treatment by bile (0.01%-0.1%) profoundly decreased $H_2O_2$ formation. S-Layer protein and slpA gene expression were also altered by the stress condition. S-Protein expression was increased in the stress condition. The slpA gene expression increased in 0.01%-0.05% bile and it decreased in 0.1% bile. However, we found that different bile salt concentrations influenced the morphology and some surface properties of L. acidophilus ATCC 4356. These changes were very different in the 0.1% bile. It appears that the bacteria respond abruptly to 0.1% bile.

• Journal of Microbiology and Biotechnology
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• v.23 no.4
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• pp.545-554
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• 2013

Plasmid isolation of kimchi-derived Weissella cibaria KLC140 revealed six different plasmids. The smallest plasmid, pKW2124, was DNA sequenced and characterized, showing 2,126 bp with a GC content of 36.39% and five putative open reading frames (ORFs). In silico analysis of these ORFs showed ORF1 encodes a putative replication protein similar to rolling circular replication proteins from other lactic acid bacteria. However, a single-stranded intermediate was not detected when S1 nuclease was treated, suggesting it may follow theta replication. Interestingly, the replication initiation site of this plasmid is 100% identical to other plasmids from lactic acid bacteria, suggesting it may function for replication initiation. To construct a surface layer expression vector, pTSLGFP, slpA encoding the surface layer protein from Lactobacillus acidophilus was PCR amplified and fused with the gfp gene, forming a SLGFP fused gene. The plasmid pKW2124 was cloned into the XbaI site of pUC19, forming an Weissella-E. coli shuttle vector pKUW22. NheI-linearized pTSLGFP was ligated into pKUWCAT containing pKUW22 and the chloramphenicol acetyltransferase gene from pEK104, resulting in an 8.6 kb pKWCSLGFP surface layer expression vector. After transformation of this vector into W. cibaria KLC140, a GFP fluorescence signal was detected on the surface of the transformant, substantiating production of SLGFP fused protein and its secretion. This is the first report for construction of a Weissella surface layer expression vector, which may be useful for surface layer production of beneficial proteins in Weissella.

• The Journal of Korean Academy of Prosthodontics
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• v.43 no.6
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• pp.751-763
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• 2005

Statement of problem. To improve a direct implant fixation to the bone, various strategies have been developed focusing on the surface of materials. The surface quality of the implant depends on the chemical, physical, mechanical and topographical properties of the surface. The different properties will interact with each other and a change in thickness of the oxide layer may also result in a change in surface energy, the surface topography and surface, chemical composition. However, there is limited the comprehensive study with regard to changed surface and biologic behavior of osteoblast by anodization. Purpose of study. The aim of this study was to analyze the characteristics of an oxide layer formed and to evaluate the cellular biologic behaviors on titanium by anodic oxidation (anodization) by cellular proliferation, differentiation, ECM formation and gene expression. And the phospholipase activity was measured on the anodized surface as preliminary study to understand how surface properties of Ti implant are transduced into downstream cellular events. Methods and Materials. The surface of a commercially pure titanium(Grade 2) was modified by anodic oxidation. The group 1 samples had a machined surface and other three experimental specimens were anodized under a constant voltage of 270 V(Group 2), 350 V(Group 3), and 450 V(Group 4). The specimen characteristics were inspected using the following five categories; the surface morphology, the surface roughness, the thickness of oxide layer, the crystallinity, and the chemical composition of the oxide layer. Cell numbers were taken as a marker for cell proliferation. While the expression of alkaline phosphatase and Runx2 (Cbfa1) was used as early differentiation marker for osteoblast. The type I collagen production was determined, which constitutes the main structural protein of the extracellular matrix. Phospholipase $A_2$ and D activity were detected. Results. (1) The anodized titanium had a porous oxide layer, and there was increase in both the size and number of pores with increasing anodizing voltage. (2) With increasing voltage, the surface roughness and thickness of the oxide film increased significantly (p<0.01), the $TiO_2$phase changed from anatase to rutile. During the anodic oxidization, Ca and P ions were more incorporated into the oxide layer. (3) The in vitro cell responses of the specimen were also dependant on the oxidation conditions. With increasing voltage, the ALP activity, type I collagen production, and Cbfa 1 gene expression increased significantly (p<0.01), while the cell proliferation decreased. (4) In preliminary study on the relation of surface property and phospholipase, PLD activity was increased but $PLA_2$ activity did not changed according to applied voltage. Conclusion. The anodized titanium shows improved surface characteristics than the machined titanium. The surface properties acquired by anodization appear to give rise more mature osteoblast characteristics and might result in increased bone growth, and contribute to the achievement of a tight fixation. The precise mechanism of surface property signaling is not known, may be related to phospholipase D.

• Fisheries and Aquatic Sciences
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• v.14 no.4
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• pp.347-354
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• 2011

Aeromonas salmonicida is an important fish pathogen commonly associated with furunculosis in salmonids. Typical A. salmonicida strains have the surface virulence A-layer protein, a major virulence determinant encoded by the vapA gene. In this study, 880 chum salmon Oncorhynchus keta were collected from the east coast of Korea during 2006-2011, including 560 wild adults and 320 artificially hatched fry pools, and the presence of typical A. salmonicida was examined by PCR using the typical A. salmonicida-specific vapA gene primers. The results demonstrated that 34.5% of the samples (304/880 samples) were PCR positive, implying that a typical A. salmonicida infection is highly prevalent among chum salmon in Korea. Twenty typical A. salmonicida isolates were recovered based on their brown pigmentation on Trypticase Soy Agar (TSA) plates, which indicates the existence of the A-layer protein. Further biochemical analyses with the four randomly selected typical A. salmonicida isolates revealed some variations in their amino acid decarboxylation and carbohydrate fermentation activity. A phylogenetic analysis based on the entire vapA gene sequence suggested that the A. salmonicida isolates from chum salmon were clustered with those isolated from Atlantic salmon in Europe. Further study is needed to resolve such an interesting relationship in detail.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.277-285
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• 2009

The nucleotide sequence of the Paenibacillus curdlanolyticus B-6 xyn10A gene, encoding a xylanase Xyn10A, consists of 3,828 nucleotides encoding a protein of 1,276 amino acids with a predicted molecular mass of 142,726 Da. Sequence analysis indicated that Xyn10A is a multidomain enzyme comprising nine domains in the following order: three family 22 carbohydrate-binding modules (CBMs), a family 10 catalytic domain of glycosyl hydrolases (xylanase), a family 9 CBM, a glycine-rich region, and three surface layer homology (SLH) domains. Xyn10A was purified from a recombinant Escherichia coli by a single step of affinity purification on cellulose. It could effectively hydrolyze agricultural wastes and pure insoluble xylans, especially low substituted insoluble xylan. The hydrolysis products were a series of short-chain xylooligosaccharides, indicating that the purified enzyme was an endo-$\beta$-1,4-xylanase. Xyn10A bound to various insoluble polysaccharides including Avicel, $\alpha$-cellulose, insoluble birchwood and oat spelt xylans, chitin, and starches, and the cell wall fragments of P. curdlanolyticus B-6, indicating that both the CBM and the SLH domains are fully functioning in the Xyn10A. Removal of the CBMs from Xyn10A strongly reduced the ability of plant cell wall hydrolysis. These results suggested that the CBMs of Xyn10A play an important role in the hydrolysis of plant cell walls.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.825-833
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• 2017

Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilutionto-extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain IMCC26207 formed a distinct lineage in the order Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously identified bacterial taxa was "Candidatus Microthrix parvicella" with 16S rRNA gene sequence similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater actinobacterium, is reported with the description of the genome properties and annotation summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. Annotation of the IMCC26207 genome showed several traits of adaptation to living in oligotrophic freshwater environments, such as phosphorus-limited condition. Comparative genomic analysis revealed that the genome of strain IMCC26207 was distinct from that of "Candidatus Microthrix" strains; therefore, we propose the name "Candidatus Limnosphaera aquatica" for this bacterium.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.320-322
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• 2017

A betaproteobacterium strain GR16-43 was isolated from a surface layer of the Geomnyong Pond in Republic of Korea by a dilution-to-extinction culturing method. We report the whole genome sequence of the strain GR16-43, which contains 4,806,848 bp with a G + C content 67.12%, and to include 4,424 protein-coding genes and 47 transfer RNA genes. The genome was determined to contain the genes encoding carbon monoxide dehydrogenase, nitrate reductase, nitrite reductase, nitric oxide reductase, and the sulfur oxidation (sox) gene cluster, highlighting the potential importance of the bacterial group represented by the strain in the cycling of inorganic elements. These results indicate that strain GR16-43 genome showed several traits indicating adaptation of the bacteria to living in freshwater environments.