• Journal of Microbiology and Biotechnology
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• v.3 no.3
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• pp.146-155
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• 1993

A DNA fragment from an alkali-tolerent Bacillus sp., conferring strong promoter activity, was subcloned into the promoter probe plasmid pPL703 and the nucleotide sequence of this promoter region was determined. The sequence analysis suggested that this highly efficient promoter region containing the complex clustered promoters comprised three kinds of promoters (P1, P2 and P3), which are transcribed by $\sigma^B (formerly \sigma^{37}), \sigma^E(formerly \sigma^{29}) and \sigma^A (formerly \sigma^{43})$ RNA polymerase holoenzymes which play major rules at the onset of endospore formation, during sporulation and at the vegetative phase of growth, respectively. S1 nuclease mapping experiments showed that all three promoters had staggered transcription initiation points. The results of chloramphenicol acetyltransferase assay after the subcloning experiments also indicated that the expression of these clustered promoters was correlated with the programs of growth and endospore development. Promoter P1, P2 and P3 were preceded by 75% AT, 79% AT and 81% AT regions, respectively, and a partial deletion of AT-rich region prevented transcription from promoter P1 in vivo. Two sets of 5 -AGTGTT-3 sequences and inverted repeat sequences located around the promoter P1 were speculated as the possible cis acting sites for the catabolite repression in B. subtilis. In vivo transcripts from these sequence regions may be able to form a secondary structure, however, the possibility that a regulatory protein induced by the excess amount of glucose could be bound to such a domain for crucial action remains to be determined.

• Journal of Plant Biology
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• v.35 no.2
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• pp.155-163
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• 1992

To elucidate the regulatory mechanism of virE operon in Agrobacterium tumefaciens pTiA6 plasmid at the molecular level, the regulatory site of virE promoter was determined using truncated virE recombinant plasmids obtained by 5' deletion analysis of virE promoter. The size of deleted nucleotides of p]S201, a functional recombinant plasmid, was found to be about 130 nucleotides from 5'-end of virE promoter. On the other hand the size of deleted nucleotides of p]S301, nonfunctional recombinant plasmid, was identified 263 nucleotides by DNA sequencing. Hence it was thought that the essential site of virE promoter was located between about 130th nucleotide and 263th nucleotide. Since the inverted repeat sequence (AACTTTGCGCTATAGGCAMGTT) is included in this essential site of virE promoter, it could be the first recognition site of the RNA polymerase in virE promoter.omoter.

• The Korean Journal of Zoology
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• v.39 no.2
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• pp.164-172
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• 1996

KP elements derived from Korean populations (Seoul, Cheonan and Taegu) of Drosophila melunoguster were examined for their molecular structure. The entire 1.15 kb sequence of the three KP elements KC-137 (Cheonan), KS-95 (Seoul) and KT-99 (Taegu) have been obtained by PCR amplification using inverted repeat primers and DNA sequencing. The 1.15 kb fragments of KP elements were cloned into pCRmll vector plasmids, and subsequently sequenced. The sequence of the three KP elements in these populations suggested that there might have been derived from the complete P element by a 1753 bp internal deletion between positions 808 and 2560. Therefore these KP elements were confirmed to be identical to that isolated from M'10 strains widely distributed in most Eurasian populations of D. melanoguster. Sequence comparison with the 2.9 kb complete P element in pn25.1 revealed that KC-137 has only shown to be two base substitutions of A to G and G to A at positions 62 and 242, respectively. The retained sequence of the two KP elements KS-95 and KT-99 shows complete homology to the P factor in pn25.1. Based on this result, the two base substitutions in KC-137 might be due to Taq DNA pollunerase errors. Finally, it is suggested that the high copy numbers of KP elements provieds an explanation for the suppression of P-mediated hybrid dvssenesis in Korean population of D. melunogoster.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.822-829
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• 2007

A gene coding for phosphoketolase, a key enzyme of carbohydrate catabolism in heterofermentative lactic acid bacteria(LAB), was cloned from a Lactobacillus paraplantarum C7 and expressed in Escherichia coli. The gene is 2,502 bp long and codes for a 788-amino-acids polypeptide with a molecular mass of 88.7 kDa. A Shine-Dalgarno sequence(aaggag) and an inverted-repeat terminator sequence are located upstream and downstream of the phosphoketolase gene, respectively. The gene exhibits an identity of >52% with phosphoketolases of other LAB. The phosphoketolase of Lb. paraplantarum C7(LBPK) contains several highly conserved phosphoketolase signature regions and typical thiamine pyrophosphate(TPP) binding sites, as reported for other TPP-dependent enzymes. The phosphoketolase gene was fused to a glutathione S-transferase(GST::LBPK) gene for purification. The GST::LBPK fusion protein was detected in the soluble fraction of a recombinant Escherichia coli BL21. The GST::LBPK fusion protein was purified with a yield of 4.32mg/400ml by GSTrap HP affinity column chromatography and analyzed by N-terminal sequencing. LBPK was obtained by factor Xa treatment of fusion protein and the final yield was 3.78mg/400ml. LBPK was examined for its N-terminal sequence and phosphoketolase activity. The $K_M\;and\;V_{max}$ values for fructose-6-phosphate were $5.08{\pm}0.057mM(mean{\pm}SD)$ and $499.21{\pm}4.33{\mu}mol/min/mg$, respectively, and the optimum temperature and pH for the production of acetyl phosphate were $45^{\circ}C$ and 7.0, respectively.

• The Transactions of the Korea Information Processing Society
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• v.6 no.7
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• pp.1832-1840
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• 1999

Since the existed Korean Web IR systems generally use boolean system, it is difficult to retrieve the information to be wanted at one time. Also, because of the feature that web documents have the frequent abbreviation and many links, the keyword extraction using the inverted document frequency extracts the improper keywords for adding ambiguous meaning problem. Therefore, users must repeat the modification of the queries until they get the proper information. In this paper, we design and implement the relevance feedback agent system for resolving the above problems. The relevance feedback agent system extracts the proper information in response to user's preferred keywords and stores these keywords in preference DB table. When users retrieve this information later, the relevance feedback agent system will search it adding relevant keywords to user's queries. As a result of this method, the system can reduce the number of modification of user's queries and improve the efficiency of the IR system.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.55-55
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• 2020

뫼제비꽃(Viola selkirkii)의 엽록체 DNA 염기서열을 차세대염기서열분석법(NGS)을 이용하여 분석하였다. 재료는 강원도 화천군 일산과 제주도 한라산의 2개체를 사용하였다. 분석결과, 염기서열의 길이는 일산의 뫼제비꽃이 156,774 bp (GC content: 36.30%), 한라산의 뫼제비꽃이 157,451 bp(GC content: 36.30%)로 한라산 개체가 길게 분석되었다. 구간별로 LSC(Large single copy)지역은 한라산 개체(85,950 bp)가 일산 개체(85,930 bp)보다 20 bp 길었으며, SSC(Small single copy)지역은 한라산 개체(17,261 bp)보다 일산 개체가 17,982 bp로 길게 분석되었다. IR(Inverted repeat)지역은 한라산 개체가 27,120 bp로 일산 개체(26,431 bp)보다 길게 분석되었다. 이러한 염기서열 길이의 차이는 종내 개체 간 빈번하게 발생하는 현상으로 IGS와 intron 구간에서 확인 된 단순반복서열의 일부 누락과 IR지역 내의 수축과 확장에 의한 것으로 판단된다. 뫼제비꽃 2개체의 엽록체 게놈을 구성하는 유전자 수는 총 111개로 동일하였으며, protein coding gene 77개, tRNA(transfer RNA) gene 30개, 그리고 rRNA (ribosomal RNA) gene 4개로 구성되어 있었다. 이는 기 발표된 엽록체 DNA 전체 염기서열이 밝혀진 제비꽃속 (Viola) 종류들과 동일한 결과이다.

• Journal of Microbiology and Biotechnology
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• v.10 no.3
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• pp.312-320
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• 2000

Abstract The full sequence of the plasmid pKJ36, which was derived from Bifidobacterium longum KJ, was determined and analyzed to construct shuttle vectors between E. coli and Bifidobacterium. The plasmid pKJ36 was composed of 3,625 base pairs with a 65.1% G+C content. The structural organization of pKJ36 was highly similar to that of pKJ50, and the three major ORFs on pKJ36 showed high amino acid sequence homologies with those of pKJ50. The putative proteins coded by these three ORFs were designated as RepB (32.0 kDa, pI=9.25), MembB (29.0 kDa, pI=12.25), and MobB (39.0 kDa, pI=IO.66), respectively. The amino acid sequence of RepB showed a 57% identity and 70% similarity with that of the RepA protein of pKJ50. Upstream of the repB gene, the so-called iteron sequence was directly repeated four-and-ahalf times and a conserved dnaA box was identified. An amino acid sequence comparison between the MobB and MobA of pKJ50 revealed a 48% identity and 61 % similarity. A conserved oriT sequence with an inverted repeat identical to that of pKJ50 was also found upstream of the mobB gene. A hydropathy analysis of MembB revealed four possible transmembrane regions. The expressions of the repB and membB genes were confirmed by RT-PCR. The in vitro translation reaction of pKJ36 showed protein bands with anticipated sizes with respect to each putative gene product. S 1 endonuclease treatment and Southern hybridization suggested that pKJ36 replicates by a rolling circle mechanism via a single-stranded DNA (ssDNA) intermediate. A shuttle vector between E. coli and Bifidobacterium sp. was constructed using the pKJ36, pBR322, and staphylococcal chloramphenicol acetyl transferase (CAT) gene. The successful transformation of the Bifidobacterium strains was shown by Southern hybridization and PCR. The transformation efficiency differed from strain to strain and, depending on the electroporation conditions, with a range between $1.2{\times}10^1-2.6{\times}10^2{\;}cfu/\mu\textrm{g}$ DNA.X> DNA.

• The Journal of the Korean Society for Microbiology
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• v.35 no.3
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• pp.263-271
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• 2000

A clinical isolate of Klebsiella pneumoniae K7746 produced the extended-spectrum ${\beta}$-lactamase (ESBL) SHV-12. A 6.6 kb BamHI fragment containing the $bla_{SHV-12}$ gene of K7746 strain was cloned into pCRScriptCAM vector resulting in the recombinant plasmid p7746-Cl. The restriction map of 3.6 kb inserted DNA and sequences immediately surrounding $bla_{SHV-12}$ of p7746-C1 were homologous to plasmid pMPA2a carrying $bla_{SHV-2a}$. In addition, both $bla_{SHV-12}$ and $bla_{SHV-2a}$ were expressed from a common hybrid promoter made of the -35 region derived from the left inverted repeat of IS26 and the -10 region from the $bla_{SHV}$ promoter itself. The results indicate that $bla_{SHV-12}$ and $bla_{SHV-2a}$ may have evolved from a common ancestor in the sequential order of $bla_{SHV-2a}$ first, followed by $bla_{SHV-12}$. Furthermore, by the PCR mapping method using primers corresponding to the IS26 and $bla_{SHV}$, the association between IS26 and $bla_{SHV}$ was studied in 12 clinical isolates carrying $bla_{SHV-2a}$, 27 clinical isolates carrying $bla_{SHV-12}$, and 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$. All 39 strains carrying $bla_{SHV-2a}$ or $bla_{SHV-12}$ were positive by the PCR, providing confirmative evidence that IS26 has been involved in the evolution and dissemination of $bla_{SHV-2a}$ and $bla_{SHV-12}$. But 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$ were negative by the PCR. Therefore, we concluded that the molecular evolutionary pathway of $bla_{SHV-2a}$ and $bla_{SHV-12}$ may be different from that of other $bla_{SHV-ESBL}$, e.g., $bla_{SHV-2}$, $bla_{SHV-3}$, $bla_{SHV-4}$, and $bla_{SHV-5}$.

• Korean Journal of Plant Taxonomy
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• v.53 no.1
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• pp.32-37
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• 2023

Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.

• Horticultural Science & Technology
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• v.34 no.2
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• pp.305-313
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• 2016

Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U's triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety 'Blackgat' was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.