• Title/Summary/Keyword: Clone library

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Functional Analysis of ESTs from the 14-year Root of Korean Ginseng

  • Yang, Deok-Chun;In, Jun-Gyo;Kim, Moo-Sung;Jeon, Jong-Seong
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2003.04a
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    • pp.125-125
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    • 2003
  • To assist genetic study of the root development in Panax ginseng, which is one of the most important medicinal plant, expressed sequence tags (EST) analysis was carried out. We constructed a cDNA library using the 14-year ginseng root. Partial sequences were obtained from 2,975 clone. The ESTs could be clustered into 1,991 (70.2%) non-redundant groups. Similarity search of the non-redundant ESTs against public non-redundant databases of both protein and DNA indicated that 1,553 groups show similarity to genes of blown function. These ESTs clones were divided into sixteen categories depending upon gene function. The most abundant transcripts were ribonuclease 1 (67) and ribonuclease 2 (65). Our extensive EST analysis of genes expressed in 14-year ginseng root not only contributes to the understanding of the dynamics of genome expression patterns in root organ but also adds data to the reperoire of all genomic genes.

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Molecular Cloning of Bacteriocin Gene and Biological Control of Plant Pathogen (Bacteriocin 생산 유전자의 Cloning 및 식물병원균에 대한 생물학적 억제)

  • 김교창;육창수;도대홍
    • Microbiology and Biotechnology Letters
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    • v.18 no.1
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    • pp.98-102
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    • 1990
  • A strain of Erwinia spp. was selected from the soil for the production of bacteriocin to the root rot plant pathogen. Bacteriocin producing gene was not located on plasmid but on chromosome. Genomic library of Erwinia spp. were made by using pLAFR 3 as a vector system for cloning of the gene. It was been cloned and expressed in E. coli DH 5 . Bacteriocin producing colony was composed of pLAFR 3 vector and 3.0 kb EcoRI fragment of Erwinia spp. ehromosomal DNA. The inserted fragment (3.0 kb) was possessed a EcoRI and BarnHI restriction sites.

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Bacterial diversity in children's dental caries (소아의 치아 우식 부위별 세균 다양성)

  • Kim, Eun-Mi;Baik, Keun-Sik;Ha, Myung-Ok
    • Journal of Korean society of Dental Hygiene
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    • v.13 no.5
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    • pp.889-900
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    • 2013
  • Objectives : Molecular biology techniques were employed to assess diversity of bacterial in children's dental caries. Methods : DNA of germs was extracted and the diversity of the 16S rRNA clones was analyzed by amplified rDNA restriction analysis and sequencing. The experimental samples were pit and fissure caries (PC), deep dentinal caries (DC), smooth surface caries (SC), and supragingival plaque (PQ) from 50 children of age less than 12 years old. The control group was healthy teeth supragingival plaque (HT). Thirty clones from each 16S rRNA clone library of 5 samples were randomly selected, thus a total of 150 clones were analyzed. Results : Amplified rDNA restriction analysis uncovered 18, 20, 11, 17, and 22 phylotypes from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and supragingival plaque, respectively. Sequencing analysis found the dominance of Actinomycs naeslundii and Fusobacterium nucleatum in the healthy teeth; Leptotrichia sp. in the pit and fissure caries; Actinomyces sp., Streptococcus mutans, and Rahnella aquatilis in the deep dentinal caries; Streptococcus mutans and Actinomyces sp. in the smooth surface caries; Enterobacter hormaechei and Streptococcus sanguinis in the supragingival plaque. Conclusions : Clonal analysis identified 6 phyla, 20 genera, and 51 species.

Cloning of a DNA Fragment Specific to Pseudomonas tolaasii Causing Bacterial Brown Blotch Disease of Oyster Mushroom (Pleurotus ostreatus) (느타리버섯 세균성갈색무늬병 병원균 Pseudomonas tolaasii의 특이적 DNA 클로닝)

  • 이혁인;차재순
    • Korean Journal Plant Pathology
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    • v.14 no.2
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    • pp.177-183
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    • 1998
  • A DNA fragment which is involved in tolassin production was cloned to obtain a molecular marker of Pseudomonas tolaasii, a casual agent of bacterial brown blotch disease of oyster mushroom (Pleurotus ostreatus). Tolaasin is a lipodepsipeptide toxin and known as a primary disease determinant of the P. tolaasii. It is responsible for formation of white line in agar when P. tolaasii were cultured against white line reacting organisms (WLROs). White line negative mutants (WL-) were generated by conjugation between rifampicin resistant strain of P. tolaasii and E. coli carrying suicidal plasmid pSUP2021 : : Tn5. The ability of tolaasin production of the WL- mutants was examined by hemolysis test, pathogenicity test, and high pressure liquid chromatography (HPLC) analysis of culture filtrate. All of the WL- mutants were lost the ability of tolaasin production (Tol-). Genomic library of the Tol- mutant was constructed in pLAFR3 and the cosmid clone containing Tn5 was selected. DNA fragment fro franking region of Tn5 was cloned from the plasmid and used as a probe in Southern blot. DNA-DNA hybridization with the probe to total DNA from group of bacteria ecologically similar to P. tolaasii including WLORs, fluorescent Pseudomonads isolated from oyster mushroom, P. agarici, P. gingeri, and some of other species of Psedomonas showed that some of the tested bacteria do not have any hybridized band and others have bands sowing RFLP. The cloned DNA fragment or its nucleotide sequence will be useful in detection and identification of the P. tolaasii.

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Genomic Organization of Penicillium chrysogenum chs4, a Class III Chitin Synthase Gene

  • Park, Yoon-Dong;Lee, Myung-Sook;Kim, Ji-Hoon;Jun Namgung;Park, Bum-Chan;Bae, Kyung-Sook;Park, Hee-Moon
    • Journal of Microbiology
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    • v.38 no.4
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    • pp.230-238
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    • 2000
  • Class III chitin synthases in filamentous fungi are important for hyphal growth and differentiation of several filamentous fungi. A genomic clone containing the full gene encoding Chs4, a class III chitin synthase in Penicillium chrysogenum, was cloned by PCR screening and colony hybridization from the genomic library. Nucleotide sequence analysis and transcript mapping of chs4 revealed an open reading frame (ORF) that consisted of 5 exons and 4 introns and encoded a putative protein of 915 amino acids. Nucleotide sequence analysis of the 5'flanking region of the ORF revealed a potential TATA box and several binding sites for transcription activators. The putative transcription initiation site at -716 position was identified by primer extension and the expression of the chs4 during the vegetative growth was confirmed by Northern blot analysis. Amino acid sequence analysis of the Chs4 revealed at least 5 transmembrane helices and several sites for past-transnational modifications. Comparison of the amino acid sequence of Chs4 with those of other fungi showed a close relationship between P chrysogenum and genus Aspergillus.

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Immunodiagnosis of clonorchiasis using a recombinant antigen (간흡충 재조합항원을 이용한 간흡충증의 면역 진단)

  • 용태순;양혜진
    • Parasites, Hosts and Diseases
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    • v.36 no.3
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    • pp.183-190
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    • 1998
  • A cDNA expression library of Clonorchis sinensis adult worm was constructed, and screened out immunologically. One clone, pBCs31, was selected ill view of its predominant reactivity with an experimentally infected rabbit serum. Recombinant C. slnensis antigen iIi 28 kDa as a if-falactosidase fusion protein produced in EscherichiG coli was identified by immunoblot analysis. The cloned gene was composed of 16 copies or a 30 base pair repeat and an additional 320 bases. The deduced amino acid seqiLence of the tandem repeat was AQPPKSGDGG. On RNA slot blot analysis, C. sinensis adult worm RNA showed a positive reaction with the cloned gene Enzyme-linked immunosorbent assay using a purified recombinant antigen of pBCs31 showed higtl specificity for diagnosis of clonorchiasis.

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Amino Acid Biosynthesis and Gene Regulation in Seed (종자내 아미노산 합성 조절 유전자에 관한 연구)

  • ;;;;;Fumio Takaiwa
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Effect of Ferrous Ion on the Formation of Exotoxin A from Pseudomonas sp. PY002 and Cloning of it's Gene (Pseudomonas sp. PY002에서 Exotoxin A의 생성에 미치는 철 이온의 영향과 Exotoxin A 유전자의 클로닝)

  • Choi, Sun-Ah;Kim, Ho-Sang;Choi, Ji-Young;Kang, Jeong-Suk;Kim, Chun-Sung;Kim, Duck-Lae;Kim, Young-Ju;Yeo, Myeong-Gu;Park, Yeol
    • Korean Journal of Microbiology
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    • v.35 no.1
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    • pp.7-12
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    • 1999
  • By SDS-polyacrylamide gel elcctrophoresis (SDS-PAGE) and immunoblot analysis that a protein with 66,000 daltons in size was recognized by P. aeruginosa anti-exotoxin A from P. sp. PY002. The yields of exotoxin A in P. sp. PY002 culture were influenced by the concentration of iron in the culture media. Increasing of the exotoxin A production and siderophore production was made slight increasing in the MKB medium. On the other hand, to clone the gene encoding the exoloxin A genomic library of P. sp. PY002 was constructed in pBluescript SK(+). From this library a exotoxin A homologous gene was isolated by immunological hybridization method using P. aemginosa anti-exoloxin A as a probe. Two putative clones were isolated and designated pETA23 and pETA42. Thc restriction analysis ol pETA42 demonstrated that thc 1760 bp insert contained one NcoI, PvuII, SstI, Kpnl and EcoRI site and three SmaI and HaeD sites.

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Diversity Analysis for Archaeal amoA Gene in Marine Sediment of Svalbard, Arctic Circle (북극 Svalbard 지역 해양 퇴적물의 고세균 amoA 유전자의 다양성 분석)

  • Park, Soo-Je;Rhee, Sung-Keun
    • Korean Journal of Microbiology
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    • v.50 no.2
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    • pp.164-168
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    • 2014
  • The ecosystem of the Arctic region has been increasingly affected by global warming. Archaeal ammonia monooxygenase alpha subunit coding gene (amoA) which is a key enzyme for nitrification was used to investigate the effect of runoff water of ice melt on microbial community of nitrogen cycle. The archaeal amoA genes at coastal area of Svalbard, Arctic region were PCR-amplified and sequenced after clone library construction. Analysis of archaeal amoA gene clone libraries suggested that the station 188 which is in the vicinity to the area of runoff water harbor lower ammonia-oxidizing archaeal diversity than the station 176 and 184. The average amino acid sequence identity within all archaeal amoA gene clones was 94% (with 91% nucleotide sequence identity). While all the clones of the station 188 were affiliated with Nitrosoarchaeaum clade containing strains isolated from low-salinity and terrestrial environments, about 45% of total clones of the station 176 and 184 were related to marine Nitosopumilus clade. Interestingly, other typical archaeal amoA gene clones of thaumarchaeal I.1b clade frequently retrieved from terrestrial environments was identified at station 188. Microbial community of nitrogen cycle in marine sediment might be affected by input of sediments caused by runoff glacier melt waters.

Characterization, Cloning and Expression of the Ferritin Gene from the Korean Polychaete, Periserrula leucophryna

  • Jeong Byeong Ryong;Chung Su-Mi;Baek Nam Joo;Koo Kwang Bon;Baik Hyung Suk;Joo Han-Seung;Chang Chung-Soon;Choi Jang Won
    • Journal of Microbiology
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    • v.44 no.1
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    • pp.54-63
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    • 2006
  • Ferritin is a major eukaryotic protein and in humans is the protein of iron storage. A partial gene fragment of ferritin (255 bp) taken from the total RNA of Periserrula leucophryna, was amplified by RT-PCR using oligonucleotide primers designed from the conserved metal binding domain of eukaryotic ferritin and confirmed by DNA sequencing. Using the $^{32}P-labeled$ partial ferritin cDNA fragment, 28 different clones were obtained by the screening of the P. leucophryna cDNA library prepared in the Uni-ZAP XR vector, sequenced and characterized. The longest clone was named the PLF (Periserrula leucophryna ferritin) gene and the nucleotide and amino acid sequences of this novel gene were deposited in the GenBank databases with accession numbers DQ207752 and ABA55730, respectively. The entire cDNA of PLF clone was 1109 bp (CDS: 129-653), including a coding nucleotide sequence of 525 bp, a 5' -untranslated region of 128 bp, and a 3'-noncoding region of 456 bp. The 5'-UTR contains a putative iron responsive element (IRE) sequence. Ferritin has an open reading frame encoding a polypeptide of 174 amino acids including a hydrophobic signal peptide of 17 amino acids. The predicted molecular weights of the immature and mature ferritin were calculated to be 20.3 kDa and 18.2 kDa, respectively. The region encoding the mature ferritin was subcloned into the pT7-7 expression vector after PCR amplification using the designed primers and included the initiation and termination codons; the recombinant clones were expressed in E. coli BL21(DE3) or E. coli BL21(DE3)pLysE. SDS-PAGE and western blot analysis showed that a ferritin of approximately 18 kDa (mature form) was produced and that by iron staining in native PAGE, it is likely that the recombinant ferritin is correctly folded and assembled into a homopolymer composed of a single subunit.