• 제목/요약/키워드: Genomic DNA library

검색결과 220건 처리시간 0.026초

Isolation of $\beta$-Lactamase Inhibitory Protein from Streptomyces exfoliatus SMF19 and Cloning of the Corresponding Gene

  • PARK, HYEON-UNG;KYE JOON LEE
    • Journal of Microbiology and Biotechnology
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    • 제6권6호
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    • pp.369-374
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    • 1996
  • The ${\beta}$-lactamase inhibitory protein (BLIP) produced by Streptomyces exfoliatus SMF19 was purified(33 kDa) and the N-terminal amino acid sequence was determined as NH2-ATSVVAWGGNND. Genomic DNA library of S. exfoliatus SMF19 was constructed in pWE15 and recombinants harbouring the corresponding gene were selected by colony hybridization to the mixture of 36-mer oligonucleotide designed from the N-terminal amino acid sequence. The corresponding gene (bliX) was isolated on a 4-kb ApaI fragment of S. exfoliatus SMF19 chromosomal DNA and then sequenced. The bliX consisting of 1, 119bp encoded a mature protein with a deduced amino acid sequence of 342 residues and also encoded a 40-amino-acid signal sequence. No significant sequence similarity to bliX was found by pairwise comparison using various protein and nucleotide sequences.

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Nickel Binding Protein (NBPI) and Its Gene from Streptomyces seoulensis

  • Kim, In-Kwon;Sa-Ouk kang
    • 한국생물물리학회:학술대회논문집
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    • 한국생물물리학회 2001년도 학술 발표회 진행표 및 논문초록
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    • pp.52-52
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    • 2001
  • Nickel-binding protein (NBP1) was purified from the crude extract of Streptomyces seoulensis using Ni$^{2+}$-charged metal chelate affinity chromatography. The molecular mass of NBPI determined on SDS-PAGE was 38kDa. An approximately 3 kb DNA fragment containing the structural gene for NBP1 was cloned from lEMBL3 genomic library of S. seoulensis using a DNA fragment PCR-amplified with the primers designed from N-terminal and internal amino acid sequences of NBP1.(omitted)

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Cloning of Isopenicillin N Synthase Gene from Lysobacter lactamgenus

  • Ryu, Jae-Kook;Nam, Doo-Hyun
    • Journal of Microbiology and Biotechnology
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    • 제7권6호
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    • pp.373-377
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    • 1997
  • The gene for isopenicillin N synthase (cyclase; IPNS) was cloned from Lysobacter lactamgenus using DNA probe amplified with primers based on the consensus sequences of isopenicillin N synthase genes of other ${\beta}$-lactam-producing microorganisms. The genomic library of L. lactamgenus using pUC18 plasmid cloned at the SacI site were screened with the PCR-generated DNA probe and three positive clones were isolated. Enzyme activities in E. coli clones were confirmed by bioassay and HPLC assay. Throughout the functional mapping, it was observed that the gene for isopenicillin N synthase is located at the 1.3-kb XhoI-BamHI fragment of insert of positive clones. Nucleotide sequencing at both ends of the XhoI-BamHI fragment revealed that IPNS of L. lactamgenus has the common amino acid sequences at amino- and carboxy-termini.

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Screening and Characterization of an Esterase from a Metagenomic Library

  • KIM JEONG-NYEO;SEO MYUNG-JI;CHO EUN-AH;LEE SANG-JAE;KIM SEONG-BO;CHEIGH CHAN-ICK;PYUN YU-RYANG
    • Journal of Microbiology and Biotechnology
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    • 제15권5호
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    • pp.1067-1072
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    • 2005
  • A metagenomic library was constructed using a fosmid vector, and total genomic DNA was extracted directly from soil at Cisolok (hot spring area, Indonesia). This library was composed of 10,214 clones and screened for lipolytic enzyme on tributyrin agar plates. An esterase gene (estMa) was subcloned and sequenced from a positive lipolytic active clone. Esterase EstMa was encoded by a 954-bp open reading frame and showed low ($11-33\%$) amino acid similarity to known esterases. The amino acid sequence analysis demonstrated that the enzyme is a new member of lipolytic enzyme family VI. The estMa gene encodes a preprotein of 317 amino acids with a predicted molecular mass of 34,799 Da. The purified enzyme exhibited optimal activity at $50^{\circ}C$ and pH 6.5. The $K_m,\;and\;V_{max}$ values of EstMa for the hydrolysis of p-nitrophenyl valerate were $45.3\;{\mu}M$ and 4.45 U/mg, respectively.

Nucleotide Sequence of Rat Transketolase and Liver-Specific Pretranslational Activation During Postnatal Development

  • Kim, Sung-Min F.;Kim, Byung-Moon;Jeng, Jingjau;Soh, Yun-Jo;Bak, Choong-Il;Huh, Jae-Wook;Song, Byoung-J.
    • BMB Reports
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    • 제29권2호
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    • pp.146-150
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    • 1996
  • A 2.1 kb cDNA clone for rat transketolase was isolated from rat liver ${\lambda}gt11$ cDNA library and its sequence was determined. The predicted rat transketolase (655 amino acids with $M_r$ 71,186) is highly similar (92%) to that of the human enzyme except that it contains an extra 32 amino acids at its N-terminus. Although it is less similar (<27%) to transketolases from non-mammalian species, the functional motifs such as the catalytic sites and thiamine binding domain are well conserved in the rat enzyme. Southern blot analysis of genomic DNA verified that transketolase appears to be derived from a single gene. Immunoblot and Northern blot analyses suggested that hepatic transketolase was activated pretranslationally by a 2.1-fold while little change was observed in brain enzyme, indicating a tissue-specific pretranslational activation during postnatal development.

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토양에서 분리한 Aeromonas sp 로 부터 \beta-mannanase 유전자의 클로닝 (Cloning of \beta-mananase gene from Aeromonas sp. in E. coli)

  • 박봉환;강대경;김하근
    • 한국미생물·생명공학회지
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    • 제29권4호
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    • pp.201-205
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    • 2001
  • 자연계로부터 locust bean gum이 들어 있는 선택배지에서 투명환을 형성하는 mannan 분해능을 갖는 미생물을 스크링 하였고 이를 Aeromonas sp. 로 동정하였다. Aero monas sp. 로부터 염색체 DNA를 분리하여 EcoRI으로 절단하여 대장균에 형질전환한 후 대장균 콜로니 주위에서 locust bean gum을 분해하여 투명환을 형성하는 대장균을 찾아냈다. 형질전환된 대장균으로부터 플라스미드를 분리하여 동일한 제한효소를 처리하여 확인한 결과 10 kd의 Aeromonas sp. 염섹체 DNA에 $\beta$-mannanase 유전자 존재하였다. 대장균에서 발현된 $\beta$-mannanase 의최적 반응 pH와 최적 반응온도는 각각 6.0과 $50^{\circ}C$로서 모균인 Aeromonas sp. 와 동일하였다.

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토양 metagenome library로부터 혈전용해효소의 탐색 (Screening of Fibrinolytic Enzymes from Soil Metagenome Library)

  • 이선이;김보혜;강주형;조효진;공은희;문상욱;김영진;안순철
    • 생명과학회지
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    • 제16권2호
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    • pp.360-364
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    • 2006
  • Fibrin clots of blood vessels are one of the serious factor caused cardiovascular disease. The development of a antithrombotic and thrombolysis solvent is necessary to prevent and treat these diseases. It has been reported that a strong fibrin-specific fibrinolytic enzyme was produced from a Korean fermented soybean paste similar to Japanese miso. We have been screened the known or novel fibrinolytic enzymes by activity-based and sequence-based screening from soil DNA metagenome library containing all kinds of environmental genomic DNA. The activity-based screening was determined the protease activity on 0.5% skim milk. For sequence-based screening, we designed a set of primer expanding gene sequence of fibrinolytic enzyme, performed PCR and selected clones showing the expected size of amplicons from metagenome library. Transformation of the gene encoding fibrinolytic enzyme was carried out with commercial vectors and their transformants were selected. Finally, we found 15 positive clones from metagenome library. Then each of sequences were analyzed and identified as similar or known the clones of nattokinase. We are going to perform full sequence of each clones, ligate with expression vector, transform into competent cells and then determine activity of expressed enzymes.

Screening and Characterization of a Novel Cellulase Gene from the Gut Microflora of Hermetia illucens Using Metagenomic Library

  • Lee, Chang-Muk;Lee, Young-Seok;Seo, So-Hyeon;Yoon, Sang-Hong;Kim, Soo-Jin;Hahn, Bum-Soo;Sim, Joon-Soo;Koo, Bon-Sung
    • Journal of Microbiology and Biotechnology
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    • 제24권9호
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    • pp.1196-1206
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    • 2014
  • A metagenomic fosmid library was constructed using genomic DNA isolated from the gut microflora of Hermetia illucens, a black soldier fly. A cellulase-positive clone, with the CS10 gene, was identified by extensive Congo-red overlay screenings for cellulase activity from the fosmid library of 92,000 clones. The CS10 gene was composed of a 996 bp DNA sequence encoding the mature protein of 331 amino acids. The deduced amino acids of CS10 showed 72% sequence identity with the glycosyl hydrolase family 5 gene of Dysgonomonas mossii, displaying no significant sequence homology to already known cellulases. The purified CS10 protein presented a single band of cellulase activity with a molecular mass of approximately 40 kDa on the SDS-PAGE gel and zymogram. The purified CS10 protein exhibited optimal activity at $50^{\circ}C$ and pH 7.0, and the thermostability and pH stability of CS10 were preserved at the ranges of $20{\sim}50^{\circ}C$ and pH 4.0~10.0. CS10 exhibited little loss of cellulase activity against various chemical reagents such as 10% polar organic solvents, 1% non-ionic detergents, and 0.5 M denaturing agents. Moreover, the substrate specificity and the product patterns by thin-layer chromatography suggested that CS10 is an endo-${\beta}$-1,4-glucanase. From these biochemical properties of CS10, it is expected that the enzyme has the potential for application in industrial processes.

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

  • 임용표;서미정;조수진;이정희;이효연
    • 한국식물학회:학술대회논문집
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    • 한국식물학회 1996년도 제10회 식물생명공학심포지움 고등식물 발생생물학의 최근 진보
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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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Construction of Various Copy Number Plasmid Vectors and Their Utility for Genome Sequencing

  • Yang, Tae-Jin;Yu, Yeisoo;Frisch, David A.;Lee, Seunghee;Kim, Hye-Ran;Kwon, Soo-Jin;Park, Beom-Suk;Wing, Rod A.
    • Genomics & Informatics
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    • 제2권4호
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    • pp.174-179
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    • 2004
  • We developed various plasmid cloning vectors that are useful in the construction of genomic and shotgun libraries. Two medium copy vectors, pCUGlblu21 (pCb21) and pAGlblu21 (pAb21), which are resistant to kanamycin ($Km^R$) and chloramphenicol ($Cam^R$), respectively, are useful for cloning DNA inserts ranging from 5kb to 15kb. Two high copy vectors, pCUGlblu31 (pCb31) and pAGlblu31 (pAb31), containing $Km^R$ and $Cam^R$, respectively, are useful for DNA inserts less than 5kb. These vectors are well adapted for large-scale genome sequencing projects by providing choice of copy number and selectable marker. The small vector size is another advantage of these vectors. All vectors contain lacZa including multicloning sites that originated from pBluscriptllsk- for easy cloning and sequencing. Two medium copy vectors contain unique and rare cutting Swal (ATTTAAAT) restriction enzyme sites for easy determination of insert size. We developed two combined vectors, pC21A31 and pC31A21, which are combinations of (pCb21 + pAb31) and (pCb31 + pAb21), respectively. These two vectors provide four choices of vectors such as $Km^R$ and medium, $Cam^R$ and high, $Cam^R$ and medium, and $Km^R$ and high copy vectors by restriction enzyme cutting, dephosphorylation, and gel purification. These vectors were successfully applied to high throughput shotgun sequencing of rice, tomato, and brassica BAC clones. With an example of extremely biased hydro sheared 3 kb shotgun library of a tomato BAC clone, which is originated from cytogenetically defined peri-centromeric region, we suggest the utility of an additional 10 kb library for sequence assembly of the difficult-to-assemble BAC clone.