• 제목/요약/키워드: Open reading frame 7 (ORF7) gene

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Molecular Cloning and Characterization of a Novel Calcium-dependent Protein Kinase Gene IiCPK2 Responsive to Polyploidy from Tetraploid Isatis indigotica

  • Lu, Beibei;Ding, Ruxian;Zhang, Lei;Yu, Xiaojing;Huang, Beibei;Chen, Wansheng
    • BMB Reports
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    • 제39권5호
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    • pp.607-617
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    • 2006
  • A novel calcium-dependent protein kinase gene (designated as IiCPK2) was cloned from tetraploid Isatis indigotica. The full-length cDNA of IiCPK2 was 2585 bp long with an open reading frame (ORF) of 1878 bp encoding a polypeptide of 625 amino acid residues. The predicted IiCPK2 polypeptide included three domains: a kinase domain, a junction domain (or autoinhibitory region), and a C-terminal calmodulin-like domain (or calcium-binding domain), which presented a typical structure of plant CDPKs. Further analysis of IiCPK2 genomic DNA revealed that it contained 7 exons, 6 introns and the length of most exons was highly conserved. Semi-quantitative RT-PCR revealed that the expression of IiCPK2 in root, stem and leaf were much higher in tetraploid sample than that in diploid progenitor. Further expression analysis revealed that gibberellin ($GA_3$), NaCl and cold treatments could up-regulate the IiCPK2 transcription. All our findings suggest that IiCPK2 might participate in the cold, high salinity and GA3 responsive pathways.

Molecular identification and expression analysis of a natural killer enhancing factor-A from black rockfish Sebastes schlegelii

  • Lee, Jeong-Ho;Kim, Joo-Won;Park, Chan-Il
    • 한국어병학회지
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    • 제22권3호
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    • pp.343-352
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    • 2009
  • Natural-killer-cell-enhancing factor (NKEF) belongs to the newly defined peroxiredoxin (Prx) family. It was originally isolated from human erythroid cells. The black rockfish NKEF cDNA was identified through the expressed sequence tag (EST) analysis of PBLs libraries. The full-length NKEF cDNA was 1433 bp long and contained an open reading frame (ORF) of 594 bp that encoded 198 amino-acid residues. The 5' UTR had a length of 39 bp, and the 3’UTR 800 bp. The deduced amino-acid sequence of the black rockfish had a density 93.4, 92.9, 87.8, 85.8, 84.8, 83.8, 80.3, 79.7, 77.2, and 75.2% that of the pufferfish, olive flounder, channel catfish, zebrafish, chicken, common carp, Myotis lucifugus, cattle, human PrxI, rat PrxI, human NKEF-A, and Xenopus tropicalis, respectively. The NKEF gene was expressed in all the tissues of the black rockfish. The RT-PCR indicated that the NKEF transcripts were predominantly in the spleen and gill, less dominantly in the PBLs, head kidney, trunk kidney, and liver, and least in the intestine and muscles. This is the first report on the existence of the NKEF-A gene in black rockfish.

Molecular Cloning and Characterization of a Bile Salt Hydrolase from Lactobacillus acidophilus PF01

  • Oh, Hae-Keun;Lee, Ji-Yoon;Lim, Soo-Jin;Kim, Min-Jeong;Kim, Geun-Bae;Kim, Jung-Hoan;Hong, Soon-Kwang;Kang, Dae-Kyung
    • Journal of Microbiology and Biotechnology
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    • 제18권3호
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    • pp.449-456
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    • 2008
  • Phenotypic screening for bile salt hydrolase (BSH) activity was performed on Lactobacillus acidophilus PF01 isolated from piglet feces. A gene encoding BSH was identified and cloned from the genomic library of L. acidophilus PF01. The bsh gene and surrounding regions were characterized by nucleotide sequence analysis and were found to contain a single open reading frame (ORF) of 951 nucleotides encoding a 316 amino acid protein. The potential bsh promoter region was located upstream of the start codon. The protein deduced from the complete ORF had high similarity with other BSHs, and four amino acid motifs located around the active site, FGRNXD, AGLNF, VLTNXP, and GXGXGXXGXPGD, were highly conserved. The bsh gene was cloned into the pET21b expression vector and expressed in Escherichia coli BLR(DE3) by induction with 0.1mM of isopropylthiogalactopyranoside. The BSH enzyme was purified with apparent homogeneity using a $Ni^{2+}$-NTA agarose column and characterized. The overexpressed recombinant BSH enzyme of L. acidophilus PF01 exhibited hydrolase activity against tauroconjugated bile salts, but not glycoconjugated bile salts. It showed the highest activity against taurocholic acid. The maximum BSH activity occurred at approximately $40^{\circ}C$. The enzyme maintained approximately 70% of its maximum activity even at $60^{\circ}C$, whereas its activity rapidly decreased at below $37^{\circ}C$. The optimum pH was 6, and BSH activity was rapidly inactivated below pH 5 and above pH 7.

Thermus thermophilus HJ6 유래 내열성 Trehalose Synthase의 유전자 클로닝 및 발현 (Gene Cloning and Expression of Trehalose Synthase from Thermus thermophilus HJ6)

  • 김현정;김한우;전숭종
    • 한국미생물·생명공학회지
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    • 제36권3호
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    • pp.182-188
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    • 2008
  • 내열성 Trehalose synthase를 생산하는 초고온성 균주 HJ6은 일본 Arima 온천수에서 분리하였다. 세포의 길이는 $2{\sim}4\;um$, 직경 0.4 um의 간균으로 생육최적 pH와 온도는 각각 6.5와 $80^{\circ}C$이였다. 분리된 균주의 16s rRNA 염기서열을 분석하고 계통학적으로 분류한 결과, HJ6 균주는 Thermus thermophilus에 속하는 것으로 동정되었다. PCR법을 이용하여 trehalose synthase(TS) 유전자를 클로닝하고 염기서열을 분석한 결과, ORF는 2,898개의 뉴클레오타이드로 구성되고 915개의 아미노산을 암호화하였다. 아마노산 서열을 바탕으로 상동성을 분석한 결과, Thermus caldophilus GK24 유래 TS와 99%, Meiothermus ruber 유래 TS와 83%의 identity를 나타내었다. 이 유전자를 온도감수성 프로모터를 포함하는 pJLA503 벡터를 이용하며 대장군에서 발현하고 정제하여 약 110 kDa 단백질을 얻을 수 있었다. 정제된 효소는 트레할로스 전환활성에 대한 최적 pH가 7.5이고, 최적온도는 $80^{\circ}C$이며, 활성의 반감기는 $90^{\circ}C$에서 40분으로 확인되어 높은 내열성을 가지는 것으로 확인되었다. 본 효소의 트레할로스 최대 전환율은 기질농도 500mM에서 55.7%를 나타내었고, 기질 농도가 증가함에 따라 더불어 증가하였기 때문에 본 효소의 트레할로스 전환율을 기질농도에 의존적인 것으로 생각되었다.

더덕의 주근에서 유래한 Dehydrin 1 (Dhn1) 유전자의 분리 및 분석 (Isolation and Characterization of Dehydrin 1 (Dhn1) gene from Codonopsis lanceolata)

  • 이강;양덕춘
    • 한국자원식물학회지
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    • 제16권3호
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    • pp.238-244
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    • 2003
  • 더덕 뿌리에서 유래한 EST 라이브러리로부터 dehydrin 유전자와 높은 상동성 을 나타내는 full clone cDNA를 얻었다. 더덕의 dehydrin, ClDhn1은 893 bp의 cDNA로 159개의 아미노산을 코딩하는 480 bp의 ORF를 가지고 있다. ClDhn1의 아미노산을 분석해 보면, 전체적으로 높은 친수성을 나타내며, lysine이 풍부한 K 반복구간(KIKEKLPG)을 카르보닐기 쪽에 2개 가지고 있다. 또한, 여러 dehydrin들의 공통적인 특징인 7개의 연속적인 serine잔기가 첫 번째 K반복 구간 앞에 위치한다. 그러나, 아미노기쪽의 DEYGNP보존 구간은 변형(DEHGNP)되어 있다. ClDhn1 유전자는 전사 단계에서 더덕의 뿌리에서 가장 높은 발현 양상을 보이며, 줄기와 잎에서는 적은 양이 발현되었다.

Molecular Characterization of Extracellular Medium-chain-length Poly(3-hydroxyalkanoate) Depolymerase Genes from Pseudomonas alcaligenes Strains

  • Kim Do Young;Kim Hyun Chul;Kim Sun Young;Rhee Young Ha
    • Journal of Microbiology
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    • 제43권3호
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    • pp.285-294
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    • 2005
  • A bacterial strain M4-7 capable of degrading various polyesters, such as poly$(\varepsilon-caprolactone)$, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3-hydroxyoctanoate), and poly(3-hydroxy-5-phenylvalerate), was isolated from a marine environment and identified as Pseudomonas alcaligenes. The relative molecular mass of a purified extracellular medium-chain-length poly(3-hydroxyalkanoate) (MCL-PHA) depolymerase $(PhaZ_{palM4-7})$ from P. alcaligenes M4-7 was 28.0 kDa, as determined by SDS-PAGE. The $PhaZ_{palM4-7}$ was most active in 50 mM glycine-NaOH buffer (pH 9.0) at $35^{\circ}C$. It was insensitive to dithiothreitol, sodium azide, and iodoacetamide, but susceptible to p-hydroxymercuribenzoic acid, N-bromosuccinimide, acetic anhydride, EDTA, diisopropyl fluorophosphate, phenylmethylsulfonyl fluoride, Tween 80, and Triton X-100. In this study, the genes encoding MCL-PHA depolymerase were cloned, sequenced, and characterized from a soil bacterium, P. alcaligenes LB19 (Kim et al., 2002, Biomacro-molecules 3, 291-296) as well as P. alcaligenes M4-7. The structural gene $(phaZ_{palLB19})$ of MCL-PHA depolymerase of P. alcaligenes LB19 consisted of an 837 bp open reading frame (ORF) encoding a protein of 278 amino acids with a deduced $M_r$ of 30,188 Da. However, the MCL-PHA depolymerase gene $(phaZ_{palM4-7})$ of P. alcaligenes M4-7 was composed of an 834 bp ORF encoding a protein of 277 amino acids with a deduced Mr of 30,323 Da. Amino acid sequence analyses showed that, in the two different polypeptides, a substrate-binding domain and a catalytic domain are located in the N-terminus and in the C-terminus, respectively. The $PhaZ_{palLB19}$ and the $PhaZ_{palM4-7}$ commonly share the lipase box, GISSG, in their catalytic domains, and utilize $^{111}Asn$ and $^{110}Ser$ residues, respectively, as oxyanions that play an important role in transition-state stabilization of hydrolytic reactions.

A Cold-Adapted Epoxide Hydrolase from a Strict Marine Bacterium, Sphingophyxis alaskensis

  • Kang, Ji-Hyun;Woo, Jung-Hee;Kang, Sung-Gyun;Hwang, Young-Ok;Kim, Sang-Jin
    • Journal of Microbiology and Biotechnology
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    • 제18권8호
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    • pp.1445-1452
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    • 2008
  • An open reading frame (ORF) encoding a putative epoxide hydrolase (EHase) was identified by analyzing the genome sequence of Sphingophyxis alaskensis. The EHase gene (seh) was cloned and expressed in E. coli. To facilitate purification, the gene was fused in-frame to 6$\times$ histidine at the C-terminus. The recombinant EHase (rSEH) was highly soluble and could be purified to apparent homogeneity by one step of metal affinity chromatography. The purified SEH displayed hydrolyzing activities toward various epoxides such as styrene oxide, glycidyl phenyl ether, epoxyhexane, epoxybutane, epichlorohydrin, and epifluorohydrin. The optimum activity toward styrene oxide was observed at pH 6.5 and $35^{\circ}C$. The purified SEH showed a cold-adapted property, displaying more than 40% of activity at low temperature of $10^{\circ}C$ compared with the optimum activity. Despite the catalytic efficiency, the purified SEH did not hydrolyze various epoxides enantioselectively. $K_m$ and $k_{cat}$ of SEH toward (R)-styrene oxide were calculated as 4$\pm$0.3 mM and 7.42$s^{-1}$ respectively, whereas $K_m$ and $k_{cat}$ of SEH toward (S)-styrene oxide were 5.25$\pm$0.3 mM and 10.08$s^{-1}$ respectively.

더덕의 주근에서 유래한 Cyclophilin 1 (ClCyP1) 유전자의 분리 및 분석 (Isolation and Characterization of Cyclophilin 1 (ClCyP1) Gene from Codonopsis lanceolata)

  • 양덕춘;이강;인준교;이범수;김종학
    • 한국자원식물학회지
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    • 제17권3호
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    • pp.239-247
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    • 2004
  • 더덕 뿌리에서 유래한 EST cDNA library로부터 cyclophilin 유전자와 높은 상동성을 나타내 는 full clone cDNA를 얻었다. 더덕의 cyclophilin, ClCyP1은 747 bp의 cDNA로 174개의 아미노산을 코딩하는 525 bp의 ORF를 가지고 있다. ClCyP1의 아미노산 서열을 분석한 결과, 기존에 보고된 식물들의 cytosolic cyclophilin들과 높은 상동성을 나타내었으며, 여러 식물의 cytosolic CyP의 공통적인 특징인 7개의 아미노산 잔기(KSGKPLH)를 가지고 있었다. RT-PCR분석 결과, 더덕의 ClCyP1은 식물의 조직 전체에서 발현되며, 저온, 고온, 그리고 염 스트레스에 대해 그 발현량이 증가하였다.

Cloning and Characterization of Squalene Synthase (SQS) Gene from Ganoderma lucidum

  • Zhao, Ming-Wen;Liang, Wan-Qi;Zhang, Da-Bing;Wang, Nan;Wang, Chen-Guang;Pan, Ying-Jie
    • Journal of Microbiology and Biotechnology
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    • 제17권7호
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    • pp.1106-1112
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    • 2007
  • This report provides the complete nucleotide sequences of the full-length cDNA encoding squalene synthase (SQS) and its genomic DNA sequence from a triterpene-producing fungus, Ganoderma lucidum. The cDNA of the squalene synthase (SQS) (GenBank Accession Number: DQ494674) was found to contain an open reading frame (ORF) of 1,404 bp encoding a 468-amino-acid polypeptide, whereas the SQS genomic DNA sequence (GenBank Accession Number: DQ494675) consisted of 1,984 bp and contained four exons and three introns. Only one gene copy was present in the G. lucidum genome. The deduced amino acid sequence of Ganoderma lucidum squalene synthase (GI-SQS) exhibited a high homology with other fungal squalene synthase genes and contained six conserved domains. A phylogenetic analysis revealed that G. lucidum SQS belonged to the fungi SQS group, and was more closely related to the SQS of U. maydis than to those of other fungi. A gene expression analysis showed that the expression level was relatively low in mycelia incubated for 12 days, increased after 14 to 20 days of incubation, and reached a relatively high level in the mushroom primordia. Functional complementation of GI-SQS in a SQS-deficient strain of Saccharomyces cerevisiae confirmed that the cloned cDNA encoded a squalene synthase.

Erwinia carotovora subsp. carotovora LY34에서 pelCI 유전자 클로닝 (Cloning and Sequencing of the pelCl Gene Encoding Pectate Lyase of Erwinia carotovora subsp. carotovora LY34)

  • 임선택;박용우;윤한대
    • Applied Biological Chemistry
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    • 제40권5호
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    • pp.380-387
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    • 1997
  • Pectate lyase isoenzymes을 분비하는 Erwinia carotovorn subsp. carotovora LY34는 식물조직을 연화시키는 연부균이다. 이 균주로부터 게놈 DNA를 분리하여 Sau3Al 제한효소로 부분 절단한 다음 pBluescript $SK^+$ 벡터에 클로닝하여 pectate Iyase를 분비하는 클론을 분리하였다 분리 결과 4.2 kb크기의 DNA 단편을 가지고 있었으며 이를 다시 재클로닝하여 3.1 kb크기의 pelCI유전자를 함유하는 pLYPA100을 구하였다. 이 유전자의 DNA 염기서열을 분석한 결과 374 개의 아미노산을 구성하는 1,122 bp의 ORF를 확인하였다. 시작코돈과 종결코돈은 ATG와 TAA였으며 초기 서열 22개의 아미노산으로 구성된 전형적인 원핵세포의 signal peptide가 존재하였다. PeICI의 단백질 염기서열을 다른 단백질과 유사성을 분석한 결과 Erwinia carotovera subsp. carotovora Er 균주의 PelIII, Erwinia carotevora subsp. carotovora SCR193 균주의 PeIC 및 Erwinia caretovora subsp. atroseptica C18 균주의 Pel3과 유사하였으며 PLbc family에 속하였다. PeICI의 분자량은 40,507, pI는 7.60으로 계산되었다.

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