• Title/Summary/Keyword: Multigene family

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Sequence Homologies of GTP-binding Domains of Rab and Rho between Plants and Yeast/Animals Suggest Structural and Functional Similarities

  • Lee, Ji-Yeon;Lee, Dong-Hee
    • Journal of Plant Biology
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    • v.39 no.2
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    • pp.85-92
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    • 1996
  • Small GTP-binding proteins are divided into three major group: Ras, Rho and Ypt/Rab. They have the conserved regions designed G1 to G5 that are critical in GDP/GTP exchange, GTP-induced conformational change and GTP hydrolysis. We isolated and characterized genomic DNA or cDNAfragments encoding G1 to G3 domains of small GTP-binding protein Rab and Rho from several plant species using two different PCR-based cloning strategies. Seven rab DNA fragments were isolated from 4 different plants, mung-bean, tobacco, rice and pepper using two degenerate primers corresponding to the GTP-binding domain G1 and G3 in small GTP-binding proteins. The amino acid sequences among these rab DNA fragments and other known small GTP-binding proteins shows that they belong to the Ypt/Rab family. Six rho DNA fragments were isolated from 5 different plants, mung-bean, rice, Arabidopsis, Allium and Gonyaulax using the nested PCR method that involves four degenerate primers corresponding to the GTP-binding domain G1, G3 and G4. The rho DNA fragments cloned show more than 90% homology to each other. Sequence comparison between plant and other known Rho family genes suggests that they are closely related (67 to 82% amino acid identity). Sequence analysis and southern blot analysis of rab and rho in mung-bean suggest than thses genes are encoded by multigene family in mung-bean.

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Isolation of a Rice Genomic Clone Encoding Ribulose-1,5-bisphosphate Carboxylase (리블로스 1,5- 이인산 탄산화효소 유전자의 분리 및 특성규명)

  • Park, Sung-Soon;Kim, Hee-Jin;Kim, Chung-Ho;Kim, Han-Jip;Lee, Jong-Seob;Lee, Kwang-Woong;Choi, Yang-Do
    • Applied Biological Chemistry
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    • v.37 no.5
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    • pp.361-369
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    • 1994
  • To study the light-induced expression mechanism and protein transport into the chloroplast, a rice genomic clone (GrbcS) for the small subunit of ribulose 1,5-bisphosphate carboxylase (rbcS) was isolated and its nucleotide sequence was determined. Nucleotide sequence analysis of GrbcS revealed that the gene consists of two exons interrupted by an intron, encoding a protein of 175 amino acids including a transit peptide of 47 amino acids. These structural features of GrbcS are consistent with those of other rbcS genes from monocot species. Genomic Southern blot analysis suggested that the rbcS genes are present as a relatively small multigene family in the rice genome. Comparison of the nucleotide and deduced amino acid sequences to other rice rbcSs shows close sequence similaritiy. Conserved DNA sequences present in other light-responsive genes are also found in the 5’ upstream region of GrbcS such as G-box, 3AF1-binding site and GATA site. The possible function of these putative regulatory elements are discussed.

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Microarray Probe Design with Multiobjective Evolutionary Algorithm (다중목적함수 진화 알고리즘을 이용한 마이크로어레이 프로브 디자인)

  • Lee, In-Hee;Shin, Soo-Yong;Cho, Young-Min;Yang, Kyung-Ae;Zhang, Byoung-Tak
    • Journal of KIISE:Software and Applications
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    • v.35 no.8
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    • pp.501-511
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    • 2008
  • Probe design is one of the essential tasks in successful DNA microarray experiments. The requirements for probes vary as the purpose or type of microarray experiments. In general, most previous works use the simple filtering approach with the fixed threshold value for each requirement. Here, we formulate the probe design as a multiobjective optimization problem with the two objectives and solve it using ${\epsilon}$-multiobjective evolutionary algorithm. The suggested approach was applied in designing probes for 19 types of Human Papillomavirus and 52 genes in Arabidopsis Calmodulin multigene family and successfully produced more target specific probes compared to well known probe design tools such as OligoArray and OligoWiz.

Differential Expression of Three Catalase Genes in the Small Radish (Rhaphanus sativus L. var. sativus)

  • Kwon, Soon Il;Lee, Hyoungseok;An, Chung Sun
    • Molecules and Cells
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    • v.24 no.1
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    • pp.37-44
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    • 2007
  • Three catalase cDNA clones were isolated from the small radish (Raphanus sativus L.). Their nucleotide and deduced amino acid sequences showed the greatest homology to those of Arabidopsis. Genomic Southern blot analysis, using RsCat1 cDNA as a probe, showed that catalases are encoded by small multigene family in the small radish. Nondenaturing polyacrylamide gels revealed the presence of several catalase isozymes, the levels of which varied among the organs examined. The isozyme activities were assigned the individual catalase genes by Northern analysis using total RNA from different organs. The three catalase genes were differentially expressed in response to treatments such as white light, xenobiotics, osmoticum, and UV. Their expression in seedlings was controlled by the circadian clock under a light/dark cycle and/or in constant light. Interestingly, RsCat1 transcripts peaked in the morning, while those of RsCat2 and RsCat3 peaked in the early evening. Our results suggest that the RsCat enzymes are involved in defense against the oxidative stress induced by environmental changes.

Regulation of Immune Responses by the Activating and Inhibitory Myeloid-Associate Immunoglobuline-Like Receptors (MAIR) (CD300)

  • Shibuya, Akira;Nakahashi-Oda, Chigusa;Tahara-Hanaoka, Satoko
    • IMMUNE NETWORK
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    • v.9 no.2
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    • pp.41-45
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    • 2009
  • Activating and inhibitory cell surface receptors play important roles in regulation of immune responses. Recent progress has demonstrated that many inhibitory receptors pair with activating, as well as inhibitory, isoforms, both of whose genes are located in small clusters on a chromosome. We and others identified paired activating and inhibitory immunoglobulin-like receptors, designated myeloid-associated immunoglobulin-like receptors (MAIR) (CD300). MAIR is a multigene family consisting of nine genes on a small segment of mouse chromosome 11. MAIR family receptors are preferentially expressed on myeloid cells, including macrophages, dendritic cells, granulocytes, and bone-marrow-derived cultured mast cells, and a subset of B cells and regulate activation of these cells. Thus, MAIR plays an important role in innate immunity mediated by myeloid cells.

Molecular Cloning and Expression of Sequence Variants of Manganese Superoxide Dismutase Genes from Wheat

  • Baek, Kwang-Hyun;Skinner, Daniel Z.
    • Korean Journal of Environmental Agriculture
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    • v.29 no.1
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    • pp.77-85
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    • 2010
  • Reactive oxygen species (ROS) are very harmful to living organisms due to the potential oxidation of membrane lipids, DNA, proteins, and carbohydrates. transformed E.coli strain QC 871, superoxide dismutase (SOD) double-mutant, with three sequence variant MnSOD1, MnSOD2, and MnSOD3 manganese superoxide dismutase (MnSOD) gene isolated from wheat. Although all QC 871 transformants grown at $37^{\circ}C$ expressed mRNA of MnSOD variants, only MnSOD2 transformant had functional SOD activity. MnSOD3 expressed active protein when grown at $22^{\circ}C$, however, MnSOD1 did not express functional protein at any growing and induction conditions. The sequence comparison of the wheat MnSOD variants revealed that the only amino acid difference between the sequence MnSOD2 and sequences MnSOD1 and 3 is phenylalanine/serine at position 58 amino acid. We made MnSOD2S58F gene, which was made by altering the phenylalaine to serine at position 58 in MnSOD2. The expressed MnSOD2S58F protein had functional SOD activity, even at higher levels than the original MnSOD2 at all observed temperatures. These data suggest that amino acid variation can result in highly active forms of MnSOD and the MnSOD2S58F gene can be an ideal target used for transforming crops to increase tolerance to environmental stresses.

GSTT1 Null Genotype Distribution in the Kumaun Region of Northern India

  • Bag, Arundhati;Upadhyay, Saloni;Jeena, Lalit M.;Pundir, Princi;Jyala, Narayan S.
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.1
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    • pp.87-89
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    • 2013
  • Glutathione S-transferases (GSTs) constitute a multigene family of multifunctional phase II metabolic enzymes. GSTT1, an important member of this group has a wide range of substrates including carcinogens. Total homozygous deletion or null genotype resulting in total lack of enzyme activity exists in populations for this enzyme. Since the null genotype may contribute to lower detoxification of carcinogens, this genotype is expected to increase cancer risk. The frequency of the GSTT1 null genotype is known to vary significantly among populations. However, little is known about its distribution in the hilly Kumaun region of northern India. Therefore, in this study, we determined the prevalence of the GSTT1 null polymorphism in the Kumaun popilation by conducting duplex PCR in 365 voluntary healthy individuals. The GSTT1 null genotype was detected in 18.4% of the individuals. Since GSTs play significant role in xenobiotic metabolism, the present data on GSTT1 genotype distribution should contribute in understanding genetic association with cancer risk in this understudied population.

Silencing of CaCDPK4 ( Capsicum annuum Calcium Dependent Protein Kinase) and ItsOrtholog, NbCDPK5 Induces Cell Death in Nicotiana benthamiana

  • Eunsook Chung;Kim, Young-Cheol;Oh, Sang-Keun;Younghee Jung;Kim, Soo-Yong;Park, Doil
    • Proceedings of the Korean Society of Plant Pathology Conference
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    • 2003.10a
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    • pp.77.1-77
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    • 2003
  • We have isolated a full-length cDNA clone, CaCDPK4 encoding a typical calcium-dependent protein kinase (CDPK) from hot pepper cDNA library. Genomic southern blot analysis showed that it belongs to a multigene family, but represents a single copy gone in hot pepper genome. RNA expression pattern of this gene revealed that it is induced by infiltration of Xanthomonas axonopodis pv. glycines Bra into hot pepper leaves but not by water deficit stress. However, high salt treatment of NaCl (0.4 M) solution to hot pepper plants strongly induced CaCDPK4 gene. In addition, this gene is weakly responsive to the exogenous application of salicylic acid or ethephon. Biochemical study of the GST-CaCDPK4 recominant protein showed that it autophosphorylates in vitro and the presence of EGTA, a calcium chelater, eliminates the kinase activity of the recombinant protein. As a way to identify the in vivo function of CaCDPK4 in plants, VIGS (Virus-Induced Gene Silencing) was employed. Agrobacterium-mediated TRV silencing construct containing the kinase and calmodulin domain of CaCDPK4 resulted in cell death of Nicotiana benthamiana plants. A highly homologous H benthamiana CDPK gene, NbCDPK5, to CaCDPK4 was cloned from N. benthamiana cDNA library. VIGS of NbCDPK5 also resulted in cell death. The molecular characterization of this cell death phenotype is being under investigation.

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