• Title, Summary, Keyword: RAG-1

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Recombination Activating Gene 1 Product Alone Possesses Endonucleolytic Activity

  • Kim, Deok-Ryong
    • BMB Reports
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    • v.36 no.2
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    • pp.201-206
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    • 2003
  • Two lymphoid-specific proteins, RAG1 and RAG2, are required for the initiation of the V(D)J recombination in vitro. The V(D)J cleavage that is mediated by RAG proteins at the border between the coding and signal sequences results in the production of a hairpin at the coding end and a double-stranded break at the signal end. Two hairpin coding ends are re-opened, modified, and sealed; whereas, the signal ends are directly ligated. Here I report that only RAG1 can carry out a distinct endonucleolytic activity in vitro using an oligonucleotide substrate that is tethered by a short single-stranded DNA. The purified RAG1 protein alone formed a nick at the near position to the recombination signal sequence. This endonucleolytic activity was eliminated by immunoprecipitation using the RAG1-specific antibody, and required the 3'-hydroxy group. All of the RAG1 mutants that were incapable of the nick and hairpin formation in the V(D)J cleavage analysis also showed this new endonucleolytic activity. This suggests that the nicking activity that was observed might be functionally different from the nick formation in the V(D)J cleavage.

Influence of Deletions in the Apoemulsan Gene Cluster on Acinetobacter venetian us RAG-l Polysaccharide Biosynthesis

  • Hanna, Dams-Kozlowska;Mercaldi, Michael P.;Ramjeawan, Aruranie;Kaplanl, David L
    • Journal of Microbiology and Biotechnology
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    • v.18 no.12
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    • pp.1890-1894
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    • 2008
  • Apoemulsan is a biopolymer with potent emulsification activity, produced by Acinetobacter venetian us RAG-1 (RAG-1). The wee gene cluster is responsible for apoemulsan biosynthesis. The analysis of (i) a putative polysaccharide copolymerase mutant (${\Delta}wzc$), (ii) a putative polymerase mutant (${\Delta}wzy$), and (iii) an apoemulsan-deficient variant (${\Delta}2$) indicated that the wee gene cluster controls the synthesis of two polysaccharides: high molecular weight (HMW) and low molecular weight (LMW). LMW polysaccharide of wee origin was present in LPS isolated from RAG-1 cells, suggesting a link to the Lipid A-core of LPS molecules. SDS-PAGE analysis indicated that apoemulsan is copurified with LPS polysaccharide, with implications in the emulsification activity of RAG-1 polymer.

Molecular Phylogenetic Position of Abbottina springeri (Cypriniformes: Cyprinidae) Based on Nucleotide Sequences of RAG1 Gene (RAG1 유전자의 염기서열에 기초한 왜매치 Abbottina springeri (잉어목, 잉어과)의 분자계통학적 위치)

  • Kim, Keun-Yong;Bang, In-Chul
    • Korean Journal of Ichthyology
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    • v.22 no.4
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    • pp.273-278
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    • 2010
  • Partial nucleotide sequences of nuclear protein-coding recombination activating gene 1 (RAG1) gene of two Abbottina and five Microphysogobio species residing in Korea were analyzed to elucidate the molecular phylogenetic position of A. springeri Banarescu and Nalbant. In RAG1 tree A. rivularis was clearly separated from the monophyletic lineage composed of A. springeri, Biwia zezera and Microphysogobio species. Within this lineage B. zezera showed sister-group relationship to the monophyletic group composed of A. springeri and five Microphysogobio species. Thus, our phylogenetic tree revealed the polyphyletic nature of two Abbottina species from Korea, which result is well congruent with the previous phyletic assumption based on osteological features. The current classification of Abbottina and Microphysogobio based on morphological criteria, such as the presence or absence of papillae on lips and size of swim bladder with or without encapsulation, does not reflect their true evolutionary history.

DNA-dependent Protein Kinase Mediates V(D)J Recombination via RAG2 Phosphorylation

  • Hah, Young-Sool;Lee, Jung-Hwa;Kim, Deok-Ryong
    • BMB Reports
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    • v.40 no.3
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    • pp.432-438
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    • 2007
  • V(D)J recombination, a site-specific gene rearrangement process occurring during the lymphocyte development, begins with DNA double strand breaks by two recombination activating gene products (RAG1/2) and finishes with the repair process by several proteins including DNA-dependent protein kinase (DNA-PK). In this report, we found that RAG2 was specifically phosphorylated by DNA-PK at the $365^{th}$ serine residue, and this phosphorylated RAG2 affected the V(D)J recombination activity in cells in the GFP expression-based assay. While the V(D)J recombination activity between wild-type RAG2 and mutant S365A RAG2 in the assay using a signal joint substrate was undistinguishable in DNA-PK deficient cells (M059J), the activity with wild-type RAG2 was largely increased in DNA-PK proficient cells (M059K) in comparison with mutant RAG2, suggesting that RAG2 phosphorylation by DNA-PK plays a crucial role in the signal joint formation during V(D)J recombination.

Identification of a Natural Hybrid between the Striped Spine Loach Cobitis tetralineata and the King Spine Loach Iksookimia longicorpa by Analyzing Mitochondrial COI and Nuclear RAG1 Sequences (미토콘드리아 COI와 핵 RAG1 유전자 분석에 의한 줄종개(Cobitis tetralineata)와 왕종개(Iksookimia longicorpa) 간 자연잡종 동정)

  • Lee, Il-Ro;Yang, Hyun;Kim, Jong-Hwan;Kim, Keun-Yong;Bang, In-Chul
    • Korean Journal of Ichthyology
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    • v.21 no.4
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    • pp.287-290
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    • 2009
  • A natural hybrid between the striped spine loach Cobitis tetralineata and the king spine loach Iksookimia longicorpa was genetically identified by sequence analyses of nuclear recombination activating gene 1 (RAG1) and mitochondrial cytochrome c oxidase I (COI) genes. Out of 850 base positions of RAG1, a total of 23 nucleotide substitutions were detected between the two parental species, whereas the electropherogram of the natural hybrid displayed double peaks at all of the 23 positions, which reflects their simple Mendelian inheritance pattern. Meanwhile, comparison of partial sequences of mitochondrial genes (COI in this study), which are well characterized by the maternal inheritance pattern, revealed that the maternal species of the hybrid was C. tetralineata because of their 100% sequence identity.

RAG-based Image Segmentation Using Multiple Windows (RAG 기반 다중 창 영상 분할 (1))

  • Lee, Sang-Hoon
    • Korean Journal of Remote Sensing
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    • v.22 no.6
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    • pp.601-612
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    • 2006
  • This study proposes RAG (Region Adjancency Graph)-based image segmentation for large imagery in remote sensing. The proposed algorithm uses CN-chain linking for computational efficiency and multi-window operation of sliding structure for memory efficiency. Region-merging due to RAG is a process to find an edge of the best merge and update the graph according to the merge. The CN-chain linking constructs a chain of the closest neighbors and finds the edge for merging two adjacent regions. It makes the computation time increase as much as an exact multiple in the increasement of image size. An RNV (Regional Neighbor Vector) is used to update the RAG according to the change in image configuration due to merging at each step. The analysis of large images requires an enormous amount of computational memory. The proposed sliding multi-window operation with horizontal structure considerably the memory capacity required for the analysis and then make it possible to apply the RAG-based segmentation for very large images. In this study, the proposed algorithm has been extensively evaluated using simulated images and the results have shown its potentiality for the application of remotely-sensed imagery.

Production of Emulsan by Acinetobacter calcoaceticus RAG-1 under Various Culture Modes (여러 배양방법하에서 Acinetobacter calcoaceticus RAG-1에 의한 Emulsan의 생산)

  • 강병철;이필경장호남
    • KSBB Journal
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    • v.6 no.4
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    • pp.389-394
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    • 1991
  • Emulsan is an extracellular emulsifying agent produced by the hydrocarbon-degrading Acinetobacter species RAG-1. In this study emulsan production of Acinetobacter calcpaceticus RAG-1 was investigated under various culture modes such as batch, fed-batch, membrane cell recycle, and continuous culture. The productions of emulsan under both ethanol-sufficient fed-batch and membrane cell recycle cultures were all 15.0U/ml, which was 53% increase in emulsan activity compared to that of pH controlled batch culture. Emulsan production was found to be strongly dependent on the residual ethanol concentration. In continuous culture the emulsan productivity increased with dilution rate.

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Genetic Identification of Hybrids between Rhodeus uyekii and R. notatus by Sequence Analysis of RAG-1 Gene (RAG-1 유전자의 염기서열 분석에 의한 각시붕어 Rhodeus uyekii와 떡납줄갱이 R. notatus 잡종의 동정)

  • Yun, Young-Eun;Lee, Il-Ro;Park, Sang-Yong;Kang, Eon-Jong;Kim, Eung-O;Yang, Sang-Keun;Nam, Yoon-Kwon;Bang, In-Chul
    • Journal of Aquaculture
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    • v.22 no.1
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    • pp.79-82
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    • 2009
  • Reciprocal interspecific hybrids between two bitterling species Rhodeus uyekii (RU) and R. notatus (RN) were genetically identified based on the partial sequence analysis of recombination activating gene-1 (RAG-1) gene. Out of 863 bp positions analyzed, 13 nucleotide substitutions were detected between the two parental species (RU and RN genotypes). Both the induced hybrids (RU female$\times$RN male; UN genotype) and their reciprocal counterparts (RN female$\times$RU male; NU genotype) displayed the double peaks (or polymorphism) of sequence chromatograms at the 13 diagnostic positions, indicating that those hybrids were actual karyogamy derived from the two parental haploid genomes. However, it was not possible to distinguish between the reciprocal interspecific hybrids.

Identification of Hybrid between the Tiger Grouper Epinephelus fuscoguttatus and the Giant Grouper E. lanceolatus by Analyzing COX I and RAG 2 Sequences (COX I 및 RAG 2 유전자 염기서열 분석에 의한 tiger grouper Epinephelus fuscoguttatus와 giant grouper E. lanceolatus 간 잡종의 동정)

  • Kim, Keun-Sik;Lee, Hyo-Ryeon;Sade, Ahemad;Bang, In-Chul
    • Korean Journal of Ichthyology
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    • v.26 no.1
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    • pp.70-73
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    • 2014
  • Interspecific hybrids between tiger grouper Epinephelus fuscoguttatus and giant grouper E. lanceolatus were genetically identified based on the partial sequence analysis of mitochondrial cytochrome c oxidase I (COX I) gene and nuclear recombination activating gene 2 (RAG 2) gene. Out of 585 base positions of RAG 2, a total of five nucleotide substitutions were detected between the two parental species (E. fuscoguttatus and E. lanceolatus). The hybrids had two distinct types of RAG 2 sequences corresponding to those of both parental species. Mitochondrial COX I gene sequencing showed that hybrids had sequences identical to E. fuscoguttatus. Molecular data clearly demonstrate that hybridization does occur between E. fuscoguttatus and E. lanceolatus, but with E. fuscoguttatus as the maternal parent.

Expression of Immune-Related Genes during Loach (Misgurnus anguillicaudatus) Embryonic and Early Larval Development

  • Lee, Jang Wook;Kim, Jung Eun;Goo, In Bon;Hwang, Ju-Ae;Im, Jea Hyun;Choi, Hye-Sung;Lee, Jeong-Ho
    • Development and Reproduction
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    • v.19 no.4
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    • pp.181-187
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    • 2015
  • Early life stage mortality in fish is one of the problems faced by loach aquaculture. However, our understanding of immune system in early life stage fish is still incomplete, and the information available is restricted to a few fish species. In the present work, we investigated the expression of immune-related transcripts in loach during early development. In fishes, recombination-activating gene 1 (RAG-1) and sacsin (SACS) have been considered as immunological function. In this study, the expression of the both genes was assessed throughout the early developmental stages of loach using real-time PCR method. maRAG-1 mRNA was first detected in 0 dph, observed the increased mostly until 40 dph. Significant expression of maRAG-1 was detected in 0 to 40 dph. These patterns of expression may suggest that the loach start to develop its function after hatching. On the other hand, maSACS was detected in unfertilized oocyte to molura stages and 0 to 40 dph. maSACS mRNA transcripts were detected in unfertilized oocytes, suggesting that they are maternally transferred.