벼 미숙종자의 발현유전자 구조특성분석

윤웅한,이강섭,이정숙,한장호,김창국,Shoshi Kikuchi,Kouji Satoh,김진아,이정화,이태호,김용환 한국식물생명공학회 2009 식물생명공학회지 Vol.36 No.2

Rice (Oryza sativa) is the most important staple crop in Korea. With its small genome size of 389Mb, rice is a model plant for genome research. We analyzed expressed sequence tag (EST) clones from immature seeds of rice (cv. Ilpum) at 20 days after heading. The 25,668 EST clones were clustered by using SeqMan program and 7,509 clones were selected as unique clones. We compared the 7,509 unique genes with KOME database including the 32,127 FL-cDNA in rice. Finally, 4,990 clones were homologous and 2,519 clones non-homologous to FL-cDNA clones. In addition, we mapped the 7,509 cDNA clones by using TIGR rice pseudomolecule version 5. Ultimately, 7,347 clones were matched to be significant clones related to the TIGR rice pseudomolecules, but 162 clones were unmapped. For the clustering of orthologous group genes, we further analyzed the 7,509 EST clones from immature seeds using NCBI clusters of orthologous groups database. Among the clones, 4,968 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 799 (14.89%), 1,536 (28.3%), 1,148 (21.2%) and 1,936 (35.7%) clones to the previous four categories, respectively. 벼는 국내에서 가장 중요한 식량작물로 게놈 크기가 389Mb이 며 식물 유전자 기능분석을 위한 모델 작물이다. 종자 발달과정에 관여하는 유전자의 기능을 분석하기 위하여 일품벼의 미숙종자(출 수 후 20일)의 발현유전자의 염기서열을 결정하였다. 염기서열이 결정된 25,668개의 발현유전자를 SeqMan 프로그램을 이용하여 cluster를 분석하여 7,509개의 unigene을 분리하였다. 일본 농업생물 자원연구소의 완전장 cDNA 32,127 클론 (KOME)과 미숙종자 발현 cDNA 7,509개를 비교분석 한 결과 4,990개는 일본의 클론과 일치 하였으며 2,519개 클론은 상동성을 나타내지 않았다. 미숙종자발 현 7,509개 unigene을 TIGR Pseudomolecule ver. 5의 염색체에 mapping 한 결과 7,347개는 각 염색체에 mapping되었으며 162개는 mapping되지 않았다. 미숙종자발현 7,509개 유전자의 기능을 NCBI COG DB를 이용 하여 분류한 결과 정보축적 및 처리 기능관련유전자 14.8%, 세포 생리기능관련 유전자 28.3%, 대사관련 유전자 21.2% 그리고 기능 미확인 유전자 35.7%의 비율을 나타내었다.

고구마 유전체 연구현황 및 전망

윤웅한,정재철,곽상수,양정욱,김태호,이형운,남상식,한장호 한국식물생명공학회 2015 식물생명공학회지 Vol.42 No.3

Sweetpotato [Ipomoea batatas (L.) Lam] grows well in harsh environmental conditions, and is cultivated as one of the top seven food crops in the world. Recently, sweetpotato is drawing interest from people as a healthy food because it is high in dietary fiber, vitamins, carotenoids and overall nutrition value. However, few studies have been conducted on sweetpotato genome sequencing in spite of its importance. This review is aimed at increasing the efficiency of sweetpotato genome sequencing research as well as establishing a base for gene utilization in order to control useful traits. Recently, animal and plant genome sequencing projects increased significantly. However, sweetpotato genome sequencing has not been performed due to polyploidy and heterogeneity problems in its genome. Meanwhile research on its transcriptome has been conducted actively. Recently, a draft of the diploid sweetpotato genome was reported in 2015 by Japanese researchers. In addition, the Korea-China- Japan Trilateral Research Association of Sweet potato (TRAS) has conducted research on gene map construction and genome sequencing of the hexaploid sweetpotato Xushu 18 since 2014. The Bill & Melinda Gates Foundation launched the ‘sweetpotato genomic sequencing to develop genomic tools for Sub-Sahara Africa breeding program’. The chloroplast genome sequence acquired during sweetpotato genome sequencing is used in evolutionary analyses. In this review, the trend of research in the sweetpotato genome sequencing was analyzed. Research trend analysis like this will provide researchers working toward sweetpotato productivity and nutrient improvement with information on the status of sweetpotato genome research. This will contribute to solving world food, energy and environmental problems.

벼 microarray를 이용한 유전자발현 profiling 연구동향

윤웅한,김연기,김창국,한장호,이태호,김동헌,이강섭,박수철,남백희 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2

As the International Rice Genome Sequencing Project (IRGSP) was completed in 2005 and opened to the public, many countries are making a lot of investments in researches on the utilization of sequence information along with system development. Also, the necessity of the functional genomics researches using microarray is increased currently to secure unique genes related with major agricultural traits and analyze metabolic pathways. Microrarray enables efficient analysis of large scale gene expression and related transcription regulation. This review aims to introduce available microarrays made based on rice genome information and current status of gene expression analysis using these microarrays integrated with the databases available to the public. Also, we introduce the researches on the large scale functional analysis of genes related with useful traits and genetic networks. Understanding of the mechanism related with mutual interaction between proteins with co-expression among rice genes can be utilized in the researches for improving major agricultural traits. The direct and indirect interactions of various genes would provide new functionality of rice. The recent results of the various expression profiling analysis in rice will promote functional genomic researches in plants including rice and provide the scientists involved in applications researches with wide variety of expression informations.

벼 glutelin 유전자 구조 및 발현특성분석

윤웅한,김창국,이강섭,한장호,이정화,김연기,지현소,문정환,이태호,김태호 한국식물생명공학회 2011 식물생명공학회지 Vol.38 No.2

벼는 세계에서 가장 중요한 작물이며 크기가 383Mb로게놈연구 모델 작물로 이용되고 있다. 또한 그 종자는 인간에게 탄수화물과 단백질 영양원을 제공한다. 벼 종자의 단백질은 약 8%를 차지하며 40%를 차지하는 콩 종자의 단백질 양에 비하여 상대적으로 적은 양을 나타낸다. 오스본의 분류에 의하면 종자 단백질은 수용성의 albumin,염용해성 globulin, 알코올 용해성 prolamin 그리고 약산또는 알카리 용해성 glutelin으로 나누어진다. Glutelin과prolamin은 벼의 주요 저장단백질이다. 벼 glutelin 저장단백질 유전자의 발현분석을 위하여 일품벼 미숙종자의 발현유전자 (EST) 분석을 행하였다. 그결과 11종의 미숙종자 발현 glutelin 유전자를 분리 하였으며 8개의 유전자는 염색체 2번에 위치하였다. Glutelin 유전자 발현양은 전체 미숙종자 발현유전자의 약 28.2%를 차지하였다. 또한 glu-04의 경우 같은 염색체 상에서4.5 kb 떨어진 곳에 역방향의 같은 염기서열로 복제되어있었다. 이와 같은 결과는 glutelin 유전자는 진화학적으로 복제되어 염색체 특이적으로 발현하는 것을 나타낸다. 종자 11개 glutelin 유전자들의 아미노산서열분석을통하여 lysin 함량을 조사한 결과 glu05-type B7에서 4.51%의 높은 lysin 함량을 나타내었다. 향후 유전자의 과발현체를 이용한 lysin 함량을 높이는 영양성 강화 연구가 요구되어진다. Rice is one of the most important crop in the world, in particular for food resources. With its small genome size of 383 Mb, the Oryza sativa is a model plant for genome research. Indeed, it’s grain provides human with a source of carbohydrates and proteins. Rice grain has relatively low protein contents (around 8%) compared to other legume seeds (around 40%). Osborne classified seed proteins into water soluble albumin, salt soluble globulin,alcohol soluble prolamin and acidic/alkaline solution soluble glutelin. Glutelin and prolamin are the major storage proteins in rice. For the gene expression study of seed storage proteins, we analyzed 33,192 EST clones at immature stages in a rice cultivar (Oryza sativa L. cv. ‘Ilpum’). Based on the expression analysis, we cloned 11 glutelin genes and figured out the 8 genes are located on Chromosome 2. The expression of glutelin genes appears to be about 28.2% of total level in immature seeds. Interestingly, glu-04 is duplicated as inverted sequences on the same chromosomes as far 4.5 kb. Our results indicate that glutelin genes, evolutionarily, were replicated on the chromosome and thus expressed as specific manners. In a whole protein composition analysis, glu05 (type B7) contains the highest lysin contents (4.51%) among the 11 rice glutelin genes. It will be an interesting future work to increase lysin contents by the gene overexpressor strategy with the aim of improved diet nutritionally fortified.

벼 발아종자 발현유전자의 발현특성분석

윤웅한,이강섭,김창국,이정숙,한장호,윤도원,지현소,이태호,이정화,박성한,김건욱,서미숙,김용환 한국식물생명공학회 2009 식물생명공학회지 Vol.36 No.3

Seed germination is the important stage to express many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mechanisms, we were analyzed the rice cDNA clones (Oryza sativa cultivar Ilpum) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,668 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as commonly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages. For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively. 종자의 발아기는 휴면기에서 에너지대사, 전분분해 및 세포분열 등 일련의 많은 유전자 발현을 나타내는 시기 이다. 종자의 발아기에 관여하는 유전자의 기능을 분석 하기 위하여 일품 벼를 48시간 발아시킨 후 얻은 발아종 자 cDNA 클론의 염기서열을 결정하였다. 염기서열이 결 정되어진 18,101개의 EST를 SeqMan 프로그램을 이용하 여 cluster 분석을 행한 결과 8,836개의 unigene을 분리 하 였다. 발아종자에서 많이 발현하는 유전자의 완전장 구 조분석을 행한 결과 발아종자 특이적으로 발현하는 키티 나아제 및 전분분해에 관여하는 아밀라제 유전자등 몇 종류의 특이발현 유전자들을 분리 하였으며 이들 유전자 들은 GenBank에 등록하였다. 미숙종자와 발아종자 공통적으로 발현하는 유전자의 분석을 위하여 미숙종자 25,668개와 발아종자 18,101개 등 43,744개의 유전자를 SeqMan 프로그램으로 cluster 분 석을 행한 결과 2,541개의 공통발현 unigene을 얻을 수 있 었다. 이들 유전자중 alpha-glubulin 및 alcohol dehydrogenase 1 등은 미숙종자와 발아종자에서만 발현을 나타내어 LEA 유전자로 추정되어진다. 발아종자 8,836개의 유전자 기능분류를 NCBI KOG DB 를 이용하여 분석한 결과 정보축적 및 처리기능관련유전 자 783개 (14.2%), 세포생리기능관련 유전자 1,484개 (27%), 대사관련 유전자 1,363개 (24.8%) 그리고 기능미확인 유 전자 1,869개 (34%)의 비율을 나타내었다.

벼 microarray를 이용한 유전자발현 profiling 연구동향

윤웅한,김연기,김창국,한장호,이태호,김동헌,이강섭,박수철,남백희,Yoon, Ung-Han,Kim, Yeon-Ki,Kim, Chang-Kug,Hahn, Jang-Ho,Kim, Dong-Hern,Lee, Tae-Ho,Lee, Gang-Seob,Park, Soo-Chul,Nahm, Baek-Hie 한국식물생명공학회 2010 식물생명공학회지 Vol.37 No.2

As the International Rice Genome Sequencing Project (IRGSP) was completed in 2005 and opened to the public, many countries are making a lot of investments in researches on the utilization of sequence information along with system development. Also, the necessity of the functional genomics researches using microarray is increased currently to secure unique genes related with major agricultural traits and analyze metabolic pathways. Microrarray enables efficient analysis of large scale gene expression and related transcription regulation. This review aims to introduce available microarrays made based on rice genome information and current status of gene expression analysis using these microarrays integrated with the databases available to the public. Also, we introduce the researches on the large scale functional analysis of genes related with useful traits and genetic networks. Understanding of the mechanism related with mutual interaction between proteins with co-expression among rice genes can be utilized in the researches for improving major agricultural traits. The direct and indirect interactions of various genes would provide new functionality of rice. The recent results of the various expression profiling analysis in rice will promote functional genomic researches in plants including rice and provide the scientists involved in applications researches with wide variety of expression informations.

myc계 단백질의 機能과 遺傳工學的 手法에 의한 human N-myc 抗體生産

尹雄漢 한국과학기술원 유전공학연구소 1993 생명공학동향 Vol.1 No.4

북한문제 : 북녘신세대 X파일 11 ; 평양 최고의 별미 숭어국

윤웅 평화문제연구소 1998 통일한국 Vol.180 No.-

통일대비 : 북녘신세대 X파일 22 ; 낙서 문화

윤웅 평화문제연구소 1999 통일한국 Vol.192 No.-

북한문제 : 북녘신세대 X파일11 ; 평야의 송신시장

윤웅 평화문제연구소 1998 통일한국 Vol.179 No.-