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Genetic Analysis of Seed-specific Gene Expression for Pigmentation in Colored Rice
김창국,Shoshi Kikuchi,Kouji Satoh,김진아,김동헌,김용환,박성한,윤웅한,이점호 한국바이오칩학회 2009 BioChip Journal Vol.3 No.2
Anthocyanin is a major class of flavonoids that tissues produce in response to environmental signals. The pigmentation of colored rice was analyzed by oligo microarray based on two factors, cultivar and developmental stage. As many as 250 and 350 genes were identified to be significantly up- and down-regulated. Using hypergeometric analysis for transcription factor function, the Myb and GT families, PBP, PBF, RAV, and STF factors were identified have potential anthocyanin-specific functions. We also obtained seventeen unknown genes which display novel functions. Among the genes within the GT-1 and Myb1 groups, three unknown genes were found to be upregulated significantly in both combinations of cultivar and developmental stage. These results showed functional diversity of TF families and that the biological functions of the particular TFs may be activated in a pigmentation pathway in rice.
Computational identification of Chinese cabbage anthocyaninspecific genes
김창국,김진아,Shoshi Kikuchi,최지원,김용갑,박현주,설영주,박동석,한장호,김용환 한국바이오칩학회 2011 BioChip Journal Vol.5 No.2
Therefore, 3,895 candidate genes related to anthocyanin biosynthesis in Chinese cabbage were identified using a 300K Brassica rapa microarray analysis. Gene expression during six stages of leaf developmental stages were examined in FC (green leaf) and FA(red leaf) Chinese cabbage cultivars. The 317 transcription factor genes found to be associated with anthocyanin were classified into 11 functional groups. The ratio of expression levels of each transcription factor between the two cultivars was examined during the six leaf developmental stages. A total of 14 genes were found to be expressed in all developmental stages commonly. Among these genes, 10 unknown and hypothetical genes were differentially revealed to be expressed between the two cultivars at each developmental stage, as determined by microarray analysis, and were verified by RT-PCR validation. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation and characterization, our results illustrate the potential usefulness of this multi-layered screening method using Chinese cabbage (Brassica rapa) microarrays.
Mitochondrial activity in illuminated leaves of chlorophyll-deficient mutant rice (OsCHLH) seedlings
Goh, Chang-Hyo,Satoh, Kouji,Kikuchi, Shoshi,Kim, Seong-Cheol,Ko, Suk-Min,Kang, Hong-Gyu,Jeon, Jong-Seong,Kim, Cheol-Soo,Park, Youn-Il The Korean Society of Plant Biotechnology 2010 Plant biotechnology reports Vol.4 No.4
The rice CHLH gene encodes the $Mg^{2+}$-chelatase H subunit, which is involved in chlorophyll biosynthesis. Growth of the chlorophyll-deficient oschlh mutant is supported by mitochondrial activity. In this study, we investigated the activity of mitochondrial respiration in the illuminated leaves during oschlh seedling development. Growth of mutant plants was enhanced in the presence of 3% sucrose, which may be used by mitochondria to meet cellular energy requirements. ATP content in these mutants was, however, significantly lowered in light conditions. Low cytosolic levels of NADH in illuminated oschlh mutant leaves further indicated the inhibition of mitochondrial metabolism. This down-regulation was particularly evident for oxidative stressresponsive genes in the mutant under light conditions. Hydrogen peroxide levels were higher in oschlh mutant leaves than in wild-type leaves; this increase was largely caused by the impairment of the expression of the antioxidant genes, such as OsAPXl, OsRACl, and OsAOXc in knockout plants. Moreover, treatment of mesophyll protoplasts with ascorbic acid or catalase recovered ATP content in the mutants. Taken together, these results suggest that the light-mediated inhibition of mitochondrial activity leads to stunted growth of CHLH rice seedlings.
cDNA Cloning and Characterization of Type II Procollagen α1 Chain in the Skate Raja kenojei
Hwang Jae-Ho,Yokoyama Yoshihiro,Mizuta Shoshi,Yoshinaka Reiji The Korean Society of Fisheries and Aquatic Scienc 2006 Fisheries and Aquatic Sciences Vol.9 No.1
We determined the partial cDNA of Type II procollagen ${\alpha}1$[pro-${\alpha}1$(II)] chain (1802 bp) of the skate Raja kenojei, which codes 581 amino acid residues. The partial structure of the pro-${\alpha}1$(II) chain consisted of a part of triple helical region (309 residues) and a C-domain (272 residues). Comparing the chain to other vertebrates showed relatively low homology (about 50%) at the amino acid level. However, eight Cys residues in the C-domain of the skate pro-${\alpha}1$(II) chain were conserved in common with those of other vertebrates. The skate pro-${\alpha}1$ (II) chain mRNA was detected by RT-PCR of various tissues, but was undetected in tissues containing Type II collagen. The low homology and unexpected expression pattern suggest the presence of another mRNA variant of the skate pro-${\alpha}1$(II) chain. The present study is the first report of the primary structure of pro-${\alpha}1$(II) chain in an elasmobranch.
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.
Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars
Cho, Kyoungwon,Shibato, Junko,Kubo, Akihiro,Kohno, Yoshihisa,Satoh, Kouji,Kikuchi, Shoshi,Sarkar, Abhijit,Agrawal, Ganesh Kumar,Rakwal, Randeep Informa UK (Taylor Francis) 2013 Plant signaling & behavior Vol.8 No.11
Cho, Kyoungwon,Shibato, Junko,Kubo, Akihiro,Kohno, Yoshihisa,Satoh, Kouji,Kikuchi, Shoshi,Agrawal, Ganesh Kumar,Sarkar, Abhijit,Rakwal, Randeep Kluwer Academic Publishers 2013 Biotechnology letters. Vol.35 No.4
<P>The 'ozone (O3)-responsive transcriptome' behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. O3 differentially and separately regulated 620 and 130 genes in the panicles and grains. Among the O3-responsive genes, 176 and 444 genes were up- and down-regulated in panicle compared to 24 and 106 genes in grain, respectively. Further mapping revealed that the majority of differentially expressed genes were mainly involved in signaling, hormonal, cell wall, transcription, proteolysis, and defense events. Many previously unknown O3-responsive novel genes were identified. Inventory of 745 O3-responsive genes and their mapping will expand our knowledge on novel regulatory processes in both panicles and grains of rice; and, serve as a resource towards the designing of rice crops for future high-O3world.</P>