• 제목/요약/키워드: rice proteins

검색결과 249건 처리시간 0.028초

OryzaGP: rice gene and protein dataset for named-entity recognition

  • Larmande, Pierre;Do, Huy;Wang, Yue
    • Genomics & Informatics
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    • 제17권2호
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    • pp.17.1-17.3
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    • 2019
  • Text mining has become an important research method in biology, with its original purpose to extract biological entities, such as genes, proteins and phenotypic traits, to extend knowledge from scientific papers. However, few thorough studies on text mining and application development, for plant molecular biology data, have been performed, especially for rice, resulting in a lack of datasets available to solve named-entity recognition tasks for this species. Since there are rare benchmarks available for rice, we faced various difficulties in exploiting advanced machine learning methods for accurate analysis of the rice literature. To evaluate several approaches to automatically extract information from gene/protein entities, we built a new dataset for rice as a benchmark. This dataset is composed of a set of titles and abstracts, extracted from scientific papers focusing on the rice species, and is downloaded from PubMed. During the 5th Biomedical Linked Annotation Hackathon, a portion of the dataset was uploaded to PubAnnotation for sharing. Our ultimate goal is to offer a shared task of rice gene/protein name recognition through the BioNLP Open Shared Tasks framework using the dataset, to facilitate an open comparison and evaluation of different approaches to the task.

벼의 생육시기에 따른 일부 광호흡효소의 활성변화 (Activities of Catalase, Glycolate Oxidase, Hydroxypyruvate and NADPH-Glyoxylate Reductases at Different Growing Stages in the Leaves of Rice Plants)

  • 권영명
    • Journal of Plant Biology
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    • 제22권3호
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    • pp.81-84
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    • 1979
  • Catalase, glycolate oxidase, hydroxypyruvate and NADPH-glyoxylate reductases activities in cell free extracts from leaves of 3 cultivars, Suwon 264, IR 36 and Jin Heung of rice plants were studied at different growing stages. Catalase and glycolate oxidase shows inclining activities toward the maximum vegetative growth whereas declining activities in either the enzymes were noticed during the maturing stage. After the photoperiodic condition exhibit increasing hydroxypyruvate and NADPH-glyoxylate reductases activities with time until maturing stage. No significant differences were found in the enzyme activities, and in analytical data of nitrogen, chlorophyll contents, dry weight and soluble proteins among the 3 cultivars.

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벼 callus로부터 재분화 과정에서 생성되는 특수한 단백질의 동정 (Indentification of Specific Proteins synthesized During Somatic Embryogenesis of Rice)

  • 원재희;최홍집;김달응
    • Current Research on Agriculture and Life Sciences
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    • 제9권
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    • pp.95-102
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    • 1991
  • 본 연구(硏究)는 식물(植物)의 발생(發生)과 분화(分化)에 관(關)한 생화학적(生化學的) 분자생물학적(分子生物學的) 구명(究明)을 위해 조직(組織) 발생(發生) 단계(段階)의 특이적인 유전자(遺傳子)의 발현조절 기작과 역할(役割)을 연구(硏究)하기 위한 기초(基礎) 지식을 얻고자 수행(遂行)되었다. 벼를 실험재료(實險材料)로 하여 현미로부터 callus를 유도(誘道)하고 이들 callus에서 여러가지 방법(方法)을 통(通)해 embryogenic callus와 nonembryogenic callus를 분리(分離)해 somatic embryogenesis에 관련된 특수한 단백질(蛋白質)을 찾고자 하였고 그 결과(結果)를 요약(要約)하면 다음과 같다. 지금까지의 보고(報告)에 의하면 재분화가 잘되는 callus와 그렇지 않은 callus간에는 여러가지 면에서 차이가 난다고 알려져 있다. 재분화가 잘되는 callus는 표면이 거칠고 흰색에 가까우며 조직(組織)이 단단하다. 반면에 재분화가 되지않는 callus는 표면(表面)에 윤기가 나며 단단하지 않다. 이러한 보고(報告)를 기초(基礎)로 하여 $N_6$ media에 1mg/1의 2,4-D가 첨가(添加)된 배지(培地)에서 2주 정도 callus를 유기시키고 유기된 callus는 다시 배양(培養)하였다. 7-8차 계대배양하면서 embryogenic callus와 nonembryogenic callus를 분리(分離)한 다음 이를 시료(試料)로 하여 protein을 추출(抽出)하여 SDS-PAGE 상에서 비교하여 보았다. 그 결과(結果) 두 callus간에 차이가 있음을 알 수 있었다. 7-8차 계대배양한 두 종류(種類)의 callus로 부터 protein을 분리하여 two-dimensional gel 전기영동에 의해 비교하여 본 결과(結果) 몇 개의 단백질(蛋白質)이 서로 다름을 알 수 있었다.

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벼의 잎 조직에서 발현되는 저온 스트레스 관련 단백질의 분리 동정 (Identification of Cold Stress-related Proteins in Rice Leaf Tissue)

  • 이동기;이상훈;이병현
    • 한국초지조사료학회지
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    • 제25권4호
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    • pp.287-296
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    • 2005
  • 프로테오믹스 기법을 이용하여 벼 저온 스트레스 관련 단백질을 분리 동정하기 위하여 저온 처리한 벼로부터 단백질을 분리하였다. 분리한 단백질로부터 Rubisco 단백질을 제거하기 위해 $15\%$ PEG fractionation을 실시한 후 $15\%$ PEG 상등액과 pellet 분획을 각각 이차원전기 영동으로 단백질을 분석하였고, MALDI-TOF MS를 이용하여 단백질을 동정하였다. $15\%$ PEG 상등액에서 8개의 단백질 spot이 증가하였고 10개의 spot 이 감소하였다. 증가한 8개 단백질 spot 중에서 epimerase/dehydratase, fructokinase, ribose-5-phosphate isomerase (Rpi), chaperonin 21 precursor, photosystem II oxygen-envolving complex (PS II OEC) protien 2 precursor, thioredoxin h-type (Trx-h) 등 6개의 단백질이 확인되어졌다. $15\%$ PEG pellet 분획에서 13개의 단백질 spot이 증가하였고 14 spot이 감소하였으며, 증가한 13개 단백질 spot중에서 OSJNB b059K02.15, hypothetical protein, mitogen-activated protein kinase kinase (MAPKK), 20S proteasome beta 7 subunit, Rubisco small subunit 등 5개의 단백질이 확인되어졌다. 확인되어진 단백질들은 기능별로 분류해 본 결과, 세포대사관련 단백질, energy 생성에 관련된 단백질, 산화환원 조절관련 단백질, 식물 병 방어관련, 단백질 합성 및 신호전달 관련 단백질 등으로 분류되었다. 이들 중 RPi와 MAPKK가 저온 스트레스에 의해 발현되는 것이 본 실험의 프로테옴 분석을 통하여 최초로 동정되었다.

한국산곡류단백질(韓國産穀類蛋白質)의 아미노산(酸) 조성비율(組成比率)에 관(關)한 연구(硏究) (On The Amino Acid Compositions of The Korean Cereal Proteins)

  • 성낙응;강희윤
    • Journal of Nutrition and Health
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    • 제3권2호
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    • pp.113-117
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    • 1970
  • 1) It was found that the polished rice is short of Iysine, methionine, cystine, and tryptophan among the essential amino acids, and that it shows no significant variations with regard to its pattern of geographical region. 2) Comparing in the contents of essential amino acids in the cereals, such as polished barley, wheat, great millet, and soy bean, the soy bean is found to be better than the polished rice, while the others to be either poorer or similar than the polished rice. 3) The aminal experiments observed with the mixed diet revealed that the most ideal composition of the mixed diet is the one composed of 70% polished rice, 20% polished barley, and 10% soy bean.

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Molecular and Cellular Studies of Seed Storage Proteins from Rice and Wheat

  • Kim, Woo-Taek
    • Applied Biological Chemistry
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    • 제32권1호
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    • pp.64-72
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    • 1989
  • Near full length cDNA clones encoding the rice seed storage protein, prolamine, were isolated and divided into two homology classes based on cross-hybridization and DNA sequencing analysis. These cDNA clones contain a single open reading frame encoding a putative rice prolamine precursor(M.W.=17,200) possessing atypical 14 amino acid signal peptide. Clones of these two homology classes diverge mainly by insertions/deletions of short nucleotide stretches and point mutations. The deduced primary structures of both types of prolamine polypeptides are devoid of any major tandem repetitive sequences, a feature prevalent in other cereal prolamines. No significant homology teas detected between the rice prolamine and other cereal prolamines, indicating that the rice gene evolved from a different ancestor that gave rise to other cereal prolamine genes. Developing wheat and rice endosperms were examined using ultrathin sections prepared from tissues harvested at various days after flowering. By immunocytochemical localization techniques, wheat prolamines are localized within vesicles from Golgi apparatus and in homogeneous regions of protein bodies. The involvement of the goli apparatus in the packaging of wheat prolamines into protein bodies indicates a pathway which differs from the mode of other cereal prolamines and resembles the mechanism employed for the storage of rice glutelin and legume globulins.

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쌀 Glutelin 유전자군의 구조 및 발현조절 (Sturcture of the Rice Glutelin Multigene Family and Its Expression)

  • 황영수
    • 한국식물학회:학술대회논문집
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    • 한국식물학회 1987년도 식물생명공학 심포지움 논문집 Proceedings of Symposia on Plant Biotechnology
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    • pp.261-282
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    • 1987
  • Plants store a significant amount of their nitrogen, sulfur and carbon reserves as storage proteins in seed tissues. The major proteins present in rice seeds are the glutelins. Glutelins are initially synthesized at 4-6 days postanthesis and deposited into protein bodies via Golgi apparatus. Based on nucleic acid sequences and Southern blot analysis, the three isolated glutelin genomic clones were representative members of three gene subfamilies each containing 5 to 8 copies. A comparison of DNA sequences displayed by relevant regions of these genomic clones showed that two subfamilies, represented by clones, Gt1 and Gt2, were closely, related and probably evolved by more recent gene duplication events. The 5' flanking and coding sequences of Gt1 and Gt2 displayed at least 87% homolgy. In contrast, Gt3 showed little or no homolgy in the 5' flanking sequences upstream of the putative CAAT boxes and exhibited significant divergence in all other portions of the gene. Conserved sequences in the 5' flanking regions of these genes were identified and discussed in light of their potential regulatory role. The derived primary sequences of all three glutelin genomic clones showed significant homology to the legume 11S storage proteins indicating a common gene origin. A comparison of the derived glutelin primary sequences showed that mutations were clustered in three peptide regions. One peptide region corresponded to the highly rautable hypervariable region of legume peptide region of legume 11S storage proteins, a potential target area for protein modification. Expression studies indicated that glutelin mRNA transcripts are differentially accumulated during endosperm development. Promoterss of Gt2 and Gt3 were functional as they direct transient expression of chloramphenicol acetyltransferase in cultured plant cell.

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고기능성 쌀단백질 소재 개발 연구 (A study on the development of high functional food protein ingredient from rice bran)

  • 이의석;김기종;김재현;홍순택
    • 농업과학연구
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    • 제37권1호
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    • pp.61-68
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    • 2010
  • Rice bran proteins from different cultivars(Youngan, Sindongjin, Suwon 511) were extracted with Xylanase using orthogonal analysis method and their functional properties were investigated. The optimum extraction conditions, based on protein content in the extract found to be at 1 wt% xylanase, pH 7 and 50:1, solvent to rice bran ratio(v/w %). Nitrogen solubility indices(NSI) of rice bran protein concentrates were shown a minimum value at pH 4 ranged 2~23%, varied with different cultivars and a maximum (NSI${\geq}$90% for all cultivars) at pH 10. As for water adsorption and fat adsorption capacity, rice bran protein concentrates were shown to be better than Na-caseinate and isolated soy protein, respectively. Emulsifying activities were observed high in order of Na-caseinate>Youngan rice bran protein>Shindongjin rice bran protein>Suwon 511 rice bran protein>isolated soy protein. In general, the surface tension of rice bran protein solution($10^{-3}$ wt%, 5 mM bis-tris, pH 7) was increased with increasing concentrations and found a minimum value near pI. On heating, it was decreased slightly with increasing temperatures up to $70^{\circ}C$ and then increased above $80^{\circ}C$. Addition of sodium chloride was made the surface tension decrease. In conclusion, with Xylanase, rice bran protein concentrate can be successfully extracted from the rice bran of different cultivars and the Youngan rice bran protein was thought to have best functionality among rice cultivars tested. It might be used as a milk protein substitute.

종자내 아미노산 합성 조절 유전자에 관한 연구 (Amino Acid Biosynthesis and Gene Regulation in Seed)

  • 임용표;서미정;조수진;이정희;이효연
    • 한국식물학회:학술대회논문집
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    • 한국식물학회 1996년도 제10회 식물생명공학심포지움 고등식물 발생생물학의 최근 진보
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Determination of the MYB Motif Interacting with WD40 and Basic Helix Loop Helix Proteins

  • Kim, Ji-Hye;Kim, Bong-Gyu;Ahn, Joong-Hoon
    • Journal of Applied Biological Chemistry
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    • 제55권1호
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    • pp.67-70
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    • 2012
  • Plant MYB transcription factors regulate secondary metabolism, cellular morphogenesis, and plant hormone signaling pathway. MYB proteins in plants consist of two repeats of 50 amino acid residues, which are referred to as R2R3 and they interact with WD40 or basic helix loop helix (bHLH) proteins. Yeast two hybrid assay was determined whether rice MYB protein interacts with either OsTTG1, which contains a WD40 domain, or with OsGL3, which contains a bHLH domain. Among 30 OsMYB proteins, three interacted with OsTTG1 and five interacted with OsGL3. A series of MYB mutants were created to determine the MYB domain important for the interaction with OsTTG1 or OsGL3. By using the yeast two hybrid assay, we found that the R3 motif of OsMYB10 and the R2 motif of OsMYB16 were required for interaction with OsTTG1 and OsGL3 proteins, respectively.