• Journal of Applied Biological Chemistry
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• 제58권4호
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• pp.355-361
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• 2015

The rice protein profiles of Oryza sativa L (Koshihikari) grown under organic and conventional cultivation regimes were compared on 2-D gels to develop diagnostic marker proteins for organic rice. The selected proteins, differentially expressed between organic and conventional rice, were compared with the differentially expressed proteins of another organic and conventional rice pairing, produced at a different location. In the first comparison among conventional, no-chemical, and organic rice grown in the same region, Korea, 13 proteins exhibiting differential expression in organic and conventionally grown plants were selected. Eight of the 13 proteins were down-regulated, and the 5 remaining proteins were up-regulated from conventional to organic rice. The second comparison pairing from Kyungju, revealed 12 differentially expressed proteins, with 8 down-regulated and 4 up-regulated proteins. Ten of the differentially expressed proteins that overlapped between the two comparison sets could not be clustered into any functional group using a functional annotation clustering tool. Further comparisons using another set of conventional and organic rice, belonging to a different variety of Oryza sativa L and produced in Sanchung, revealed 8 differentially expressed proteins, 5 of which were down-regulated and 3 of which were upregulated in the organic rice. Overall, 3 differentially expressed proteins were commonly found in all three organic rice crops. These 3 proteins, along with other overlapping differentially expressed proteins, can provide a good starting point for the development of signature proteins that can be used for the authentication of organic rice with a follow-up studies with more comparison sets.

• Food Science and Biotechnology
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• 제15권3호
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• pp.385-391
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• 2006

In Korea, different kinds of genetically modified (GM) crops are under development, including GM-rice expressing insecticidal crystal (Cry) proteins of Bacillus thuringiensis (Bt) modified to change a single amino acid. In this study, amino acid (aa) sequences of modified Cry proteins were compared to that of known allergens, and Cry proteins expressed in GM-rice were identified by using Cry protein specific polyclonal antibody. The antigen-antibody reactions were compared between GM and commercial rice to assess the allergic risk of Cry proteins. This analysis showed no known allergen to have more than 35% aa sequence homology with modified Cry proteins in Bt rice over an 80 aa window or to have more than 8 consecutive identical aa. Sera from allergic patients showed some IgE reactivity via immunoblotting and enzyme-linked immunosorbent assay (ELISA), although no differences were seen between GM and commercial rice. Based on these results we conclude that GM rice with modified Cry proteins has no differences in its protein composition or allergenicity relative to commercial rice.

• 한국작물학회지
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• 제58권4호
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• pp.388-392
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• 2013

The proteins from functional rice cultivars (Nogwonchalbyeo, Giant embryonic, Arhyangchalbyeo, and Goamibyeo) and general white rice were extracted and separated using two-dimensional (2D) gel electrophoresis. A wide variation in the molecular weight (MW) and pH range of the expressed proteins in rice samples were observed. The green-kerneled rice (Nogwonchalbyeo) exhibited proteins with MW of 9-57 kDa and appeared at a pH range of 4-7. The Giant embryonic contained proteins with MW of 31-63 kDa and a pH range of 5-6. The aromatic glutinous rice (Arhyangchalbyeo) showed proteins with MW of 24-28 and pH of 5.8-6.8. The high-amylose rice (Goamibyeo) exhibited proteins with MW of 3-63 and pH of 5.2-5.6. The identified proteins uniquely found and highly expressed in each cultivar may have a significant role on rice functionality. The results illustrate that the 2D gel electrophoresis is a valuable method in the determination of the protein expression profiles in functional rice grains and may be useful in the identification of specific marker proteins associated with the functional property of rice.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2004년도 춘계 학술대회지
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• pp.12-27
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• 2004

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant sciences. Plant proteomics would be most useful when combined with other functional genomics tools and approaches. A combination of microarray and proteomics analysis will indicate whether gene regulation is controlled at the level of transcription or translation and protein accumulation. In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is a most prevalent technique to identify rapidly a large of proteins in proteome analysis. However, the conventional Western blotting/sequencing technique us still used in many laboratories. As a first step to efficiently construct protein data-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein spots are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins (i. e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 30% of total rice cDNA have been deposited in the database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that fumed out to be calreticulin, gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activate in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins (http://genome .c .kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Recently, we are separated proteins from grain filling and seed maturation in rice to perform ESI-Q-TOF/MS and MALDI-TOF/MS. This experiment shows a possibility to easily and rapidly identify a number of 2-DE separated proteins of rice by ESI-Q-TOF/MS and MALDI-TOF/MS. Therefore, the Information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful in the plant molecular breeding. Also, information from our study could provide a venue to plant breeder and molecular biologist to design their research strategies precisely.

• Journal of Plant Biotechnology
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• 제30권3호
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• pp.281-291
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• 2003

In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is the most prevalent technique to rapidly identify a large number of proteome analysis. However, the conventional Western blotting/sequencing technique has been used in many laboratories. As a first step to efficiently construct protein cata-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein sports are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins(i, e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 45% of total rice cDNA have been deposited in the EMBL database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that tuned out to be calreticulin, gibberellin-binding protein, which is ribulose-1.5-bisphosphate carboxylase/oxygense active in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins(http://genome.c.kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Also, the information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful be in the plant molecular breeding.

• Journal of Applied Biological Chemistry
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• 제42권4호
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• pp.180-185
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• 1999

Protein concentrate was produced and succinylated from rice bran to assess and improve its functional properties for the purpose of expanding the uses of rice bran proteins. The most effective solvent for the extraction of rice bran proteins was 20% aqueous ethanol at pH 9. The protein content of rice bran protein concentrate produced was 70.0% and the total protein yield was 64.3%. The extent of succinylation of free amino groups in the modified products was 72.8%. Though the modified protein products showed good functional properties including solubility, emulsion properties, and oil absorption capacity, it did not form gel. Succinylation improved solubility and emulsion and gelling properties. These improvements in functionality will enhance the value of rice bran proteins, thus enabling them to be more competitive with other food proteins.

• Journal of Applied Biological Chemistry
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• 제55권2호
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• pp.79-83
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• 2012

벼의 발아에서부터 생장 결실기에까지 토양, 온도, 시비조건 등의 재배환경은 벼에 발현되는 단백질체의 profile을 변화시키는 것이 잘 알려져 있다. 온도를 포함한 재배환경이 다른 경상북도 칠곡과 강원도 출원에서 재배된 오대 백미의 단백질체 profile을 2-dimensional (D) gel 상에서 분리하여 비교함으로써 재배환경에 의해 현저하게 발현양의 차이를 보이는 단백질들의 기능을 분석하였다. 오대 백미에 발현되는 112개의 단백질들의 기능을 고려할 때 재배환경에 의해 가장 유의적인 차이를 보이는 단백질 군들은 철원 오대백미의 스트레스 대응 단백질로 지베렐린 합성에 관여하는 ent-kaur-16-ene synthase이며 칠곡 오대백미의 스트레스 대응 단백질은 heat shock protein으로 재배환경에 따라 발현되는 스트레스 대응 단백질의 종류도 다르게 나타났다. 등숙온도가 높은 칠곡에서 재배된 오대 백미에는 곰팡이나 Bacillus 병원균에 대응하는 xylanase inhibitor protein이 유의적으로 발현되었으며, 철원 백미에서는 세포벽 합성관련 효소, 세포주기 관련 단백질 등이 선별적으로 발현의 증가를 보였고 수송관여 단백질들은 철원 및 칠곡 백미에서 모두 변화를 보였다. 단백질 함량과 단백질 profile을 종합적으로 분석할 때 철원 백미에는 칠곡 백미에 비해 새로운 주종 단백질들의 발현이 많았으며 칠곡 백미는 전체적인 단백질의 발현이 높게 나타났음을 보여, 재배환경에 따라 단백질 profile이 변화되는 특성이 다름을 보였는데, 이 결과는 지구온난화와 같은 기후 변화에 따른 작물의 단백질체 변화와 고급미 생산을 위해 적절한 단백질체 profile을 갖게 하는 재배조건 확립 등의 연구에 활용될 수 있다.

• Molecules and Cells
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• 제38권8호
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• pp.685-696
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• 2015

Rice is a model plant widely used for basic and applied research programs. Plant cell wall proteins play key roles in a broad range of biological processes. However, presently, knowledge on the rice cell wall proteome is rudimentary in nature. In the present study, the tightly-bound cell wall proteome of rice callus cultured cells using sequential extraction protocols was developed using mass spectrometry and bioinformatics methods, leading to the identification of 1568 candidate proteins. Based on bioinformatics analyses, 389 classical rice cell wall proteins, possessing a signal peptide, and 334 putative non-classical cell wall proteins, lacking a signal peptide, were identified. By combining previously established rice cell wall protein databases with current data for the classical rice cell wall proteins, a comprehensive rice cell wall proteome, comprised of 496 proteins, was constructed. A comparative analysis of the rice and Arabidopsis cell wall proteomes revealed a high level of homology, suggesting a predominant conservation between monocot and eudicot cell wall proteins. This study importantly increased information on cell wall proteins, which serves for future functional analyses of these identified rice cell wall proteins.

• The Plant Pathology Journal
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• 제27권1호
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• pp.37-43
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• 2011

Rice stripe virus (RSV) is one of serious epidemic pathogens for rice species grown in many Asian countries. Therefore, it is necessary to produce a diagnostic detection kit applicable in fields for RSV detection. In this study, RSV proteins that were derived from recombinant proteins and synthetic polypeptides as antigens were generated and were raised in rabbits for antiserum production. Among seven proteins in RSV, genes that code for NCP and NS3 proteins were cloned and subcloned into vector carrying His-tag protein and were expressed in E. coli. Of two recombinant proteins, only anti-NCP displayed stable hybridization signals in western blot analysis. Alternately, synthetic RSV polypeptides for CP, NCP, NS3 and NSvc4 we also generated and only antibodies against CP and NCP were very effective to detect RSV in both RSV infected rice and weed plants. However, antibodies against NS3 and NSvc4 showed weak specific bands as well as strong non-specific background due to the difference of viral proteins produced in the infected leaves. In summary, the antibodies generated against RSV proteins produced in this study will be useful for various assays such as for RSV diagnostic detection, immunoprecipitation, protein purification, and western blot analysis.

• The Plant Pathology Journal
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• 제26권2호
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• pp.110-114
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• 2010

WRKY transcription factors are known to be involved in many different biological processes including plant response to biotic stress, abiotic stress, and plant development. WRKY proteins are extensively studied in Arabidopsis. Recently, reports on WRKY proteins are rapidly increasing in the other plant species, especially in rice. Therefore, this review will discuss the function of rice WRKY proteins reported so far.