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Kubo T, Yamagata Y, Matsusaka H, Toyoda A, Sato Y, Kumamaru T. MiRiQ Database: A Platform for In Silico Rice Mutant Screening. PLANT & CELL PHYSIOLOGY 2024; 65:169-174. [PMID: 37930817 PMCID: PMC10799713 DOI: 10.1093/pcp/pcad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/15/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
Genetic studies using mutant resources have significantly contributed to elucidating plant gene function. Massive mutant libraries sequenced by next-generation sequencing technology facilitate mutant identification and functional analysis of genes of interest. Here, we report the creation and release of an open-access database (https://miriq.agr.kyushu-u.ac.jp/index.php), called Mutation-induced Rice in Kyushu University (MiRiQ), designed for in silico mutant screening based on a whole-genome-sequenced mutant library. This database allows any user to easily find mutants of interest without laborious efforts such as large-scale screening by PCR. The initial version of the MiRiQ database (version 1.0) harbors a total of 1.6 million single-nucleotide variants (SNVs) and InDels of 721 M1 plants that were mutagenized by N-methyl-N-nitrosourea treatment of the rice cultivar Nipponbare (Oryza sativa ssp. japonica). The SNVs were distributed among 87% of all 35,630 annotated protein-coding genes of the Nipponbare genome and were predicted to induce missense and nonsense mutations. The MiRiQ database provides built-in tools, such as a search tool by keywords and JBrowse for mutation searches. Users can request mutant seeds in the M2 or M3 generations from a request form linked to this database. We believe that the availability of a wide range of gene mutations in this database will benefit the plant science community and breeders worldwide by accelerating functional genomic research and crop improvement.
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Affiliation(s)
- Takahiko Kubo
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan
| | - Yutaka Sato
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
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Qing D, Deng G, Pan Y, Gao L, Liang H, Zhou W, Chen W, Li J, Huang J, Gao J, Lu C, Wu H, Liu K, Dai G. ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress. BREEDING SCIENCE 2022; 72:150-168. [PMID: 36275934 PMCID: PMC9522529 DOI: 10.1270/jsbbs.21081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/11/2021] [Indexed: 06/16/2023]
Abstract
Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for a relative and absolute quantification (iTRAQ) labeling-based quantitative proteomics approach was used to detected changes in protein levels. Two-week-old seedlings of the cold tolerant rice variety Kongyu131 were treated at 8°C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to the control group. Functional analysis revealed that most of the regulated proteins are involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulated proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is that it provides new insights into cold stress responses in rice with respect to proteomics and provides candidate genes for cold-tolerance rice breeding.
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Affiliation(s)
- Dongjin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Lijun Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Jingcheng Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Ju Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Chunju Lu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Hao Wu
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Kaiqiang Liu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
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Farooq A, Bhat KA, Mir RA, Mahajan R, Nazir M, Sharma V, Zargar SM. Emerging trends in developing biosensor techniques to undertake plant phosphoproteomic analysis. J Proteomics 2021; 253:104458. [PMID: 34923172 DOI: 10.1016/j.jprot.2021.104458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
Protein modifications particularly phosphorylation is governed by a complex array of mechanisms to attain a functional conformation and regulate important biological processes in organisms during external environmental stimuli and hormone signaling. Phosphoproteomics is a promising field of proteomics for identification of proteins with phosphate groups and their impact on structure, function and localization of proteins. Techniques that allow quantitative detection of proteins and their post-translational modifications (PTMs) have immensely led to understand the structural and functional dynamics of proteins. Biosensor systems are a relatively new biotechnological approach that works on the principle of transforming the interactions of different biological samples viz proteins, enzymes, aptamers, nucleic acids and so on into the signals such as electrochemical, colorimetric, optical or magnetic which have been effectively useful in the detection and characterization of phosphoproteins. The focus of our review is to provide a comprehensive account of the critical role and utility of novel biosensors such as, fluorescence based, enrichment based, nanobody based biosensors, as promising technical intercessions to identify phosphoproteins and their influence on structural dynamics of proteins. Furthermore, by studying the innovative phosphoprotein biosensors we will be able to identify the aberrant phosphorylation patterns to precisely diagnose diseases.
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Affiliation(s)
- Asmat Farooq
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India; Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (SKUAST-J), Chatha, Jammu 180009, India
| | - Kaisar Ahmad Bhat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India; Department of Biotechnology, School of Biosciences & Biotechnology, BGSB University, Rajouri, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences & Biotechnology, BGSB University, Rajouri, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India
| | - Muslima Nazir
- CORD, University of Kashmir, Hazratbal, Srinagar, Jammu & Kashmir, India
| | - Vikas Sharma
- Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (SKUAST-J), Chatha, Jammu 180009, India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India.
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Goto C, Hashizume S, Fukao Y, Hara-Nishimura I, Tamura K. Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction. Nucleus 2020; 10:81-92. [PMID: 30961429 PMCID: PMC6527390 DOI: 10.1080/19491034.2019.1603093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In eukaryotes, the nucleus plays key roles in fundamental cellular processes, including DNA replication, chromatin maintenance, transcription, and translation. To better understand the functional diversity of nuclei, we developed a method for the comprehensive extraction of the nuclear proteome from Arabidopsis. We used a buffer with a high sucrose concentration to purify nuclei and then conducted solubility-based fractionation to increase proteome coverage. We identified 1539 proteins and two novel nuclear envelope (NE) proteins in the nuclear fraction of Arabidopsis cultured cells. The localization of 25 proteins was determined by GFP fusion analyses; 23 of these proteins were localized either in the nucleus or the NE-associated endoplasmic reticulum. This result was indicative of the high quality of the proteome. These findings will be useful for clarifying novel nuclear functions in plants.
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Affiliation(s)
- Chieko Goto
- a Graduate School of Agricultural and Life Sciences , University of Tokyo , Tokyo , Japan
| | - Shoko Hashizume
- b Department of Botany , Graduate School of Science, Kyoto University , Kyoto , Japan
| | - Yoichiro Fukao
- c Department of Bioinformatics , College of Life Sciences, Ritsumeikan University , Shiga , Japan
| | | | - Kentaro Tamura
- e Department of Environmental and Life Sciences , University of Shizuoka , Shizuoka , Japan
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Graziano S, Marmiroli N, Gullì M. Proteomic analysis of reserve proteins in commercial rice cultivars. Food Sci Nutr 2020; 8:1788-1797. [PMID: 32328244 PMCID: PMC7174207 DOI: 10.1002/fsn3.1375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/25/2022] Open
Abstract
Rice consumption is rising in western countries with the adoption of new nutritional styles, which require the avoidance of gluten. Nevertheless, there are reports of rice allergic reactions. Rice grains contain a low amount of proteins most of which are storage proteins represented by glutelins, prolamins, albumins, and globulins. Some of these proteins are seed allergenic proteins as α-amylase/trypsin inhibitor, globulins, β-glyoxylase, and several glutelins. Italy is the major rice producer in Europe, and for this, seed reserve proteins of four Italian rice cultivars were characterized by 2D-GE analysis. Some differentially abundant proteins were identified and classified as allergenic proteins, prompting a further characterization of the genes encoding some of these proteins. In particular, a deletion in the promoter region of the 19 KDa globulin gene has been identified, which may be responsible for the different abundance of the protein in the Karnak cultivar. This polymorphism can be applied for cultivar identification in commercial samples. Seed proteome was characterized by a variable combination of several proteins, which may determine a different allergenic potential. Proteomic and genomic allowed to identify the protein profile of four commercial cultivars and to develop a molecular marker useful for the analysis of commercial products.
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Affiliation(s)
- Sara Graziano
- Interdepartmental Center SITEIA.PARMAUniversity of ParmaParco Area delle ScienzeParmaItaly
| | - Nelson Marmiroli
- Interdepartmental Center SITEIA.PARMAUniversity of ParmaParco Area delle ScienzeParmaItaly
| | - Mariolina Gullì
- Interdepartmental Center SITEIA.PARMAUniversity of ParmaParco Area delle ScienzeParmaItaly
- Department of ChemistryLife Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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Rakwal R, Hayashi G, Shibato J, Deepak SA, Gundimeda S, Simha U, Padmanaban A, Gupta R, Han SI, Kim ST, Kubo A, Imanaka T, Fukumoto M, Agrawal GK, Shioda S. Progress Toward Rice Seed OMICS in Low-Level Gamma Radiation Environment in Iitate Village, Fukushima. J Hered 2019; 109:206-211. [PMID: 28992201 DOI: 10.1093/jhered/esx071] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 09/08/2017] [Indexed: 11/13/2022] Open
Abstract
Here, we present an update on the next level of experiments studying the impact of the gamma radiation environment, created post-March, 2011 nuclear accident at Fukushima Daiichi nuclear power plant, on rice plant and its next generation-the seed. Japonica-type rice (Oryza sativa L. cv. Koshihikari) plant was exposed to low-level gamma radiation (~4 μSv/h) in the contaminated Iitate Farm field in Iitate village (Fukushima). Seeds were harvested from these plants at maturity, and serve as the treated group. For control group, seeds (cv. Koshihikari) were harvested from rice grown in clean soil in Soma city, adjacent to Iitate village, in Fukushima. Focusing on the multi-omics approach, we have investigated the dry mature rice seed transcriptome, proteome, and metabolome following cultivation of rice in the radionuclide contaminated soil and compared it with the control group seed (non-radioactive field-soil environment). This update article presents an overview of both the multi-omics approach/technologies and the first findings on how rice seed has changed or adapted its biology to the low-level radioactive environment.
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Affiliation(s)
- Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo, Japan.,Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE Academy Private Limited, Birgunj, Nepal
| | - Gohei Hayashi
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Junko Shibato
- Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo, Japan
| | | | | | | | | | - Ravi Gupta
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, Republic of Korea
| | - Sang-Ik Han
- National Institute of Crop Science, Rural Development Administration (RDA), Miryang, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, Republic of Korea
| | - Akihiro Kubo
- Environmental Stress Mechanisms Section, Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan (Kubo)
| | | | - Manabu Fukumoto
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE Academy Private Limited, Birgunj, Nepal
| | - Seiji Shioda
- Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo, Japan
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Ji Z, Zeng Y, Liang Y, Qian Q, Yang C. Proteomic dissection of the rice-Fusarium fujikuroi interaction and the correlation between the proteome and transcriptome under disease stress. BMC Genomics 2019; 20:91. [PMID: 30691406 PMCID: PMC6350333 DOI: 10.1186/s12864-019-5435-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/07/2019] [Indexed: 02/08/2023] Open
Abstract
Background Bakanae disease, caused by the fungus Fusarium fujikuroi, occurs widely throughout Asia and Europe and sporadically in other rice production areas. Recent changes in climate and cropping patterns have aggravated this disease. To gain a better understanding of the molecular mechanisms of rice bakanae disease resistance, we employed a 6-plex tandem mass tag approach for relative quantitative proteomic comparison of infected and uninfected rice seedlings 7 days post-inoculation with two genotypes: the resistant genotype 93–11 and the susceptible genotype Nipponbare. Results In total, 123 (77.2% up-regulated, 22.8% down-regulated) and 91 (94.5% up-regulated, 5.5% down-regulated) differentially expressed proteins (DEPs) accumulated in 93–11 and Nipponbare, respectively. Only 11 DEPs were both shared by the two genotypes. Clustering results showed that the protein regulation trends for the two genotypes were highly contrasting, which suggested obviously different interaction mechanisms of the host and the pathogen between 93 and 11 and Nipponbare. Further analysis showed that a noticeable aquaporin, PIP2–2, was sharply upregulated with a fold change (FC) of 109.2 in 93–11, which might be related to pathogen defense and the execution of bakanae disease resistance. Certain antifungal proteins were regulated in both 93–11 and Nipponbare with moderate FCs. These proteins might participate in protecting the cellular integrity required for basic growth of the susceptible genotype. Correlation analysis between the transcriptome and proteome revealed that Pearson correlation coefficients of R = 0.677 (P = 0.0005) and R = − 0.097 (P = 0.702) were obtained for 93–11 and Nipponbare, respectively. Our findings raised an intriguing result that a significant positive correlation only in the resistant genotype, while no correlation was found in the susceptible genotype. The differences in codon usage was hypothesized for the cause of the result. Conclusions Quantitative proteomic analysis of the rice genotypes 93-11and Nipponbare after F. fujikuroi infection revealed that the aquaporin protein PIP2–2 might execute bakanae disease resistance. The difference in the correlation between the transcriptome and proteome might be due to the differences in codon usage between 93-11and Nipponbare. Overall, the protein regulation trends observed under bakanae disease stress are highly contrasting, and the molecular mechanisms of disease defense are obviously different between 93 and 11 and Nipponbare. In summary, these findings deepen our understanding of the functions of proteins induced by bakanae disease and the mechanisms of rice bakanae disease resistance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5435-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhijuan Ji
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China
| | - Yuxiang Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China
| | - Yan Liang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China.
| | - Changdeng Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China.
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Zhang X, Yin F, Xiao S, Jiang C, Yu T, Chen L, Ke X, Zhong Q, Cheng Z, Li W. Proteomic analysis of the rice (Oryza officinalis) provides clues on molecular tagging of proteins for brown planthopper resistance. BMC PLANT BIOLOGY 2019; 19:30. [PMID: 30658570 PMCID: PMC6339371 DOI: 10.1186/s12870-018-1622-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 12/27/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Among various pests, the brown planthopper (BPH) that damages rice is the major destructive pests. Understanding resistance mechanisms is a critical step toward effective control of BPH. This study investigates the proteomics of BPH interactions with three rice cultivars: the first resistant (PR) to BPH, the second susceptible (PS), and the third hybrid (HR) between the two, in order to understand mechanisms of BPH resistance in rice. RESULTS Over 4900 proteins were identified from these three rice cultivars using iTRAQ proteomics study. A total of 414, 425 and 470 differentially expressed proteins (DEPs) were detected from PR, PS and HR, respectively, after BPH infestation. Identified DEPs are mainly enriched in categories related with biosynthesis of secondary metabolites, carbon metabolism, and glyoxylate and dicarboxylate metabolism. A two-component response regulator protein (ORR22) may participate in the early signal transduction after BPH infestation. In the case of the resistant rice cultivar (PR), 6 DEPs, i.e. two lipoxygenases (LOXs), a lipase, two dirigent proteins (DIRs) and an Ent-cassa-12,15-diene synthase (OsDTC1) are related to inheritable BPH resistance. A heat shock protein (HSP20) may take part in the physiological response to BPH infestation, making it a potential target for marker-assisted selection (MAS) of rice. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed eight genes encoding various metabolic proteins involved in BPH resistance. During grain development the expressions of these genes varied at the transcriptional and translational levels. CONCLUSIONS This study provides comprehensive details of key proteins under compatible and incompatible interactions during BPH infestation, which will be useful for further investigation of the molecular basis of rice resistance to BPH and for breeding BPH-resistant rice cultivars.
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Affiliation(s)
- Xiaoyun Zhang
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Fuyou Yin
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Suqin Xiao
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Chunmiao Jiang
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Tengqiong Yu
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Ling Chen
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Xue Ke
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Qiaofang Zhong
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Zaiquan Cheng
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan People’s Republic of China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan People’s Republic of China
| | - Weijiao Li
- Faculty of Chinese Materia Medica, Yunnan University of Traditional Chinese Medicine, Kunming, Yunnan People’s Republic of China
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11
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Meng Q, Gupta R, Min CW, Kwon SW, Wang Y, Je BI, Kim YJ, Jeon JS, Agrawal GK, Rakwal R, Kim ST. Proteomics of Rice- Magnaporthe oryzae Interaction: What Have We Learned So Far? FRONTIERS IN PLANT SCIENCE 2019; 10:1383. [PMID: 31737011 PMCID: PMC6828948 DOI: 10.3389/fpls.2019.01383] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/07/2019] [Indexed: 05/21/2023]
Abstract
Rice blast disease, caused by Magnaporthe oryzae, is one of the major constraints to rice production, which feeds half of the world's population. Proteomic technologies have been used as effective tools in plant-pathogen interactions to study the biological pathways involved in pathogen infection, plant response, and disease progression. Advancements in mass spectrometry (MS) and apoplastic and plasma membrane protein isolation methods facilitated the identification and quantification of subcellular proteomes during plant-pathogen interaction. Proteomic studies conducted during rice-M. oryzae interaction have led to the identification of several proteins eminently involved in pathogen perception, signal transduction, and the adjustment of metabolism to prevent plant disease. Some of these proteins include receptor-like kinases (RLKs), mitogen-activated protein kinases (MAPKs), and proteins related to reactive oxygen species (ROS) signaling and scavenging, hormone signaling, photosynthesis, secondary metabolism, protein degradation, and other defense responses. Moreover, post-translational modifications (PTMs), such as phosphoproteomics and ubiquitin proteomics, during rice-M. oryzae interaction are also summarized in this review. In essence, proteomic studies carried out to date delineated the molecular mechanisms underlying rice-M. oryzae interactions and provided candidate proteins for the breeding of rice blast resistant cultivars.
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Affiliation(s)
- Qingfeng Meng
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard, New Delhi, India
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Soon Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Byoung Il Je
- Department of Horticultural Bioscience, Pusan National University, Miryang, South Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
- *Correspondence: Sun Tae Kim,
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12
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Physiological and TMT-based proteomic analysis of oat early seedlings in response to alkali stress. J Proteomics 2018; 193:10-26. [PMID: 30576833 DOI: 10.1016/j.jprot.2018.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/07/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
Oats are an important cereal crop worldwide, and they also serve as a phytoremediation crop to ameliorate salinized and alkalized soils. However, the mechanism of the oat response to alkali remains unclear. Physiological and tandem mass tag (TMT)-based proteomic analyses were employed to elucidate the mechanism of the oat response to alkali stress. Physiological and phenotypic data showed that oat root growth was inhibited more severely than shoot growth after alkali stress. In total, 164 proteins were up-regulated and 241 proteins were down-regulated in roots, and 93 proteins were up-regulated and 139 proteins were down-regulated in shoots. Under high pH stress, transmembrane proton transporters were down-regulated; conversely, organic acid synthesis related enzymes were increased. Transporters of N, P, Fe, Cu and Ca in addition to N assimilation enzymes in the root were highly increased. This result revealed that higher efficiency of P, Fe, Cu and Ca transport, especially higher efficiency of N intake and assimilation, greatly promoted oat root resistance to alkali stress. Furthermore, many resistance proteins, such as late embryogenesis abundant (LEA) mainly in shoots, GDSL esterase lipase mainly in roots, and WD40-like beta propeller repeat families, greatly accumulated to contribute to oat resistance to alkali stress. SIGNIFICANCE: In this study, physiological and tandem mass tag (TMT)-based proteomic analyses were employed to elucidate oats early seedlings in response to alkali stress. Many difference expression proteins were found involving in oats response to alkali stress. Also, higher efficiency transport of P, Fe, Cu, Ca and N greatly promoted oat resistance to alkali stress.
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13
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Wang J, Wang J, Wang X, Li R, Chen B. Proteomic response of hybrid wild rice to cold stress at the seedling stage. PLoS One 2018; 13:e0198675. [PMID: 29879216 PMCID: PMC5991693 DOI: 10.1371/journal.pone.0198675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
Low temperature at the seedling stage is a major damaging factor for rice production in southern China. To better understand the cold response of cultivated and wild rice, cold-sensitive cultivar 93–11 (Oryza sativa L. ssp. Indica) and cold-resistant hybrid wild rice DC907 with a 93–11 genetic background were used for a quantitative proteomic analysis with tandem mass tags (TMT) in parallel. Rice seedlings grown for four weeks at a normal temperature (25°C) were treated at 8–10°C for 24, 72 and 120 h. The number of differentially expressed proteins increased gradually over time in the cold-exposed rice in comparison with the untreated rice. A total of 366 unique proteins involved in ATP synthesis, photosystem, reactive oxygen species, stress response, cell growth and integrity were identified as responding to cold stress in DC907. While both DC907 and 93–11 underwent similar alterations in proteomic profiles in response to cold stress, DC907 responded in a prompter manner in terms of expressing cold-responding proteins, maintained a higher level of photosynthesis to power the cells, and possessed a stable and higher level of DIR proteins to prevent the plant from obtaining irreversible cell structure damage. The observations made in this study may lay a new foundation for further investigation of cold sensitivity or tolerance mechanisms in rice.
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Affiliation(s)
- Jinzi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| | - Jun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xin Wang
- College of Agriculture, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
- * E-mail: (BC); (RL)
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
- * E-mail: (BC); (RL)
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14
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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15
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Barnabas L, Ashwin NMR, Kaverinathan K, Trentin AR, Pivato M, Sundar AR, Malathi P, Viswanathan R, Rosana OB, Neethukrishna K, Carletti P, Arrigoni G, Masi A, Agrawal GK, Rakwal R. Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum. Proteomics 2016; 16:1111-22. [PMID: 26857420 DOI: 10.1002/pmic.201500245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 01/05/2016] [Accepted: 02/02/2016] [Indexed: 02/05/2023]
Abstract
Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum.
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Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - N M R Ashwin
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - K Kaverinathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Anna Rita Trentin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Micaela Pivato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - A Ramesh Sundar
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - P Malathi
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - R Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - O B Rosana
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - K Neethukrishna
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center of Padova University, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal.,Tsukuba International Academy for Sport Studies (TIAS) and Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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16
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Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
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Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
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17
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Barnabas L, Ramadass A, Amalraj RS, Palaniyandi M, Rasappa V. Sugarcane proteomics: An update on current status, challenges, and future prospects. Proteomics 2016; 15:1658-70. [PMID: 25641866 DOI: 10.1002/pmic.201400463] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/27/2014] [Accepted: 01/09/2015] [Indexed: 12/23/2022]
Abstract
Sugarcane is one of the most important commercial crops cultivated worldwide for the production of crystal sugar, ethanol, and other related by-products. Unlike other comparable monocots like sorghum, maize, and rice, sugarcane genome by virtue of its polyploidy nature remains yet to be fully deciphered. Proteomics-an established complementary tool to genomics is at its infancy in sugarcane as compared to the other monocots. However, with the surge in genomics research accomplished by next-generation sequencing platforms, sugarcane proteomics has gained momentum. This review summarizes the available literature from 1970 to 2014, which ensures a comprehensive coverage on sugarcane proteomics-a topic first of its kind to be reviewed. We herewith compiled substantial contributions in different areas of sugarcane proteomics, which include abiotic and biotic stresses, cell wall, organelle, and structural proteomics. The past decade has witnessed a paradigm shift in the pace with which sugarcane proteomics is progressing, as evident by the number of research publications. In addition to extensively reviewing the progress made thus far, we intend to highlight the scope in sugarcane proteomics, with an aspiration to instigate focused research on sugarcane to harness its full potential for the human welfare.
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Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Ashwin Ramadass
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Ramesh Sundar Amalraj
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Malathi Palaniyandi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Viswanathan Rasappa
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
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18
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Wang L, Cao H, Chen C, Yue C, Hao X, Yang Y, Wang X. Complementary transcriptomic and proteomic analyses of a chlorophyll-deficient tea plant cultivar reveal multiple metabolic pathway changes. J Proteomics 2015; 130:160-9. [PMID: 26344129 DOI: 10.1016/j.jprot.2015.08.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/04/2015] [Accepted: 08/27/2015] [Indexed: 02/03/2023]
Abstract
To uncover the mechanisms that underlie the chlorina phenotype of the tea plant, this study employs morphological, biochemical, transcriptomic, and iTRAQ-based proteomic analyses to compare the green tea cultivar LJ43 and the yellow-leaf tea cultivar ZH1. ZH1 exhibited the chlorina phenotype, with significantly decreased chlorophyll content and abnormal chloroplast development compared with LJ43. ZH1 also displayed higher theanine and free amino acid content and lower carotenoid and catechin content. Microarray and iTRAQ analyses indicated that the differentially expressed genes and proteins could be mapped to the following pathways: 'phenylpropanoid biosynthesis,' 'glutathione metabolism,' 'phenylalanine metabolism,' 'photosynthesis,' and 'flavonoid biosynthesis.' Altered gene and protein levels in these pathways may account for the increased amino acid content and reduced chlorophyll and flavonoid content of ZH1. Altogether, this study combines transcriptomic and proteomic approaches to better understand the mechanisms responsible for the chlorina phenotype.
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Affiliation(s)
- Lu Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Hongli Cao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu'an 355000, China.
| | - Chuan Yue
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Yajun Yang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Xinchao Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
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19
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Proteomic changes in rice leaves grown under open field high temperature stress conditions. Mol Biol Rep 2015; 42:1545-58. [PMID: 26323334 DOI: 10.1007/s11033-015-3923-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 08/25/2015] [Indexed: 12/18/2022]
Abstract
The interactive effect of temperature with other climatic and soil factors has profound influences on the growth and development of rice. The responses of rice to high temperatures under field conditions are more important than those under the controlled conditions. To understand the genes associated with high temperature stress response in general and tolerance in particular, the expression of all those genes associated with adaptation and tolerance in rice requires proteomic analysis. High temperature stress-tolerant cv. N22 was subjected to 28/18 °C (control) and 42/32 °C (high temperature stress) at flowering stage. The plants were grown in the field under the free air temperature increment condition. The proteomic changes in rice leaves due to high temperature stress were discussed. The proteomes of leaves had about 3000 protein spots, reproducibly detected on 2-dimensional electrophoretic gels with 573 proteins differentially expressed between the control and the high temperature treatments. Putative physiological functions suggested five categories such as growth (15.4%), heat shock proteins (7.7%), regulatory proteins (26.9%), redox homeostasis proteins (11.5%) and energy and metabolism (38.5%) related proteins. The results of the present study suggest that cv. N22, an agronomically recognized temperature tolerant rice cultivar copes with high temperature stress in a complex manner. Several functional proteins play important roles in its responses. The predicted climate change events necessitate more studies using this cultivar under different simulated ecological conditions to identify proteomic changes and the associated genes to be used as biomarkers and to gain a better understanding on the biochemical pathways involved in tolerance.
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20
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Wang B, Hajano JUD, Ren Y, Lu C, Wang X. iTRAQ-based quantitative proteomics analysis of rice leaves infected by Rice stripe virus reveals several proteins involved in symptom formation. Virol J 2015; 12:99. [PMID: 26113023 PMCID: PMC4489111 DOI: 10.1186/s12985-015-0328-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/18/2015] [Indexed: 01/17/2023] Open
Abstract
Background Rice plants infected by Rice stripe virus (RSV) usually leads to chlorosis and death of newly emerged leaves. However, the mechanism of RSV-induced these symptoms was not clear. Methods We used an iTRAQ approach for a quantitative proteomics comparison of non-infected and infected rice leaves. RT-qPCR and Northern blot analyses were performed for assessing the transcription of candidate genes. Results As a whole, 681 (65.8 % downregulated, 34.2 % upregulated infected vs. non-infected) differentially accumulated proteins were identified. A bioinformatics analysis indicated that ten of these regulated proteins are involved in chlorophyll biosynthesis and three in cell death processes. Subsequent RT-qPCR results showed that downregulation of magnesium chelatase was due to reduced expression levels of the genes encoding subunits CHLI and CHLD, which resulted in chlorophyll reduction involved in leaf chlorosis. Three aspartic proteases expressed higher in RSV-infected leaves than those in the control leaves, which were also implicated in RSV-induced cell death. Northern blot analyses of CHLI and p0026h03.19 confirmed the RT-qPCR results. Conclusions The magnesium chelatase and aspartic proteases may be associated with RSV-induced leaf chlorosis and cell death, respectively. The findings may yield new insights into mechanisms underlying rice stripe disease symptom formation. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0328-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
| | - Jamal-U-Ddin Hajano
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
| | - Yingdang Ren
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, China.
| | - Chuantao Lu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
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21
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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Gupta R, Kim ST. Depletion of RuBisCO protein using the protamine sulfate precipitation method. Methods Mol Biol 2015; 1295:225-33. [PMID: 25820725 DOI: 10.1007/978-1-4939-2550-6_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a major high-abundant protein (HAP) in the plant leaves which hinders analysis of low-abundant proteins (LAP). In this chapter, we describe a highly simple RuBisCO depletion method using protamine sulfate (PS). Addition of 0.1 % PS is sufficient to precipitate the RuBisCO from the leaf extracts of diverse plants including monocots and dicots. Our results of SDS-PAGE, Western blotting, and two-dimensional gel electrophoresis showed that both large and small subunits of RuBisCO were precipitated in the pellet fractions, while LAPs were enriched in the supernatant fraction after PS precipitation.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, Republic of Korea
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Phelix CF, Feltus FA. Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome (TTM) technology - effects of drought stress on rice. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:63-73. [PMID: 24985701 DOI: 10.1111/plb.12221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
Measuring biomarkers from plant tissue samples is challenging and expensive when the desire is to integrate transcriptomics, fluxomics, metabolomics, lipidomics, proteomics, physiomics and phenomics. We present a computational biology method where only the transcriptome needs to be measured and is used to derive a set of parameters for deterministic kinetic models of metabolic pathways. The technology is called Transcriptome-To-Metabolome (TTM) biosimulations, currently under commercial development, but available for non-commercial use by researchers. The simulated results on metabolites of 30 primary and secondary metabolic pathways in rice (Oryza sativa) were used as the biomarkers to predict whether the transcriptome was from a plant that had been under drought conditions. The rice transcriptomes were accessed from public archives and each individual plant was simulated. This unique quality of the TTM technology allows standard analyses on biomarker assessments, i.e. sensitivity, specificity, positive and negative predictive values, accuracy, receiver operator characteristics (ROC) curve and area under the ROC curve (AUC). Two validation methods were also used, the holdout and 10-fold cross validations. Initially 17 metabolites were identified as candidate biomarkers based on either statistical significance on binary phenotype when compared with control samples or recognition from the literature. The top three biomarkers based on AUC were gibberellic acid 12 (0.89), trehalose (0.80) and sn1-palmitate-sn2-oleic-phosphatidylglycerol (0.70). Neither heat map analyses of transcriptomes nor all 300 metabolites clustered the stressed and control groups effectively. The TTM technology allows the emergent properties of the integrated system to generate unique and useful 'Omics' information.
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Affiliation(s)
- C F Phelix
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA; AL Phahelix Biometrics, Inc., San Antonio, TX, USA
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Proteomic analysis of upland rice (Oryza sativa L.) exposed to intermittent water deficit. Protein J 2014; 33:221-30. [PMID: 24652039 DOI: 10.1007/s10930-014-9554-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Rice is the most important crop consumed all over the world. In Brazil, irrigated rice covers 50 % of the rice producing area and is responsible for 75 % of the national production. Upland rice covers most of the remaining area, and is therefore, a very important production system in the country. In the present study, we have used the drought tolerant upland rice variety Três Meses Antigo to investigate the proteomic changes that occur during drought stress. Plants were submitted to drought by the reposition of 50 % of the water lost daily. Twenty days after the beginning of the drought stress period, leaves were harvested and used for protein extraction. The 2D maps obtained from treated and control plants revealed 408 reproducible spots, 44 of which were identified by mass spectrometry, including 15 differential proteins. Several unaltered proteins were also identified (39 spots) and were mainly involved in photosynthesis. Taken together, the results obtained suggest that the tolerant upland rice up-regulates anti-oxidant and energy production related proteins in order to cope with water deficit.
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Martínez-Cortés T, Pomar F, Merino F, Novo-Uzal E. A proteomic approach to Physcomitrella patens rhizoid exudates. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1671-8. [PMID: 25179523 DOI: 10.1016/j.jplph.2014.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 08/09/2014] [Accepted: 08/11/2014] [Indexed: 05/07/2023]
Abstract
The interaction between plants and the surrounding environment has been widely studied, specially the defence reactions and the plant-plant interactions. One of the most remarkable metabolic features of plant roots is the ability to secrete a vast array of compounds into the rhizosphere, not only of low molecular weight but also polysaccharides and proteins. Here, we took advantage of proteomics to study the rhizoid exudates of Physcomitrella patens at early and late development stages (7 and 28 days of culture in liquid medium). Samples were extracted, separated and detected with nanoLC-MALDI-TOF/TOF MS/MS, identifying 47 proteins at the development stage of 7 days, and 66 proteins at 28 days. Moreover, 21 proteins were common to the two analyzed periods. All the identified proteins were classified into 8 functional categories: response to stress, response to stimulus, oxido-reduction, cell wall modification, photosynthesis and carbohydrate metabolism, transport, DNA metabolic process and regulation/signalling. Our results show important differences in the protein expression profile along the development of P. patens, mainly at the level of regulation- and senescence-related proteins. Defence-related proteins, such as chitinases, thaumatins and peroxidases have a major role in the interaction of P. patens with the environment.
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Affiliation(s)
- Teresa Martínez-Cortés
- Department of Animal Biology, Plant Biology and Ecology. University of A Coruña, E-15071 A Coruña, Spain; Present address: IBMC. University of Porto, E- 4150-180 Porto, Portugal
| | - Federico Pomar
- Department of Animal Biology, Plant Biology and Ecology. University of A Coruña, E-15071 A Coruña, Spain
| | - Fuencisla Merino
- Department of Animal Biology, Plant Biology and Ecology. University of A Coruña, E-15071 A Coruña, Spain
| | - Esther Novo-Uzal
- Department of Plant Biology. University of Murcia. E-30100 Murcia, Spain.
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Wongpia A, Mahatheeranont S, Lomthaisong K, Niamsup H. Evaluation of Sample Preparation Methods from Rice Seeds and Seedlings Suitable for Two-Dimensional Gel Electrophoresis. Appl Biochem Biotechnol 2014; 175:1035-51. [DOI: 10.1007/s12010-014-1333-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022]
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Yang Y, Zhu K, Xia H, Chen L, Chen K. Comparative proteomic analysis of indica and japonica rice varieties. Genet Mol Biol 2014; 37:652-61. [PMID: 25505840 PMCID: PMC4261965 DOI: 10.1590/s1415-47572014005000015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/10/2014] [Indexed: 11/24/2022] Open
Abstract
Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93–11 and Nipponbare). In all, 47 proteins that differed significantly between 93–11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was expressed specifically in 93–11; these differences were confirmed by quantitative real-time PCR and proteomic analysis of other indica and japonica rice varieties. This is the first report to successfully demonstrate differences in the protein composition of indica and japonica rice varieties and to identify candidate proteins and genes for future investigation of their roles in the differentiation of indica and japonica rice.
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Affiliation(s)
- Yanhua Yang
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Keming Zhu
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Hengchuan Xia
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Liang Chen
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Keping Chen
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
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Kim JY, Wu J, Kwon SJ, Oh H, Lee SE, Kim SG, Wang Y, Agrawal GK, Rakwal R, Kang KY, Ahn IP, Kim BG, Kim ST. Proteomics of rice and Cochliobolus miyabeanus
fungal interaction: Insight into proteins at intracellular and extracellular spaces. Proteomics 2014; 14:2307-18. [DOI: 10.1002/pmic.201400066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/16/2014] [Accepted: 07/17/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Jin Yeong Kim
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - Jingni Wu
- Department of Plant Microbe Interactions; Max-Planck Institute for Plant Breeding Research; Cologne Germany
| | - Soon Jae Kwon
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - Haram Oh
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - So Eui Lee
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
| | - Sang Gon Kim
- National Institute of Crop Science; Rural Development Administration; Suwon South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions; Max-Planck Institute for Plant Breeding Research; Cologne Germany
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Pvt. Ltd; Birgunj Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Pvt. Ltd; Birgunj Nepal
- Organization for Educational Initiatives; University of Tsukuba; Tsukuba Ibaraki Japan
- Department of Anatomy I; Showa University School of Medicine; Shinagawa Tokyo Japan
| | - Kyu Young Kang
- Division of Applied Life Science; Gyeongsang National University; Jinju South Korea
| | - Il-Pyung Ahn
- Molecular Breeding division; National Academy of Agricultural Science, RDA; Suwon South Korea
| | - Beom-Gi Kim
- Molecular Breeding division; National Academy of Agricultural Science, RDA; Suwon South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience; Life and Industry Convergence Research Institute, Pusan National University; Miryang South Korea
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Hayashi G, Shibato J, Imanaka T, Cho K, Kubo A, Kikuchi S, Satoh K, Kimura S, Ozawa S, Fukutani S, Endo S, Ichikawa K, Agrawal GK, Shioda S, Fukumoto M, Rakwal R. Unraveling Low-Level Gamma Radiation-Responsive Changes in Expression of Early and Late Genes in Leaves of Rice Seedlings at litate Village, Fukushima. J Hered 2014; 105:723-38. [DOI: 10.1093/jhered/esu025] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Jaiswal DK, Ray D, Choudhary MK, Subba P, Kumar A, Verma J, Kumar R, Datta A, Chakraborty S, Chakraborty N. Comparative proteomics of dehydration response in the rice nucleus: new insights into the molecular basis of genotype-specific adaptation. Proteomics 2014; 13:3478-97. [PMID: 24133045 DOI: 10.1002/pmic.201300284] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/10/2013] [Accepted: 09/23/2013] [Indexed: 01/04/2023]
Abstract
Dehydration is the most crucial environmental factor that considerably reduces the crop harvest index, and thus has become a concern for global agriculture. To better understand the role of nuclear proteins in water-deficit condition, a nuclear proteome was developed from a dehydration-sensitive rice cultivar IR-64 followed by its comparison with that of a dehydration-tolerant c.v. Rasi. The 2DE protein profiling of c.v. IR-64 coupled with MS/MS analysis led to the identification of 93 dehydration-responsive proteins (DRPs). Among those identified proteins, 78 were predicted to be destined to the nucleus, accounting for more than 80% of the dataset. While the detected number of protein spots in c.v. IR-64 was higher when compared with that of Rasi, the number of DRPs was found to be less. Fifty-seven percent of the DRPs were found to be common to both sensitive and tolerant cultivars, indicating significant differences between the two nuclear proteomes. Further, we constructed a functional association network of the DRPs of c.v. IR-64, which suggests that a significant number of the proteins are capable of interacting with each other. The combination of nuclear proteome and interactome analyses would elucidate stress-responsive signaling and the molecular basis of dehydration tolerance in plants.
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31
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Proteome alterations of reverse photoperiod-sensitive genic male sterile rice (Oryza sativa L.) at fertility transformation stage. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0205-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Dupae J, Bohler S, Noben JP, Carpentier S, Vangronsveld J, Cuypers A. Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions. J Proteomics 2014; 108:30-54. [PMID: 24821411 DOI: 10.1016/j.jprot.2014.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/07/2014] [Accepted: 04/15/2014] [Indexed: 01/14/2023]
Abstract
UNLABELLED This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed. BIOLOGICAL SIGNIFICANCE This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.
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Affiliation(s)
- Joke Dupae
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Sacha Bohler
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Jean-Paul Noben
- Biomedical Institute, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Sebastien Carpentier
- Afdeling Plantenbiotechniek, Catholic University Leuven, Willem de Croylaan 42 - bus 2455, 3001 Leuven, Belgium.
| | - Jaco Vangronsveld
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Ann Cuypers
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
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Abstract
Substantial evidences implicate that sample preparation and protein extraction in proteomic studies of plant-pathogen interactions are critical to understand cross talk between host and pathogen. Therefore, interest is growing in applying proteomics techniques to investigate simultaneously secreted proteins from rice and pathogen. We have found, however, that most proteins of interest are low abundant so that proper prefractionation or extraction of secreted proteins from extracellular space (ECS) in the rice leaf is required to excavate relevant protein. This chapter describes the preparation of sample and extraction procedure to enrich the proteins interested before separation by 2-DE or LC-MS/MS. This method significantly increases the sensitivity of proteomic comparisons.
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Li Y, Nie Y, Zhang Z, Ye Z, Zou X, Zhang L, Wang Z. Comparative proteomic analysis of methyl jasmonate-induced defense responses in different rice cultivars. Proteomics 2014; 14:1088-101. [DOI: 10.1002/pmic.201300104] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 01/20/2014] [Accepted: 01/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Yunfeng Li
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Yanfang Nie
- College of Natural Resources and Environment; South China Agricultural University; Guangzhou P. R. China
| | - Zhihui Zhang
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Zhijian Ye
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Xiaotao Zou
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Zhenzhong Wang
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
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Kim ST, Kim SG, Agrawal GK, Kikuchi S, Rakwal R. Rice proteomics: a model system for crop improvement and food security. Proteomics 2014; 14:593-610. [PMID: 24323464 DOI: 10.1002/pmic.201300388] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/24/2013] [Accepted: 11/07/2013] [Indexed: 12/14/2022]
Abstract
Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.
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Affiliation(s)
- Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
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36
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Neilson KA, George IS, Emery SJ, Muralidharan S, Mirzaei M, Haynes PA. Analysis of rice proteins using SDS-PAGE shotgun proteomics. Methods Mol Biol 2014; 1072:289-302. [PMID: 24136530 DOI: 10.1007/978-1-62703-631-3_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.
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Affiliation(s)
- Karlie A Neilson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
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37
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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38
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Collado-Romero M, Alós E, Prieto P. Unravelling the proteomic profile of rice meiocytes during early meiosis. FRONTIERS IN PLANT SCIENCE 2014; 5:356. [PMID: 25104955 PMCID: PMC4109522 DOI: 10.3389/fpls.2014.00356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/03/2014] [Indexed: 05/06/2023]
Abstract
Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene, or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodeling, nucleic acid binding, cell-cycle regulation, and cytoskeleton. Moreover, the putative roles of 16 proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins [such as SKP1 (OSK), a putative CDK2 like effector], a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs. The data have been deposited to the ProteomeXchange with the PXD001058 identifier.
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Affiliation(s)
| | | | - Pilar Prieto
- *Correspondence: Pilar Prieto, Plant Breeding Department, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Av. Menéndez Pidal s/n, Campus Alameda del Obispo, Apartado 4084, Córdoba 14080, Spain e-mail:
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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J Proteomics 2013; 93:5-19. [DOI: 10.1016/j.jprot.2013.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
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40
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Zi J, Zhang J, Wang Q, Zhou B, Zhong J, Zhang C, Qiu X, Wen B, Zhang S, Fu X, Lin L, Liu S. Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One 2013; 8:e74229. [PMID: 24058531 PMCID: PMC3776822 DOI: 10.1371/journal.pone.0074229] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.
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Affiliation(s)
- Jin Zi
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiyuan Zhang
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Quanhui Wang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Baojin Zhou
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Junyan Zhong
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | | | - Xuemei Qiu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Bo Wen
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Shenyan Zhang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiqin Fu
- Hunan Hybrid Rice Research Center, Changsha, China
| | - Liang Lin
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- * E-mail: (LL); (SL)
| | - Siqi Liu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (LL); (SL)
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41
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Singh R, Jwa NS. Understanding the Responses of Rice to Environmental Stress Using Proteomics. J Proteome Res 2013; 12:4652-69. [DOI: 10.1021/pr400689j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raksha Singh
- Department of Molecular Biology,
College of Life Sciences, Sejong University, Gunja-dong, Gwangjin-gu, Seoul 143-747, Republic of Korea
| | - Nam-Soo Jwa
- Department of Molecular Biology,
College of Life Sciences, Sejong University, Gunja-dong, Gwangjin-gu, Seoul 143-747, Republic of Korea
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42
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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43
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Neilson KA, Scafaro AP, Chick JM, George IS, Van Sluyter SC, Gygi SP, Atwell BJ, Haynes PA. The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings. Proteomics 2013; 13:1922-33. [DOI: 10.1002/pmic.201200475] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/06/2012] [Accepted: 02/07/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Karlie A. Neilson
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
| | - Andrew P. Scafaro
- Department of Biological Sciences, Macquarie University; New South Wales Australia
| | - Joel M. Chick
- Department of Cell Biology, Harvard Medical School; MA USA
| | - Iniga S. George
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
| | - Steven C. Van Sluyter
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School; MA USA
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University; New South Wales Australia
| | - Paul A. Haynes
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
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44
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Yang Y, Dai L, Xia H, Zhu K, Liu H, Chen K. Protein profile of rice (Oryza sativa) seeds. Genet Mol Biol 2013; 36:87-92. [PMID: 23569412 PMCID: PMC3615530 DOI: 10.1590/s1415-47572013000100012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/23/2012] [Indexed: 11/21/2022] Open
Abstract
Seeds are the most important plant storage organ and play a central role in the life cycle of plants. Since little is known about the protein composition of rice (Oryza sativa) seeds, in this work we used proteomic methods to obtain a reference map of rice seed proteins and identify important molecules. Overall, 480 reproducible protein spots were detected by two-dimensional electrophoresis on pH 4-7 gels and 302 proteins were identified by MALDI-TOF MS and database searches. Together, these proteins represented 252 gene products and were classified into 12 functional categories, most of which were involved in metabolic pathways. Database searches combined with hydropathy plots and gene ontology analysis showed that most rice seed proteins were hydrophilic and were related to binding, catalytic, cellular or metabolic processes. These results expand our knowledge of the rice proteome and improve our understanding of the cellular biology of rice seeds.
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Affiliation(s)
- Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, PR China
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45
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Proteome Analysis of Rice (Oryza sativa L.) Mutants Reveals Differentially Induced Proteins during Brown Planthopper (Nilaparvata lugens) Infestation. Int J Mol Sci 2013; 14:3921-45. [PMID: 23434671 PMCID: PMC3588078 DOI: 10.3390/ijms14023921] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 01/20/2013] [Accepted: 01/22/2013] [Indexed: 01/02/2023] Open
Abstract
Although rice resistance plays an important role in controlling the brown planthopper (BPH), Nilaparvata lugens, not all varieties have the same level of protection against BPH infestation. Understanding the molecular interactions in rice defense response is an important tool to help to reveal unexplained processes that underlie rice resistance to BPH. A proteomics approach was used to explore how wild type IR64 and near-isogenic rice mutants with gain and loss of resistance to BPH respond during infestation. A total of 65 proteins were found markedly altered in wild type IR64 during BPH infestation. Fifty-two proteins associated with 11 functional categories were identified using mass spectrometry. Protein abundance was less altered at 2 and 14 days after infestation (DAI) (T1, T2, respectively), whereas higher protein levels were observed at 28 DAI (T3). This trend diminished at 34 DAI (T4). Comparative analysis of IR64 with mutants showed 22 proteins that may be potentially associated with rice resistance to the brown planthopper (BPH). Ten proteins were altered in susceptible mutant (D1131) whereas abundance of 12 proteins including S-like RNase, Glyoxalase I, EFTu1 and Salt stress root protein “RS1” was differentially changed in resistant mutant (D518). S-like RNase was found in greater quantities in D518 after BPH infestation but remained unchanged in IR64 and decreased in D1131. Taken together, this study shows a noticeable level of protein abundance in the resistant mutant D518 compared to the susceptible mutant D1131 that may be involved in rendering enhanced level of resistance against BPH.
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46
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Liang C, Tian J, Liao H. Proteomics dissection of plant responses to mineral nutrient deficiency. Proteomics 2013. [PMID: 23193087 DOI: 10.1002/pmic.201200263] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plants require at least 17 essential nutrients to complete their life cycle. Except for carbon, hydrogen, and oxygen, other essential nutrients are mineral nutrients, which are mainly acquired from soils by roots. In natural soils, the availability of most essential mineral nutrients is very low and hard to meet the demand of plants. Developing crops with high nutrient efficiency is essential for sustainable agriculture, which requires more understandings of crop responses to mineral nutrient deficiency. Proteomic techniques provide a crucial and complementary tool to dissect molecular mechanisms underlying crop adaptation to mineral nutrient deficiency in the rapidly processing postgenome era. This review gives a comparative overview about identification of mineral nutrient deficiency responsive proteins using proteomic analysis, and discusses the current status for crop proteomics and its challenges to be integrated into systems biology approaches for developing crops with high mineral nutrient efficiency.
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Affiliation(s)
- Cuiyue Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, South China Agricultural University, Guangzhou, P. R. China
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47
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Kim SG, Wang Y, Lee KH, Park ZY, Park J, Wu J, Kwon SJ, Lee YH, Agrawal GK, Rakwal R, Kim ST, Kang KY. In-depth insight into in vivo apoplastic secretome of rice-Magnaporthe oryzae interaction. J Proteomics 2013; 78:58-71. [DOI: 10.1016/j.jprot.2012.10.029] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/04/2012] [Accepted: 10/26/2012] [Indexed: 12/22/2022]
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48
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Gong CY, Wang T. Proteomic evaluation of genetically modified crops: current status and challenges. FRONTIERS IN PLANT SCIENCE 2013; 4:41. [PMID: 23471542 PMCID: PMC3590489 DOI: 10.3389/fpls.2013.00041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/19/2013] [Indexed: 05/07/2023]
Abstract
Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. "Omics" techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques.
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Affiliation(s)
| | - Tai Wang
- *Correspondence: Tai Wang, Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Haidianqu, Beijing 100093, China. e-mail:
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49
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Agrawal GK, Jwa NS, Jung YH, Kim ST, Kim DW, Cho K, Shibato J, Rakwal R. Rice proteomic analysis: sample preparation for protein identification. Methods Mol Biol 2013; 956:151-84. [PMID: 23135851 DOI: 10.1007/978-1-62703-194-3_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Rice is one of the most important food and cereal crop plants in the world. Rice proteomics began in the 1990s. Since then, considerable progress has been made in establishing protocols from isolation of rice proteins from different tissues, organs, and organelles, to separation of complex proteins and to their identification by mass spectrometry. Since the year 2000, global proteomics studies have been performed during growth and development under numerous biotic and abiotic environmental conditions. Two-dimensional (2-D) gel-based proteomics platform coupled with mass spectrometry has been retained as the workhorse for proteomics of a variety of rice samples. In this chapter, we describe in detail the different protocols used for isolation of rice proteins, their separation, detection, and identification using gel-based proteomics and mass spectrometry approaches.
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50
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Alam I, Sharmin SA, Kim KH, Kim YG, Lee JJ, Lee BH. An improved plant leaf protein extraction method for high resolution two-dimensional polyacrylamide gel electrophoresis and comparative proteomics. Biotech Histochem 2012; 88:61-75. [DOI: 10.3109/10520295.2012.729863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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