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Hong WJ, Jiang X, Choi SH, Kim YJ, Kim ST, Jeon JS, Jung KH. A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity. PLANTS 2021; 10:plants10081690. [PMID: 34451735 PMCID: PMC8401045 DOI: 10.3390/plants10081690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 02/01/2023]
Abstract
Carbohydrate metabolism is an important biochemical process related to developmental growth and yield-related traits. Due to global climate change and rapid population growth, increasing rice yield has become vital. To understand whole carbohydrate metabolism pathways and find related clues for enhancing yield, genes in whole carbohydrate metabolism pathways were systemically dissected using meta-transcriptome data. This study identified 866 carbohydrate genes from the MapMan toolkit and the Kyoto Encyclopedia of Genes and Genomes database split into 11 clusters of different anatomical expression profiles. Analysis of functionally characterized carbohydrate genes revealed that source activity and eating quality are the most well-known functions, and they each have a strong correlation with tissue-preferred clusters. To verify the transcriptomic dissection, three pollen-preferred cluster genes were used and found downregulated in the gori mutant. Finally, we summarized carbohydrate metabolism as a conceptual model in gene clusters associated with morphological traits. This systemic analysis not only provided new insights to improve rice yield but also proposed novel tissue-preferred carbohydrate genes for future research.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Xu Jiang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Seok-Hyun Choi
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
| | - Sun-Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
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Hong WJ, Kim YJ, Kim EJ, Kumar Nalini Chandran A, Moon S, Gho YS, Yoou MH, Kim ST, Jung KH. CAFRI-Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:532-545. [PMID: 32652789 DOI: 10.1111/tpj.14926] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 05/03/2023]
Abstract
Rice (Oryza sativa L.) is a staple crop with agricultural traits that have been intensively investigated. However, despite the variety of mutant population and multi-omics data that have been generated, rice functional genomic research has been bottlenecked due to the functional redundancy in the genome. This phenomenon has masked the phenotypes of knockout mutants by functional compensation and redundancy. Here, we present an intuitive tool, CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice (CAFRI-Rice; cafri-rice.khu.ac.kr). To create this tool, we generated a phylogenetic heatmap that can estimate the similarity between protein sequences and expression patterns, based on 2,617 phylogenetic trees and eight tissue RNA-sequencing datasets. In this study, 33,483 genes were sorted into 2,617 families, and about 24,980 genes were tested for functional redundancy using a phylogenetic heatmap approach. It was predicted that 7,075 genes would have functional redundancy, according to the threshold value validated by an analysis of 111 known genes functionally characterized using knockout mutants and 5,170 duplicated genes. In addition, our analysis demonstrated that an anther/pollen-preferred gene cluster has more functional redundancy than other clusters. Finally, we showed the usefulness of the CAFRI-Rice-based approach by overcoming the functional redundancy between two root-preferred genes via loss-of-function analyses as well as confirming the functional dominancy of three genes through a literature search. This CAFRI-Rice-based target selection for CRISPR/Cas9-mediated mutagenesis will not only accelerate functional genomic studies in rice but can also be straightforwardly expanded to other plant species.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Eui-Jung Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Myeong-Hyun Yoou
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
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Rice Senescence-Induced Receptor-Like Kinase ( OsSRLK) Is Involved in Phytohormone-Mediated Chlorophyll Degradation. Int J Mol Sci 2019; 21:ijms21010260. [PMID: 31905964 PMCID: PMC6982081 DOI: 10.3390/ijms21010260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 01/26/2023] Open
Abstract
Chlorophyll breakdown is a vital catabolic process of leaf senescence as it allows the recycling of nitrogen and other nutrients. In the present study, we isolated rice senescence-induced receptor-like kinase (OsSRLK), whose transcription was upregulated in senescing rice leaves. The detached leaves of ossrlk mutant (ossrlk) contained more green pigment than those of the wild type (WT) during dark-induced senescence (DIS). HPLC and immunoblot assay revealed that degradation of chlorophyll and photosystem II proteins was repressed in ossrlk during DIS. Furthermore, ultrastructural analysis revealed that ossrlk leaves maintained the chloroplast structure with intact grana stacks during dark incubation; however, the retained green color and preserved chloroplast structures of ossrlk did not enhance the photosynthetic competence during age-dependent senescence in autumn. In ossrlk, the panicles per plant was increased and the spikelets per panicle were reduced, resulting in similar grain productivity between WT and ossrlk. By transcriptome analysis using RNA sequencing, genes related to phytohormone, senescence, and chlorophyll biogenesis were significantly altered in ossrlk compared to those in WT during DIS. Collectively, our findings indicate that OsSRLK may degrade chlorophyll by participating in a phytohormone-mediated pathway.
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Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84 T and Silicon. Int J Mol Sci 2019; 20:ijms20235883. [PMID: 31771205 PMCID: PMC6928808 DOI: 10.3390/ijms20235883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023] Open
Abstract
Plant-growth-promoting bacteria (PGPB) are beneficial microorganisms that can also protect against disease and environmental stress. Silicon (Si) is the second most abundant element in soil, and is known to increase plant growth, grain yield, resistance to biotic stress, and tolerance to abiotic stress. Combined treatment of PGPB and Si has been shown to further enhance plant growth and crop yield. To determine the global effects of the PGPB and Si on rice growth, we compared rice plants treated with Paenibacillus yonginensis DCY84T (DCY84T) and Si with untreated rice. To identify the genes that respond to DCY84T+Si treatment in rice, we performed an RNA-Seq transcriptome analysis by sampling treated and untreated roots on a weekly basis for three weeks. Overall, 576 genes were upregulated, and 394 genes were downregulated in treated roots, using threshold fold-changes of at least 2 (log2) and p-values < 0.05. Gene ontology analysis showed that phenylpropanoids and the L-phenylalanine metabolic process were prominent in the upregulated genes. In a metabolic overview analysis using the MapMan toolkit, pathways involving phenylpropanoids and ethylene were strongly associated with upregulated genes. The functions of seven upregulated genes were identified as being associated with drought stress through a literature search, and a stress experiment confirmed that plants treated with DCY84T+Si exhibited greater drought tolerance than the untreated control plants. Furthermore, the predicted protein–protein interaction network analysis associated with DCY84T+ Si suggests mechanisms underlying growth promotion and stress tolerance.
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A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6534745. [PMID: 31396532 PMCID: PMC6668530 DOI: 10.1155/2019/6534745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/18/2022]
Abstract
Chloroplasts are intracellular semiautonomous organelles central to photosynthesis and are essential for plant growth and yield. The significance of the function of chloroplast-related genes in response to climate change has not been well studied in crops. In the present study, the initial focus was on genes that were predicted to be located in the chloroplast genome in rice, a model crop plant, with genes either preferentially expressed in the leaf or ubiquitously expressed in all organs. The characteristics were analyzed by Gene Ontology (GO) enrichment and MapMan functional classification tools. It was then identified that 110 GO terms (45 for leaf expression and 65 for ubiquitous expression) and 1,695 genes mapped to MapMan overviews were strongly associated with chloroplasts. In particular, the MapMan cellular response overview revealed a close association between heat stress response and chloroplast-related genes in rice. Moreover, features of these genes in response to abiotic stress were analyzed using a large-scale publicly available transcript dataset. Consequently, the expression of 215 genes was found to be upregulated in response to high temperature stress. Conversely, genes that responded to other stresses were extremely limited. In other words, chloroplast-related genes were found to affect abiotic stress response mainly through high temperature response, with little effect on response to drought and salinity stress. These results suggest that genes involved in diurnal rhythm in the leaves participate in the reaction to recognize temperature changes in the environment. Furthermore, the predicted protein–protein interaction network analysis associated with high temperature stress is expected to provide a very important basis for the study of molecular mechanisms by which chloroplasts will respond to future climate changes.
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Zhong Z, Lin L, Chen M, Lin L, Chen X, Lin Y, Chen X, Wang Z, Norvienyeku J, Zheng H. Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection. RICE (NEW YORK, N.Y.) 2019; 12:12. [PMID: 30825020 PMCID: PMC6397267 DOI: 10.1186/s12284-019-0270-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/18/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited. RESULTS Here, we explored gene expression divergence between a japonica rice cultivar Nipponbare and an indica rice cultivar 93-11 in response to invasion by the filamentous ascomycete fungus Magnaporthe oryzae (Pyricularia oryzae), a plant pathogen that causes significant loss to rice production worldwide. We investigated differentially expressed genes in the two cultivars and observed that evolutionarily conserved orthologous genes showed highly variable expression patterns under rice blast infection. Analysis of promoter region of these differentially expressed orthologous genes revealed the existence of cis-regulatory elements associated with the differentiated expression pattern of these genes in the two rice cultivars. Further comparison of these regions in global rice population indicated their fixation and close relationship with rice population divergence. CONCLUSION We proposed that variation in the expression patterns of these orthologous genes mediated by cis-regulatory elements in the two rice cultivars, may constitute an alternative evolutionary mechanism that distinguishes these two genetically and ecologically divergent rice cultivars in response to M. oryzae infection.
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Affiliation(s)
- Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Meilian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaofeng Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yahong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xi Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Institute of Oceanography, Minjiang University, Fuzhou, 350108 China
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huakun Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Moon S, Oo MM, Kim B, Koh HJ, Oh SA, Yi G, An G, Park SK, Jung KH. Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development. RICE (NEW YORK, N.Y.) 2018; 11:28. [PMID: 29687350 PMCID: PMC5913055 DOI: 10.1186/s12284-018-0219-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Understanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development. RESULTS We performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer. CONCLUSION Through the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea
| | - Moe Moe Oo
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Backki Kim
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, South Korea
| | - Hee-Jong Koh
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, South Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Gihwan Yi
- College of Agriculture and Life Science, Daegu, 702-701, South Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea.
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Tripathi A, Chacon O, Singla-Pareek SL, Sopory SK, Sanan-Mishra N. Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice. Curr Genomics 2018; 19:21-35. [PMID: 29491730 PMCID: PMC5817874 DOI: 10.2174/1389202918666170228134530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants. In this study, the Next Generation Sequencing (NGS) was employed to profile miRNA expression levels from glyoxalase overexpressing transgenic lines. The associated targets of differentially expressed miRNAs were predicted and their functional annotation was carried out using Gene Ontology (GO) and KEGG Orthology (KO), which showed their involvement in several crucial biological pathways. The analysis of NGS datasets also identified other isoforms or isomiRs of selected miRNAs, which may have an active role in developing tolerance against salt stress. Different aspects of miRNA modifications were also studied in glyoxalase overexpressing lines.
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Affiliation(s)
- Anita Tripathi
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Osmani Chacon
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sneh Lata Singla-Pareek
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sudhir K. Sopory
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Neeti Sanan-Mishra
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D. Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. Sci Rep 2017; 7:8792. [PMID: 28821707 PMCID: PMC5562787 DOI: 10.1038/s41598-017-07035-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/21/2017] [Indexed: 01/31/2023] Open
Abstract
Flag leaves (FL) and second leaves (SL) in rice show differential aging patterns during monocarpic senescence. Coordination of aging programs between FL and SL is important for grain yield and quality. However, the molecular bases for differential aging programs between FL and SL have not been systematically explored in rice. Here, we performed mRNA-sequencing of FL and SL at six time points during grain-filling and identified four molecular bases for differential aging programs between FL and SL: phenylpropanoid biosynthesis, photosynthesis, amino acid (AA) transport, and hormone response. Of them, photosynthesis (carbon assimilation) and AA transport (nitrogen remobilization) predominantly occurred in FL and SL, respectively, during grain-filling. Unlike other molecular bases, AA transport showed consistent differential expression patterns between FL and SL in independent samples. Moreover, long-distance AA transporters showed invariant differential expression patterns between FL and SL after panicle removal, which was consistent to invariant differential nitrogen contents between FL and SL after panicle removal. Therefore, our results suggest that the supplies of carbon and nitrogen to seeds is functionally segregated between FL and SL and that long-distance AA transport is an invariant core program for high nitrogen remobilization in SL.
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Affiliation(s)
- Shinyoung Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Hyobin Jeong
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Sichul Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Jinwon Lee
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Sun-Ji Kim
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Ji-Won Park
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea. .,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea.
| | - Daehee Hwang
- Center for Plant Ageing Research, IBS, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea. .,Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, Republic of Korea.
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Kim SW, Lee SK, Jeong HJ, An G, Jeon JS, Jung KH. Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves. Sci Rep 2017; 7:8214. [PMID: 28811563 PMCID: PMC5557844 DOI: 10.1038/s41598-017-08473-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/30/2017] [Indexed: 12/13/2022] Open
Abstract
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56.6% are diurnally expressed while 47.6% of the 761 that are down-regulated by drought are also diurnal. Using the β-glucuronidase reporter system and qRT-PCR analyses, we validated expression patterns of two candidate genes, thereby supporting the reliability of our transcriptome data. MapMan analysis indicated that diurnal genes up-regulated by drought are closely associated with the starch-sucrose pathway while those that are down-regulated are involved in photosynthesis. We then confirmed that starch-sucrose contents and chlorophyll fluorescence are altered in a diurnal manner under drought stress, suggesting these metabolic diurnal alterations as a novel indicator to evaluate the drought response in rice leaves. We constructed a functional gene network associated with the starch-sucrose KEGG metabolic pathway for further functional studies, and also developed a regulatory pathway model that includes OsbZIP23 transcription factor.
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Affiliation(s)
- Seo-Woo Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sang-Kyu Lee
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Hee-Jeong Jeong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Yoo YH, Nalini Chandran AK, Park JC, Gho YS, Lee SW, An G, Jung KH. OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies. FRONTIERS IN PLANT SCIENCE 2017; 8:580. [PMID: 28491065 PMCID: PMC5405136 DOI: 10.3389/fpls.2017.00580] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/30/2017] [Indexed: 05/18/2023]
Abstract
Water deficiencies are one of the most serious challenges to crop productivity. To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from 4-week-old rice seedlings grown in soil that had been subjected to drought conditions for 2-3 d. In all, 1,098 genes were up-regulated in response to soil moisture stress for 3 d, which causes severe damage in root development after recovery, unlikely that of 2 d. Comparison with previous transcriptome data produced in drought condition indicated that more than 68% of our candidate genes were not previously identified, emphasizing the novelty of our transcriptome analysis for drought response in soil condition. We then validated the expression patterns of two candidate genes using a promoter-GUS reporter system in planta and monitored the stress response with novel molecular markers. An integrating omics tool, MapMan analysis, indicated that RING box E3 ligases in the ubiquitin-proteasome pathways are significantly stimulated by induced drought. We also analyzed the functions of 66 candidate genes that have been functionally investigated previously, suggesting the primary roles of our candidate genes in resistance or tolerance relating traits including drought tolerance (29 genes) through literature searches besides diverse regulatory roles of our candidate genes for morphological traits (15 genes) or physiological traits (22 genes). Of these, we used a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates a plant's degree of tolerance to water deficiencies through the control of total leaf area and stomatal density based on previous finding. Unlike previous result, we found that OsPhyB represses the activity of ascorbate peroxidase and catalase mediating reactive oxygen species (ROS) processing machinery required for drought tolerance of roots in soil condition, suggesting the potential significance of remaining uncharacterized candidate genes for manipulating drought tolerance in rice.
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Kumar M, Gho YS, Jung KH, Kim SR. Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:1120. [PMID: 28713404 PMCID: PMC5491850 DOI: 10.3389/fpls.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/09/2017] [Indexed: 05/14/2023]
Abstract
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.
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Affiliation(s)
- Manu Kumar
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
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Systematic Analysis of the 4-Coumarate:Coenzyme A Ligase (4CL) Related Genes and Expression Profiling during Fruit Development in the Chinese Pear. Genes (Basel) 2016; 7:genes7100089. [PMID: 27775579 PMCID: PMC5083928 DOI: 10.3390/genes7100089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/24/2016] [Accepted: 10/07/2016] [Indexed: 12/31/2022] Open
Abstract
In plants, 4-coumarate:coenzyme A ligases (4CLs), comprising some of the adenylate-forming enzymes, are key enzymes involved in regulating lignin metabolism and the biosynthesis of flavonoids and other secondary metabolites. Although several 4CL-related proteins were shown to play roles in secondary metabolism, no comprehensive study on 4CL-related genes in the pear and other Rosaceae species has been reported. In this study, we identified 4CL-related genes in the apple, peach, yangmei, and pear genomes using DNATOOLS software and inferred their evolutionary relationships using phylogenetic analysis, collinearity analysis, conserved motif analysis, and structure analysis. A total of 149 4CL-related genes in four Rosaceous species (pear, apple, peach, and yangmei) were identified, with 30 members in the pear. We explored the functions of several 4CL and acyl-coenzyme A synthetase (ACS) genes during the development of pear fruit by quantitative real-time PCR (qRT-PCR). We found that duplication events had occurred in the 30 4CL-related genes in the pear. These duplicated 4CL-related genes are distributed unevenly across all pear chromosomes except chromosomes 4, 8, 11, and 12. The results of this study provide a basis for further investigation of both the functions and evolutionary history of 4CL-related genes.
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Chandran AKN, Priatama RA, Kumar V, Xuan Y, Je BI, Kim CM, Jung KH, Han CD. Genome-wide transcriptome analysis of expression in rice seedling roots in response to supplemental nitrogen. JOURNAL OF PLANT PHYSIOLOGY 2016; 200:62-75. [PMID: 27340859 DOI: 10.1016/j.jplph.2016.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/29/2016] [Accepted: 06/11/2016] [Indexed: 05/09/2023]
Abstract
Nitrogen (N) is the most important macronutrient for plant growth and grain yields. For rice crops, nitrate and ammonium are the major N sources. To explore the genomic responses to ammonium supplements in rice roots, we used 17-day-old seedlings grown in the absence of external N that were then exposed to 0.5mM (NH4)2SO4 for 3h. Transcriptomic profiles were examined by microarray experiments. In all, 634 genes were up-regulated at least two-fold by the N-supplement when compared with expression in roots from untreated control plants. Gene Ontology (GO) enrichment analysis revealed that those upregulated genes are associated with 23 GO terms. Among them, metabolic processes for diverse amino acids (i.e., aspartate, threonine, tryptophan, glutamine, l-phenylalanine, and thiamin) as well as nitrogen compounds are highly over-represented, demonstrating that our selected genes are suitable for studying the N-response in roots. This enrichment analysis also indicated that nitrogen is closely linked to diverse transporter activities by primary metabolites, including proteins (amino acids), lipids, and carbohydrates, and is associated with carbohydrate catabolism and cell wall organization. Integration of results from omics analysis of metabolic pathways and transcriptome data using the MapMan tool suggested that the TCA cycle and pathway for mitochondrial electron transport are co-regulated when rice roots are exposed to ammonium. We also investigated the expression of N-responsive marker genes by performing a comparative analysis with root samples from plants grown under different NH4(+) treatments. The diverse responses to such treatment provide useful insight into the global changes related to the shift from an N-deficiency to an enhanced N-supply in rice, a model crop plant.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Ryza A Priatama
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Vikranth Kumar
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yuanhu Xuan
- College of Plant Protection, Shengyang Agricultural University, Dongling Road 120, Shengyang 110866, China
| | - Byoung Il Je
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chul Min Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Chang-Deok Han
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea.
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Cho H, Chou HH. Thermodynamically optimal whole-genome tiling microarray design and validation. BMC Res Notes 2016; 9:305. [PMID: 27295952 PMCID: PMC4906886 DOI: 10.1186/s13104-016-2113-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
Background Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Findings Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. Conclusions This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2113-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyejin Cho
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Hui-Hsien Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Department of Computer Science, Iowa State University, Ames, IA, 50011, USA.
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Pandey V, Ansari M, Tula S, Sahoo R, Bains G, Kumar J, Tuteja N, Shukla A. Ocimum sanctum leaf extract induces drought stress tolerance in rice. PLANT SIGNALING & BEHAVIOR 2016; 11:e1150400. [PMID: 26890603 PMCID: PMC4977457 DOI: 10.1080/15592324.2016.1150400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
Ocimum leaves are highly enriched in antioxidant components. Thus, its leaf extract, if applied in plants, is believed to efficiently scavenge ROS, thereby preventing oxidative damage under drought stress. Thus, the present study was performed in kharif 2013 and rabi 2014 season to evaluate the effect of aqueous leaf extract of Ocimum sanctum against drought stress in 2 rice genotype under glass house conditions. Here we show that various morpho- physiological (chlorophyll fluorescence, leaf rolling score, leaf tip burn, number of senesced leaves and total dry matter) and biochemical parameters (proline, malondialdehyde and superoxide dismutase content) were amended by Ocimum treatment in both the seasons. Application of Ocimum extract increased expression of dehydrin genes, while reducing expression of aquaporin genes in drought stressed rice plant. Thus, application of Ocimum leaf extract under drought stress can be suggested as a promising strategy to mitigate drought stress in economical, accessible and ecofriendly manner.
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Affiliation(s)
- Veena Pandey
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - M.W. Ansari
- Department of Botany, Zakir Husain Delhi College, Jawahar Lal Nehru Marg, New Delhi, India
| | - Suresh Tula
- Plant Molecular Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - R.K. Sahoo
- Plant Molecular Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Gurdeep Bains
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - J. Kumar
- Department of Plant Pathology, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Narendra Tuteja
- Amity Institute of Microbial Technology, Amity University, Noida, UP, India
| | - Alok Shukla
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
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Pandey V, Ansari MW, Tula S, Yadav S, Sahoo RK, Shukla N, Bains G, Badal S, Chandra S, Gaur AK, Kumar A, Shukla A, Kumar J, Tuteja N. Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes. PLANTA 2016; 243:1251-64. [PMID: 26898554 DOI: 10.1007/s00425-016-2482-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 01/29/2016] [Indexed: 05/25/2023]
Abstract
This study demonstrates a dose-dependent response of Trichoderma harzianum Th-56 in improving drought tolerance in rice by modulating proline, SOD, lipid peroxidation product and DHN / AQU transcript level, and the growth attributes. In the present study, the effect of colonization of different doses of T. harzianum Th-56 strain in rice genotypes were evaluated under drought stress. The rice genotypes treated with increasing dose of T. harzianum strain Th-56 showed better drought tolerance as compared with untreated control plant. There was significant change in malondialdehyde, proline, higher superoxide dismutase level, plant height, total dry matter, relative chlorophyll content, leaf rolling, leaf tip burn, and the number of scorched/senesced leaves in T. harzianum Th-56 treated rice genotypes under drought stress. This was corroborated with altered expression of aquaporin and dehydrin genes in T. harzianum Th-56 treated rice genotypes. The present findings suggest that a dose of 30 g/L was the most effective in improving drought tolerance in rice, and its potential exploitation will contribute to the advancement of rice genotypes to sustain crop productivity under drought stress. Interaction studies of T. harzianum with three aromatic rice genotypes suggested that PSD-17 was highly benefitted from T. harzianum colonization under drought stress.
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Affiliation(s)
- Veena Pandey
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Mohammad W Ansari
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Jawahar Lal Nehru Marg, New Delhi, 110002, India
| | - Suresh Tula
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Sandep Yadav
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ranjan K Sahoo
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Nandini Shukla
- Department of Plant Pathology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Gurdeep Bains
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Shail Badal
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Subhash Chandra
- Department of Agronomy, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - A K Gaur
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Atul Kumar
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Alok Shukla
- Department of Plant Physiology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India.
| | - J Kumar
- Department of Plant Pathology, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India.
| | - Narendra Tuteja
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Jawahar Lal Nehru Marg, New Delhi, 110002, India.
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
- Amity Institute of Microbial Technology, Amity University, E2-Block, 4th Floor, Room 404A, Sector 125, Noida, 201313, UP, India.
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Birla BS, Chou HH. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction. PLoS One 2015; 10:e0145682. [PMID: 26716828 PMCID: PMC4696799 DOI: 10.1371/journal.pone.0145682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/07/2015] [Indexed: 11/19/2022] Open
Abstract
Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.
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Affiliation(s)
- Bhagyashree S. Birla
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Hui-Hsien Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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Guo Z, Song G, Liu Z, Qu X, Chen R, Jiang D, Sun Y, Liu C, Zhu Y, Yang D. Global epigenomic analysis indicates that epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice. BMC Genomics 2015; 16:232. [PMID: 25886904 PMCID: PMC4394419 DOI: 10.1186/s12864-015-1454-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 03/09/2015] [Indexed: 12/05/2022] Open
Abstract
Background For heterozygous genes, alleles on the chromatin from two different parents exhibit histone modification variations known as allele-specific histone modifications (ASHMs). The regulation of allele-specific gene expression (ASE) by ASHMs has been reported in animals. However, to date, the regulation of ASE by ASHM genes remains poorly understood in higher plants. Results We used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL × 93-11 and GL × TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study. Conclusions Our results demonstrate that epialleles from parents can be inherited by the F1 to produce ASHMs in the F1 hybrid. Our findings indicate that ASHM-H3K36me3, rather than H3K27me3, mainly regulates ASE in hybrid rice. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1454-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhibin Guo
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Gaoyuan Song
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Zhenwei Liu
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Xuefeng Qu
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Rong Chen
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Daiming Jiang
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Yunfang Sun
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Chuan Liu
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
| | - Daichang Yang
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China.
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Jung KH, Kim SR, Giong HK, Nguyen MX, Koh HJ, An G. Genome-wide identification and functional analysis of genes expressed ubiquitously in rice. MOLECULAR PLANT 2015; 8:276-89. [PMID: 25624149 DOI: 10.1016/j.molp.2014.10.013] [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: 05/19/2014] [Revised: 10/07/2014] [Accepted: 10/07/2014] [Indexed: 05/10/2023]
Abstract
Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.
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Affiliation(s)
- Ki-Hong Jung
- Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea.
| | - Sung-Ruyl Kim
- Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
| | - Hoi-Khoanh Giong
- Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
| | - Minh Xuan Nguyen
- Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
| | - Hyun-Jung Koh
- Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea.
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Yadav R, Prasad R. Identification and functional characterization of sorbitol-6-phosphate dehydrogenase protein from rice and structural elucidation by in silico approach. PLANTA 2014; 240:223-238. [PMID: 24817585 DOI: 10.1007/s00425-014-2076-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
The sorbitol-6-phosphate dehydrogenase (S6PDH) is a key enzyme for sorbitol synthesis and plays an important role in the alleviation of salinity stress in plants. Despite the huge significance, the structure and the mode of action of this enzyme are still not known. In the present study, sequence analysis, cloning, expression, activity assays and enzyme kinetics using various substrates (glucose-6-phosphate, sorbitol-6-phosphate and mannose-6-phosphate) were performed to establish the functional role of S6PDH protein from rice (Oryza sativa). For the structural analysis of the protein, a comparative homology model was prepared on the basis of percentage sequence identity and substrate similarity using the crystal structure of human aldose reductase in complex with glucose-6-phosphate and NADP(+) (PDB ID: 2ACQ) as a template. Molecular docking was performed for studying the structural details of substrate binding and possible enzyme mechanism. The cloned sequence resulted into an active recombinant protein when expressed into a bacterial expression system. The purified recombinant protein was found to be active with glucose-6-phosphate and sorbitol-6-phosphate; however, activity against mannose-6-phosphate was not found. The K m values for glucose-6-phosphate and sorbitol-6-phosphate were found to be 15.9 ± 0.2 and 7.21 ± 0.5 mM, respectively. A molecular-level analysis of the active site of OsS6PDH provides valuable information about the enzyme mechanism and requisite enantioselectivity for its physiological substrates. Thus, the fundamental studies of structure and function of OsS6PDH could serve as the basis for the future studies of bio-catalytic applications of this enzyme.
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Affiliation(s)
- Rajbala Yadav
- Molecular Biology and Proteomics Lab, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India,
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22
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Oo MM, Bae HK, Nguyen TD, Moon S, Oh SA, Kim JH, Soh MS, Song JT, Jung KH, Park SK. Evaluation of rice promoters conferring pollen-specific expression in a heterologous system, Arabidopsis. PLANT REPRODUCTION 2014; 27:47-58. [PMID: 24550073 DOI: 10.1007/s00497-014-0239-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Promoters can direct gene expression specifically to targeted tissues or cells. Effective with both crop species and model plant systems, these tools can help researchers overcome the practical obstacles associated with transgenic protocols. Here, we identified promoters that allow one to target the manipulation of gene expression during pollen development. Utilizing published transcriptomic databases for rice, we investigated the promoter activity of selected genes in Arabidopsis. From various microarray datasets, including those for anthers and pollen grains at different developmental stages, we selected nine candidate genes that showed high levels of expression in the late stages of rice pollen development. We named these Oryza sativa late pollen-specific genes. Their promoter regions contained various cis-acting elements that could be responsible for anther-/pollen-specific expression. Promoter::GUS-GFP reporters were constructed and introduced into Arabidopsis plants. Histochemical GUS staining revealed that six of the nine rice promoters conferred strong GUS expression that was restricted to the anthers in Arabidopsis. Further analysis showed that although the GUS signals were not detected at the unicellular stage, they strengthened in the bicellular or tricellular stages, peaking at the mature pollen stage. This paralleled their transcriptomic profiles in rice. Based on our results, we proposed that these six rice promoters, which are active in the late stages of pollen formation in the dicot Arabidopsis, can aid molecular breeders in generating new varieties of a monocot plant, rice.
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Affiliation(s)
- Moe Moe Oo
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
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23
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Alqurashi M, Meier S. Inferring biological functions of guanylyl cyclases with computational methods. Methods Mol Biol 2013; 1016:225-34. [PMID: 23681582 DOI: 10.1007/978-1-62703-441-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens.
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Affiliation(s)
- May Alqurashi
- Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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24
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Pashaj A, Yi X, Xia M, Canny S, Riethoven JJM, Moreau R. Characterization of genome-wide transcriptional changes in liver and adipose tissues of ZDF (fa/fa) rats fed R-α-lipoic acid by next-generation sequencing. Physiol Genomics 2013; 45:1136-43. [DOI: 10.1152/physiolgenomics.00138.2013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We report on the characterization of lipogenic tissue transcriptional networks that support physiological responses of obese rats to a lipid-lowering bioactive food compound, R-α-lipoic acid (LA). Nine-week-old male Zucker diabetic fatty (fa/fa) rats were fed a chow diet supplemented with 3 g LA per kg diet or pair fed for 2 wk. At the end of the trial, high-quality RNA was extracted from the liver and epididymal fat and subjected to transcriptome analysis by RNA-Seq technology. Results showed a substantially higher number of differentially expressed genes [DEG, false discovery rate adjusted P ≤ 0.05 and absolute log2 (fold change) ≥ 1] in the liver (110 genes) vs. epididymal fat (10 genes). Most epididymal fat DEG were also differentially expressed in liver and shared directionality of change. Gene Ontology (GO) analysis of these transcripts revealed significant enrichment of GO categories related to immune response, stress response, lipid metabolism, and carboxylic acid metabolic processes. Of interest, interferon-related genes involved in defense against microorganisms and innate immune response were induced by LA. Lipid metabolism-related transcript changes observed in LA-fed animals included downregulation of lipogenic genes ( Pnpla3, Pnpla5, Elovl6, Acly, Gpam, and Aacs) and concomitant upregulation of short-, medium-, and long-chain fatty acid metabolic processes ( Acot1, Acot2, Acsf2, and Crat). Transcriptional changes were accompanied by the lowering of abdominal adiposity and blood triacylglycerol levels. We conclude that LA dietary supplementation induces prominent gene expression changes in liver in support of significant improvement of whole-body lipid status.
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Affiliation(s)
- Anjeza Pashaj
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska; and
| | - Xiaohua Yi
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska; and
| | - Mengna Xia
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska; and
| | - Stephanie Canny
- Beadle Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska
| | | | - Régis Moreau
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska; and
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Edstam MM, Blomqvist K, Eklöf A, Wennergren U, Edqvist J. Coexpression patterns indicate that GPI-anchored non-specific lipid transfer proteins are involved in accumulation of cuticular wax, suberin and sporopollenin. PLANT MOLECULAR BIOLOGY 2013; 83:625-49. [PMID: 23893219 DOI: 10.1007/s11103-013-0113-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/12/2013] [Indexed: 05/03/2023]
Abstract
The non-specific lipid transfer proteins (nsLTP) are unique to land plants. The nsLTPs are characterized by a compact structure with a central hydrophobic cavity and can be classified to different types based on sequence similarity, intron position or spacing between the cysteine residues. The type G nsLTPs (LTPGs) have a GPI-anchor in the C-terminal region which attaches the protein to the exterior side of the plasma membrane. The function of these proteins, which are encoded by large gene families, has not been systematically investigated so far. In this study we have explored microarray data to investigate the expression pattern of the LTPGs in Arabidopsis and rice. We identified that the LTPG genes in each plant can be arranged in three expression modules with significant coexpression within the modules. According to expression patterns and module sizes, the Arabidopsis module AtI is functionally equivalent to the rice module OsI, AtII corresponds to OsII and AtIII is functionally comparable to OsIII. Starting from modules AtI, AtII and AtIII we generated extended networks with Arabidopsis genes coexpressed with the modules. Gene ontology analyses of the obtained networks suggest roles for LTPGs in the synthesis or deposition of cuticular waxes, suberin and sporopollenin. The AtI-module is primarily involved with cuticular wax, the AtII-module with suberin and the AtIII-module with sporopollenin. Further transcript analysis revealed that several transcript forms exist for several of the LTPG genes in both Arabidopsis and rice. The data suggests that the GPI-anchor attachment and localization of LTPGs may be controlled to some extent by alternative splicing.
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Narsai R, Devenish J, Castleden I, Narsai K, Xu L, Shou H, Whelan J. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:1057-73. [PMID: 24147765 PMCID: PMC4253041 DOI: 10.1111/tpj.12357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 05/04/2023]
Abstract
Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
- Centre for Computational Systems Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - James Devenish
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Ian Castleden
- Centre for Computational Systems Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Kabir Narsai
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Lin Xu
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang UniversityHangzhou, 310058, China
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, University of Western AustraliaMCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
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27
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Jung KH, Gho HJ, Giong HK, Chandran AKN, Nguyen QN, Choi H, Zhang T, Wang W, Kim JH, Choi HK, An G. Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data. RICE (NEW YORK, N.Y.) 2013; 6:19. [PMID: 24280533 PMCID: PMC4883688 DOI: 10.1186/1939-8433-6-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/07/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Accumulation of genome-wide transcriptome data provides new insight on a genomic scale which cannot be gained by analyses of individual data. The majority of rice (O. sativa) species are japonica and indica cultivars. Genome-wide identification of genes differentially expressed between japonica and indica cultivars will be very useful in understanding the domestication and evolution of rice species. RESULTS In this study, we analyzed 983 of the 1866 entries in the Affymetrix array data in the public database: 595 generated from indica and 388 from japonica rice cultivars. To discover differentially expressed genes in each cultivar, we performed significance analysis of microarrays for normalized data, and identified 490 genes preferentially expressed in japonica and 104 genes in indica. Gene Ontology analyses revealed that defense response-related genes are significantly enriched in both cultivars, indicating that japonica and indica might be under strong selection pressure for these traits during domestication. In addition, 36 (34.6%) of 104 genes preferentially expressed in indica and 256 (52.2%) of 490 genes preferentially expressed in japonica were annotated as genes of unknown function. Biotic stress overview in the MapMan toolkit revealed key elements of the signaling pathway for defense response in japonica or indica eQTLs. CONCLUSIONS The percentage of screened genes preferentially expressed in indica was 4-fold higher (34.6%) and that in japonica was 5-fold (52.2%) higher than expected (11.1%), suggesting that genes of unknown function are responsible for the novel traits that distinguish japonica and indica cultivars. The identification of 10 functionally characterized genes expressed preferentially in either japonica or indica highlights the significance of our candidate genes during the domestication of rice species. Functional analysis of the roles of individual components of stress-mediated signaling pathways will shed light on potential molecular mechanisms to improve disease resistance in rice.
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Affiliation(s)
- Ki-Hong Jung
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Hyun-Jung Gho
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Hoi-Khoanh Giong
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Anil Kumar Nalini Chandran
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Quynh-Nga Nguyen
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - HeeBak Choi
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Tian Zhang
- />CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Wen Wang
- />CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Jin-Hyun Kim
- />Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- />Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Gynheung An
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
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28
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Tong YA, Peng H, Zhan C, Fan L, Ai T, Wang S. Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function. PLoS One 2013; 8:e63938. [PMID: 23717514 PMCID: PMC3661559 DOI: 10.1371/journal.pone.0063938] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 04/08/2013] [Indexed: 11/18/2022] Open
Abstract
Intronic microRNAs (in-miRNAs) as a class of miRNA family that regulates gene expression are still poorly understood in plants. In this study, we systematically identified rice in-miRNAs by re-mining eight published small RNA-sequencing datasets of rice. Furthermore, based on the collected expression, annotation, and putative target data, we investigated the structures, potential functions, and expression features of these in-miRNAs and the expression patterns of their host genes. A total of 153 in-miRNAs, which account for over 1/4 of the total rice miRNAs, were identified. In silico expression analysis showed that most of them (∼63%) are tissue or stage-specific. However, a majority of their host genes, especially those containing clustered in-miRNAs, exhibit stable high-level expressions among 513 microarray datasets. Although in-miRNAs show diversity in function and mechanism, the DNA methylation directed by 24 nt in-miRNAs may be the main pathway that controls the expressions of target genes, host genes, and even themselves. These findings may enhance our understanding on special functions of in-miRNAs, especially in mediating DNA methylation that was concluded to affect the stability of expression and structure of host and target genes.
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Affiliation(s)
- Yong-ao Tong
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Hua Peng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Cheng Zhan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - LinHong Fan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Taobo Ai
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Shenghua Wang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
- * E-mail:
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29
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Hudson D, Guevara DR, Hand AJ, Xu Z, Hao L, Chen X, Zhu T, Bi YM, Rothstein SJ. Rice cytokinin GATA transcription Factor1 regulates chloroplast development and plant architecture. PLANT PHYSIOLOGY 2013; 162:132-44. [PMID: 23548780 PMCID: PMC3641198 DOI: 10.1104/pp.113.217265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 03/29/2013] [Indexed: 05/18/2023]
Abstract
Chloroplast biogenesis has been well documented in higher plants, yet the complex methods used to regulate chloroplast activity under fluctuating environmental conditions are not well understood. In rice (Oryza sativa), the CYTOKININ-RESPONSIVE GATA TRANSCRIPTION FACTOR1 (Cga1) shows increased expression following light, nitrogen, and cytokinin treatments, while darkness and gibberellin reduce expression. Strong overexpression of Cga1 produces dark green, semidwarf plants with reduced tillering, whereas RNA interference knockdown results in reduced chlorophyll and increased tillering. Coexpression, microarray, and real-time expression analyses demonstrate a correlation between Cga1 expression and the expression of important nucleus-encoded, chloroplast-localized genes. Constitutive Cga1 overexpression increases both chloroplast biogenesis and starch production but also results in delayed senescence and reduced grain filling. Growing the transgenic lines under different nitrogen regimes indicates potential agricultural applications for Cga1, including manipulation of biomass, chlorophyll/chloroplast content, and harvest index. These results indicate a conserved mechanism by which Cga1 regulates chloroplast development in higher plants.
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Affiliation(s)
- Darryl Hudson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - David R. Guevara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Andrew J. Hand
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Zhenhua Xu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Lixin Hao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Xi Chen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Tong Zhu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
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30
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Ma NL, Rahmat Z, Lam SS. A review of the "Omics" approach to biomarkers of oxidative stress in Oryza sativa. Int J Mol Sci 2013; 14:7515-41. [PMID: 23567269 PMCID: PMC3645701 DOI: 10.3390/ijms14047515] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/20/2013] [Accepted: 03/20/2013] [Indexed: 12/27/2022] Open
Abstract
Physiological and ecological constraints that cause the slow growth and depleted production of crops have raised a major concern in the agriculture industry as they represent a possible threat of short food supply in the future. The key feature that regulates the stress signaling pathway is always related to the reactive oxygen species (ROS). The accumulation of ROS in plant cells would leave traces of biomarkers at the genome, proteome, and metabolome levels, which could be identified with the recent technological breakthrough coupled with improved performance of bioinformatics. This review highlights the recent breakthrough in molecular strategies (comprising transcriptomics, proteomics, and metabolomics) in identifying oxidative stress biomarkers and the arising opportunities and obstacles observed in research on biomarkers in rice. The major issue in incorporating bioinformatics to validate the biomarkers from different omic platforms for the use of rice-breeding programs is also discussed. The development of powerful techniques for identification of oxidative stress-related biomarkers and the integration of data from different disciplines shed light on the oxidative response pathways in plants.
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Affiliation(s)
- Nyuk Ling Ma
- Department of Biology, Faculty of Science and Technology, University Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Zaidah Rahmat
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, University Technology Malaysia, 81310 Johor Bahru, Johor, Malaysia; E-Mail:
| | - Su Shiung Lam
- Department of Engineering Science, Faculty of Science and Technology, University Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; E-Mail:
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31
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Huang S, Jacoby RP, Shingaki-Wells RN, Li L, Millar AH. Differential induction of mitochondrial machinery by light intensity correlates with changes in respiratory metabolism and photorespiration in rice leaves. THE NEW PHYTOLOGIST 2013; 198:103-115. [PMID: 23356873 DOI: 10.1111/nph.12123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 11/27/2012] [Indexed: 05/04/2023]
Abstract
The light responsiveness of mitochondrial function was investigated through changes in mitochondrial composition and metabolism in rice (Oryza sativa) shoots. The mitochondrial proteome and metabolite abundances under low light, (LL, 100 μmol m(-2) s(-1) ), and high light (HL, 700 μmol m(-2) s(-1) ) were measured along with information on shoot photosynthetic, respiratory and photorespiratory activity. Specific steps in mitochondrial tricarboxylic acid (TCA) cycle metabolism were decreased under HL, correlating with lower respiration rate under HL. The abundance of mitochondrial enzymes in branch chain metabolism was reduced under HL/LL, and correlated with a decrease in the abundance of a range of amino acids in the HL/LL. Mitochondrial nucleoside diphosphate kinase was increased under LL/HL treatments. Significant accumulation of glycine decarboxylase P, T subunits and serine hydroxymethyltransferase occurred in response to light. The abundance of the glycine decarboxylase (GDC) H subunit proteins was not changed by HL/LL treatments, and the abundance of GDC L subunit protein was halved under HL, indicating a change in the stoichiometry of GDC subunits, while photorespiration was fourfold higher in LL- than in HL-treated plants. Insights into these light-dependent phenomena and their importance for understanding the initiation of photorespiration in rice and adaptation of mitochondria to function in photosynthetic cells are discussed.
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Affiliation(s)
- Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Richard P Jacoby
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Rachel N Shingaki-Wells
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
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32
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Huang S, Jacoby RP, Shingaki-Wells RN, Li L, Millar AH. Differential induction of mitochondrial machinery by light intensity correlates with changes in respiratory metabolism and photorespiration in rice leaves. THE NEW PHYTOLOGIST 2013. [PMID: 23356873 DOI: 10.1111/nph.12123 [epub ahead of print]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The light responsiveness of mitochondrial function was investigated through changes in mitochondrial composition and metabolism in rice (Oryza sativa) shoots. The mitochondrial proteome and metabolite abundances under low light, (LL, 100 μmol m(-2) s(-1) ), and high light (HL, 700 μmol m(-2) s(-1) ) were measured along with information on shoot photosynthetic, respiratory and photorespiratory activity. Specific steps in mitochondrial tricarboxylic acid (TCA) cycle metabolism were decreased under HL, correlating with lower respiration rate under HL. The abundance of mitochondrial enzymes in branch chain metabolism was reduced under HL/LL, and correlated with a decrease in the abundance of a range of amino acids in the HL/LL. Mitochondrial nucleoside diphosphate kinase was increased under LL/HL treatments. Significant accumulation of glycine decarboxylase P, T subunits and serine hydroxymethyltransferase occurred in response to light. The abundance of the glycine decarboxylase (GDC) H subunit proteins was not changed by HL/LL treatments, and the abundance of GDC L subunit protein was halved under HL, indicating a change in the stoichiometry of GDC subunits, while photorespiration was fourfold higher in LL- than in HL-treated plants. Insights into these light-dependent phenomena and their importance for understanding the initiation of photorespiration in rice and adaptation of mitochondria to function in photosynthetic cells are discussed.
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Affiliation(s)
- Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Richard P Jacoby
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Rachel N Shingaki-Wells
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (CABiN), The University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Transcriptional profiling of rice early response to Magnaporthe oryzae identified OsWRKYs as important regulators in rice blast resistance. PLoS One 2013; 8:e59720. [PMID: 23544090 PMCID: PMC3609760 DOI: 10.1371/journal.pone.0059720] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/17/2013] [Indexed: 01/25/2023] Open
Abstract
Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive. Therefore, we carried out a transcriptome study on rice early defense response to M. oryzae. We found that the transcriptional profiles of rice compatible and incompatible interactions with M. oryzae were mostly similar, with genes regulated more prominently in the incompatible interactions. The functional analysis showed that the genes involved in signaling and secondary metabolism were extensively up-regulated. In particular, WRKY transcription factor genes were significantly enriched among the up-regulated genes. Overexpressing one of these WRKY genes, OsWRKY47, in transgenic rice plants conferred enhanced resistance against rice blast fungus. Our results revealed the sophisticated transcriptional reprogramming of signaling and metabolic pathways during rice early response to M. oryzae and demonstrated the critical roles of WRKY transcription factors in rice blast resistance.
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Sun H, Huang X, Xu X, Lan H, Huang J, Zhang HS. ENAC1, a NAC transcription factor, is an early and transient response regulator induced by abiotic stress in rice (Oryza sativa L.). Mol Biotechnol 2013; 52:101-10. [PMID: 22161313 DOI: 10.1007/s12033-011-9477-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The plant-specific NAC (NAM, ATAF, and CUC)-domain proteins play important roles in plant development and stress responses. In this research, a full-length cDNA named ENAC1 (early NAC-domain protein induced by abiotic stress 1) was isolated from rice. ENAC1 possess one NAC domain in the N-terminus. Comparative time-course expression analysis indicated that ENAC1 expression, similar with OsDREB1A, was induced very quickly by various abiotic stresses including salt, drought, cold, and exogenous abscisic acid. However, the induction of ENAC1 by abiotic stress was transient and lasted up to 3 h, whereas that of OsDREB1A maintained longer. The promoter sequence of ENAC1 harbors several cis-elements including ABA response elements, but the well-known dehydration responsive element/C-repeat element is absent. The ENAC1-GFP (green fluorescent protein) fusion protein was localized in the nucleus of rice protoplast cell. Yeast hybrid assays revealed that ENAC1 was a transcription activator and bound to NAC recognition sequence (NACRS). Co-expression analysis suggested that ENAC1 co-expressed with a number of stress-related genes. Taken together, ENAC1 may be an early transcription activator of stress responses and function in the regulation of NACRS-mediated gene expression under abiotic stress.
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Affiliation(s)
- Hui Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Kudo T, Akiyama K, Kojima M, Makita N, Sakurai T, Sakakibara H. UniVIO: a multiple omics database with hormonome and transcriptome data from rice. PLANT & CELL PHYSIOLOGY 2013; 54:e9. [PMID: 23314752 PMCID: PMC3583028 DOI: 10.1093/pcp/pct003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/02/2013] [Indexed: 05/20/2023]
Abstract
Plant hormones play important roles as signaling molecules in the regulation of growth and development by controlling the expression of downstream genes. Since the hormone signaling system represents a complex network involving functional cross-talk through the mutual regulation of signaling and metabolism, a comprehensive and integrative analysis of plant hormone concentrations and gene expression is important for a deeper understanding of hormone actions. We have developed a database named Uniformed Viewer for Integrated Omics (UniVIO: http://univio.psc.riken.jp/), which displays hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map. At the present time, hormonome and transcriptome data obtained from 14 organ parts of rice plants at the reproductive stage and seedling shoots of three gibberellin signaling mutants are included in the database. The hormone concentration and gene expression data can be searched by substance name, probe ID, gene locus ID or gene description. A correlation search function has been implemented to enable users to obtain information of correlated substance accumulation and gene expression. In the correlation search, calculation method, range of correlation coefficient and plant samples can be selected freely.
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Affiliation(s)
- Toru Kudo
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- These authors equally contributed to this study
- Present address: PMCB Program, Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Kenji Akiyama
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- These authors equally contributed to this study
| | - Mikiko Kojima
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Nobue Makita
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Hitoshi Sakakibara
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
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Sharma R, Cao P, Jung KH, Sharma MK, Ronald PC. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. FRONTIERS IN PLANT SCIENCE 2013; 4:330. [PMID: 23986771 PMCID: PMC3752443 DOI: 10.3389/fpls.2013.00330] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/05/2013] [Indexed: 05/19/2023]
Abstract
Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.
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Affiliation(s)
- Rita Sharma
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Feedstocks Divison, Joint BioEnergy InstituteEmeryville, CA, USA
| | - Peijian Cao
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research InstituteZhengzhou, China
| | - Ki-Hong Jung
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Manoj K. Sharma
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Feedstocks Divison, Joint BioEnergy InstituteEmeryville, CA, USA
| | - Pamela C. Ronald
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Feedstocks Divison, Joint BioEnergy InstituteEmeryville, CA, USA
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Pamela C. Ronald, Department of Plant Pathology and the Genome Center, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA e-mail:
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Jung KH, An G. Functional characterization of rice genes using a gene-indexed T-DNA insertional mutant population. Methods Mol Biol 2013; 956:57-67. [PMID: 23135844 DOI: 10.1007/978-1-62703-194-3_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite the availability of the finished genome sequence and tools for its analyses, few rice genes have been characterized. Because Agrobacterium-mediated transformation causes random T-DNA insertions across the genome, T-DNA can be a good mutagen for functional genomics. Gene-indexed mutants with flanking sequences around inserted T-DNA are valuable resources for accelerating functional characterizations of rice genes. Such mutant lines, covering at least half the rice genome, have been generated through international efforts. Here, we describe approaches that use functional genomics with T-DNA insertional mutagenesis.
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Affiliation(s)
- Ki-Hong Jung
- Department of Plant Pathology, University of California, Davis, CA, USA
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Tripathi AK, Pareek A, Sopory SK, Singla-Pareek SL. Narrowing down the targets for yield improvement in rice under normal and abiotic stress conditions via expression profiling of yield-related genes. RICE (NEW YORK, N.Y.) 2012; 5:37. [PMID: 24280046 PMCID: PMC4883727 DOI: 10.1186/1939-8433-5-37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 12/12/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Crop improvement targeting high yield and tolerance to environmental stresses has become the need of the hour. Yield improvement via breeding or gene pyramiding aiming comprehensive incorporation of the agronomically favored traits requires an in-depth understanding of the molecular basis of these traits. The present study describes expression profiling of yield-related genes in rice with respect to different developmental stages and various abiotic stress conditions. RESULTS Our analysis indicates developmental regulation of the yield-related genes pertaining to the genetic reprogramming involved at the corresponding developmental stage. The gene expression data can be utilized to specifically select particular genes which can potentially function synergistically for enhancing the yield while maintaining the source-sink balance. Furthermore, to gain some insights into the molecular basis of yield penalty during various abiotic stresses, the expression of selected yield-related genes has also been analyzed by qRT-PCR under such stress conditions. Our analysis clearly showed a tight transcriptional regulation of a few of these yield-related genes by abiotic stresses. The stress-responsive expression patterns of these genes could explain some of the most important stress-related physiological manifestations such as reduced tillering, smaller panicles and early completion of the life cycle owing to reduced duration of vegetative and reproductive phases. CONCLUSIONS Development of high yielding rice varieties which maintain their yield even under stress conditions may be achieved by simultaneous genetic manipulation of certain combination of genes such as LRK1 and LOG, based on their function and expression profile obtained in the present study. Our study would aid in investigating in future, whether over-expressing or knocking down such yield-related genes can improve the grain yield potential in rice.
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Affiliation(s)
- Amit K Tripathi
- />Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067 India
| | - Ashwani Pareek
- />Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Sudhir K Sopory
- />Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067 India
| | - Sneh L Singla-Pareek
- />Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067 India
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Umate P. Comparative genomics of the lipid-body-membrane proteins oleosin, caleosin and steroleosin in magnoliophyte, lycophyte and bryophyte. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:345-53. [PMID: 23317702 PMCID: PMC5054715 DOI: 10.1016/j.gpb.2012.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/08/2012] [Accepted: 08/01/2012] [Indexed: 11/17/2022]
Abstract
Lipid bodies store oils in the form of triacylglycerols. Oleosin, caleosin and steroleosin are unique proteins localized on the surface of lipid bodies in seed plants. This study has identified genes encoding lipid body proteins oleosin, caleosin and steroleosin in the genomes of five plants: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Selaginella moellendorffii and Physcomitrella patens. The protein sequence alignment indicated that each oleosin protein contains a highly-conserved proline knot motif, and proline knob motif is well conserved in steroleosin proteins, while caleosin proteins possess the Dx[D/N]xDG-containing calcium-binding motifs. The identification of motifs (proline knot and knob) and conserved amino acids at active site was further supported by the sequence logos. The phylogenetic analysis revealed the presence of magnoliophyte- and bryophyte-specific subgroups. We analyzed the public microarray data for expression of oleosin, caleosin and steroleosin in Arabidopsis and rice during the vegetative and reproductive stages, or under abiotic stresses. Our results indicated that genes encoding oleosin, caleosin and steroleosin proteins were expressed predominantly in plant seeds. This work may facilitate better understanding of the members of lipid-body-membrane proteins in diverse organisms and their gene expression in model plants Arabidopsis and rice.
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Affiliation(s)
- Pavan Umate
- Department of Botany, Kakatiya University, Warangal 506009, India.
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40
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Zhang X, Li J, Liu A, Zou J, Zhou X, Xiang J, Rerksiri W, Peng Y, Xiong X, Chen X. Expression profile in rice panicle: insights into heat response mechanism at reproductive stage. PLoS One 2012; 7:e49652. [PMID: 23155476 PMCID: PMC3498232 DOI: 10.1371/journal.pone.0049652] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/11/2012] [Indexed: 12/20/2022] Open
Abstract
Rice at reproductive stage is more sensitive to environmental changes, and little is known about the mechanism of heat response in rice panicle. Here, using rice microarray, we provided a time course gene expression profile of rice panicle at anther developmental stage 8 after 40°C treatment for 0 min, 20 min, 60 min, 2 h, 4 h, and 8 h. The identified differentially expressed genes were mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response. The predominant transcription factor gene families responsive to heat stress were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat stress. The motif co-occurrence analysis on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3 in response to heat stress. The regulation model central to ROS combined with transcriptome and ROS quantification data in rice panicle indicated the great importance to maintain ROS balance and the existence of wide cross-talk in heat response. The present study increased our understanding of the heat response in rice panicle and provided good candidate genes for crop improvement.
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Affiliation(s)
- Xianwen Zhang
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiaping Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Ailing Liu
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jie Zou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiaoyun Zhou
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jianhua Xiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Wirat Rerksiri
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yan Peng
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Xingyao Xiong
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- * E-mail: (XX); (XC)
| | - Xinbo Chen
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- * E-mail: (XX); (XC)
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Abstract
Transcriptome analysis using oligonucleotide microarrays is a powerful tool for detecting changes in genome-wide transcripts under a given biological condition. Although the rice genome sequence is available, the number of functionally characterized genes in rice is still very limited. Genome-wide transcriptome analysis is a useful tool for elucidating the functions of rice genes that have not yet been determined. Currently, more than 3,000 arrays are publicly available. Here, we introduce methods for genome-wide transcriptome analysis in rice.
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Chinpongpanich A, Limruengroj K, Phean-o-pas S, Limpaseni T, Buaboocha T. Expression analysis of calmodulin and calmodulin-like genes from rice, Oryza sativa L. BMC Res Notes 2012; 5:625. [PMID: 23134977 PMCID: PMC3532322 DOI: 10.1186/1756-0500-5-625] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/29/2012] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In plants, a large family of calmodulin (CaM) and CaM-like (CML) proteins transduce the increase in cytosolic Ca2+ concentrations by binding to and altering the activities of target proteins, and thereby affecting the physiological responses to a vast array of stimuli. Here, transcript expression analysis of Cam and CML gene family members in rice (Oryza sativa L.) was extensively examined. RESULTS Cam and CML genes in rice exhibited differential expression patterns in tissues/organs. Under osmotic stress and salt stress, expression of OsCam1-1, OsCML4, 5, 8, and 11 was induced with different kinetics and magnitude. OsCML4 and 8 mRNA levels significantly increased by 3 h after treatment and remained elevated for at least 24 h while expression of OsCam1-1, OsCML5 and 11 was up-regulated as early as 1-3 h before rapidly returning to normal levels. Several cis-acting elements in response to abiotic stresses, including DREs (important promoter elements responsive to drought, high salt, and cold stress), were detected in the 5' upstream regions of these genes. The observed induction of the GUS activity of transgenic rice plants via the OsCam1-1 promoter appeared to be biphasic and dependent on the severity of salt stress. CONCLUSIONS Large OsCam and OsCML gene family members likely play differential roles as signal transducers in regulating various developmental processes and represent important nodes in the signal transduction and transcriptional regulation networks in abiotic stresss responses mediated by the complex Ca2+ signals in plants, which are rich in both spatial and temporal information.
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Affiliation(s)
- Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kampon Limruengroj
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Srivilai Phean-o-pas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tipaporn Limpaseni
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Teerapong Buaboocha
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Chen L, Hu W, Tan S, Wang M, Ma Z, Zhou S, Deng X, Zhang Y, Huang C, Yang G, He G. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One 2012; 7:e46744. [PMID: 23082129 PMCID: PMC3474763 DOI: 10.1371/journal.pone.0046744] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/04/2012] [Indexed: 01/31/2023] Open
Abstract
MAPK cascades are universal signal transduction modules and play important roles in plant growth, development and in response to a variety of biotic and abiotic stresses. Although MAPKs and MAPKKs have been systematically investigated in several plant species including Arabidopsis, rice and poplar, no systematic analysis has been conducted in the emerging monocot model plant Brachypodium distachyon. In the present study, a total of 16 MAPK genes and 12 MAPKK genes were identified from B. distachyon. An analysis of the genomic evolution showed that both tandem and segment duplications contributed significantly to the expansion of MAPK and MAPKK families. Evolutionary relationships within subfamilies were supported by exon-intron organizations and the architectures of conserved protein motifs. Synteny analysis between B. distachyon and the other two plant species of rice and Arabidopsis showed that only one homolog of B. distachyon MAPKs was found in the corresponding syntenic blocks of Arabidopsis, while 13 homologs of B. distachyon MAPKs and MAPKKs were found in that of rice, which was consistent with the speciation process of the three species. In addition, several interactive protein pairs between the two families in B. distachyon were found through yeast two hybrid assay, whereas their orthologs of a pair in Arabidopsis and other plant species were not found to interact with each other. Finally, expression studies of closely related family members among B. distachyon, Arabidopsis and rice showed that even recently duplicated representatives may fulfill different functions and be involved in different signal pathways. Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles.
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Affiliation(s)
- Lihong Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Wei Hu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Shenglong Tan
- Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Min Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Zhanbing Ma
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Shiyi Zhou
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Xiaomin Deng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Yang Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Chao Huang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
- * E-mail: (GY); (GH)
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science & Technology (HUST), Wuhan, China
- * E-mail: (GY); (GH)
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Rana RM, Dong S, Ali Z, Huang J, Zhang HS. Regulation of ATG6/Beclin-1 homologs by abiotic stresses and hormones in rice (Oryza sativa L.). GENETICS AND MOLECULAR RESEARCH 2012; 11:3676-87. [PMID: 22930426 DOI: 10.4238/2012.august.17.3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Autophagy, a complex and conserved mechanism, serving as a defense response in all eukaryotic organisms, is regulated by several proteins, among which ATG proteins are the most important due to their involvement in autophagosome formation. ATG6/Beclin-1 proteins, reported to be essential for autophagosome formation and assigned as a conserved domain, were subjected to database searches. We found three homologs in the rice (Oryza sativa) genome. A phylogeny tree was constructed to establish their across species relationship, which divided them into three distinct groups; two for plants, i.e., monocots and dicots, and one for animals. Evolutionary study of this family by critical amino acid conservation analysis revealed significant functional divergence. The finding of important stress-related cis-acting elements in the promoter region of rice ATG6 genes demonstrated their involvement in abiotic stress responses. Furthermore, expression profiling of rice ATG6 genes based on microarray data, as well as by semi-quantitative RT-PCR showed differential expression when subjected to different stresses suggesting the involvement of OsATG6 genes in abiotic stresses (heat, cold and drought) and hormone (abscisic acid) responses. Analysis of co-expressed genes showed that most of them annotated to DNA repair pathways and proteolysis, etc. Collectively, these results suggest the involvement of OsATG6 genes in different stresses, and provide a basis for further functional studies to investigate the biological mechanism of action of these genes under abiotic stresses.
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Affiliation(s)
- R M Rana
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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van Eekelen JAM, Ellis JA, Pennell CE, Craig J, Saffery R, Mattes E, Olsson CA. Stress-sensitive neurosignalling in depression: an integrated network biology approach to candidate gene selection for genetic association analysis. Ment Illn 2012; 4:e21. [PMID: 25478122 PMCID: PMC4253374 DOI: 10.4081/mi.2012.e21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 07/06/2012] [Accepted: 08/01/2012] [Indexed: 01/18/2023] Open
Abstract
Genetic risk for depressive disorders is poorly understood despite consistent suggestions of a high heritable component. Most genetic studies have focused on risk associated with single variants, a strategy which has so far only yielded small (often non-replicable) risks for depressive disorders. In this paper we argue that more substantial risks are likely to emerge from genetic variants acting in synergy within and across larger neurobiological systems (polygenic risk factors). We show how knowledge of major integrated neurobiological systems provides a robust basis for defining and testing theoretically defensible polygenic risk factors. We do this by describing the architecture of the overall stress response. Maladaptation via impaired stress responsiveness is central to the aetiology of depression and anxiety and provides a framework for a systems biology approach to candidate gene selection. We propose principles for identifying genes and gene networks within the neurosystems involved in the stress response and for defining polygenic risk factors based on the neurobiology of stress-related behaviour. We conclude that knowledge of the neurobiology of the stress response system is likely to play a central role in future efforts to improve genetic prediction of depression and related disorders.
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Affiliation(s)
- J. Anke M. van Eekelen
- Developmental Neuroscience, Telethon Institute for Child Health Research and Centre for Child Health Research, University of Western Australia, Perth
| | - Justine A. Ellis
- Environmental and Genetic Epidemiology, Murdoch Childrens Research Institute, The Royal Children's Hospital and Department of Physiology, University of Melbourne
| | - Craig E. Pennell
- The School of Women's and Infants' Health, University of Western Australia at King Edward Memorial Hospital
| | - Jeff Craig
- Developmental Epigenetics, Early Development and Disease, Department of Paediatrics, Murdoch Childrens Research Institute, Royal Children's Hospital
| | - Richard Saffery
- Developmental Epigenetics, Early Development and Disease, Department of Paediatrics, Murdoch Childrens Research Institute, Royal Children's Hospital
| | - Eugen Mattes
- Developmental Neuroscience, Telethon Institute for Child Health Research and Centre for Child Health Research, University of Western Australia, Perth
| | - Craig A. Olsson
- School of Psychology, Deakin University Australia; Murdoch Childrens Research Institute; University of Melbourne, Australia
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Cao P, Jung KH, Choi D, Hwang D, Zhu J, Ronald PC. The Rice Oligonucleotide Array Database: an atlas of rice gene expression. RICE (NEW YORK, N.Y.) 2012; 5:17. [PMID: 24279809 PMCID: PMC4883718 DOI: 10.1186/1939-8433-5-17] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. RESULTS In this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD's user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. CONCLUSIONS The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.
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Affiliation(s)
- Peijian Cao
- />Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Ki-Hong Jung
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Korea
| | - Daeseok Choi
- />School of Interdisciplinary Bioscience and Bioengineering & Integrative Biosciences and Biotechnology, POSTECH, Pohang, 790-784 Korea
| | - Daehee Hwang
- />School of Interdisciplinary Bioscience and Bioengineering & Integrative Biosciences and Biotechnology, POSTECH, Pohang, 790-784 Korea
| | - Jun Zhu
- />Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Pamela C Ronald
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Korea
- />Department of Plant Pathology and the Genome Center, University of California, Davis, 95616 USA
- />Joint Bioenergy Institute, Emeryville, 94710 USA
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Bradbury LMT, Shumskaya M, Tzfadia O, Wu SB, Kennelly EJ, Wurtzel ET. Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms. Proc Natl Acad Sci U S A 2012; 109:E1888-97. [PMID: 22706644 PMCID: PMC3390835 DOI: 10.1073/pnas.1206002109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In photosynthetic organisms, carotenoids serve essential roles in photosynthesis and photoprotection. A previous report designated CruP as a secondary lycopene cyclase involved in carotenoid biosynthesis [Maresca J, et al. (2007) Proc Natl Acad Sci USA 104:11784-11789]. However, we found that cruP KO or cruP overexpression plants do not exhibit correspondingly reduced or increased production of cyclized carotenoids, which would be expected if CruP was a lycopene cyclase. Instead, we show that CruP aids in preventing accumulation of reactive oxygen species (ROS), thereby reducing accumulation of β-carotene-5,6-epoxide, a ROS-catalyzed autoxidation product, and inhibiting accumulation of anthocyanins, which are known chemical indicators of ROS. Plants with a nonfunctional cruP accumulate substantially higher levels of ROS and β-carotene-5,6-epoxide in green tissues. Plants overexpressing cruP show reduced levels of ROS, β-carotene-5,6-epoxide, and anthocyanins. The observed up-regulation of cruP transcripts under photoinhibitory and lipid peroxidation-inducing conditions, such as high light stress, cold stress, anoxia, and low levels of CO(2), fits with a role for CruP in mitigating the effects of ROS. Phylogenetic distribution of CruP in prokaryotes showed that the gene is only present in cyanobacteria that live in habitats characterized by large variation in temperature and inorganic carbon availability. Therefore, CruP represents a unique target for developing resilient plants and algae needed to supply food and biofuels in the face of global climate change.
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Affiliation(s)
- Louis M. T. Bradbury
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
| | - Maria Shumskaya
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
| | - Oren Tzfadia
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
- Graduate School and University Center, City University of New York, New York, NY 10016-4309
| | - Shi-Biao Wu
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
| | - Edward J. Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
- Graduate School and University Center, City University of New York, New York, NY 10016-4309
| | - Eleanore T. Wurtzel
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
- Graduate School and University Center, City University of New York, New York, NY 10016-4309
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Cserháti M, Turóczy Z, Dudits D, Györgyey J. The rice word landscape: a detailed catalogue of the rice motif content in the non-coding regions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:334-42. [PMID: 22702246 DOI: 10.1089/omi.2011.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Among the different areas of molecular biology concerning the detailed study of different parts of the cell, such as genomics, proteomics, and metabolomics, different new areas of study are emerging which entail the analysis of different parts of the genome, such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study was to construct and analyze a catalogue of all statistically relevant putative functional octamer words or motifs (which we have termed the "motifome" of a given organism) found within first introns, promoters, the 5' and 3' untranslated regions (UTRs), and the entire genome of japonica rice, and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of non-coding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. While common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.
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Affiliation(s)
- Mátyás Cserháti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary.
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Cserháti M, Turóczy Z, Dudits D, Györgyey J. The rice word landscape--a detailed catalog of the rice motif content in the noncoding regions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 15:819-28. [PMID: 22122670 DOI: 10.1089/omi.2011.0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Among the different areas of molecular biology concerning the detailed study of different parts of the cell such as genomics, proteomics, or metabolomics, different new areas of study are emerging that entail the analysis of different parts of the genome such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study is to draw up and analyze a catalog of all statistically relevant putative functional octamer words or motifs found within first introns, promoters, the 5' and 3' UTRs, and the entire genome of japonica rice and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of noncoding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. Although common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.
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Affiliation(s)
- Mátyás Cserháti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary.
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Vega-Sánchez ME, Verhertbruggen Y, Christensen U, Chen X, Sharma V, Varanasi P, Jobling SA, Talbot M, White RG, Joo M, Singh S, Auer M, Scheller HV, Ronald PC. Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice. PLANT PHYSIOLOGY 2012; 159:56-69. [PMID: 22388489 PMCID: PMC3375985 DOI: 10.1104/pp.112.195495] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 02/29/2012] [Indexed: 05/17/2023]
Abstract
Mixed-linkage glucan (MLG) is a cell wall polysaccharide containing a backbone of unbranched (1,3)- and (1,4)-linked β-glucosyl residues. Based on its occurrence in plants and chemical characteristics, MLG has primarily been associated with the regulation of cell wall expansion due to its high and transient accumulation in young, expanding tissues. The Cellulose synthase-like F (CslF) subfamily of glycosyltransferases has previously been implicated in mediating the biosynthesis of this polymer. We confirmed that the rice (Oryza sativa) CslF6 gene mediates the biosynthesis of MLG by overexpressing it in Nicotiana benthamiana. Rice cslf6 knockout mutants show a slight decrease in height and stem diameter but otherwise grew normally during vegetative development. However, cslf6 mutants display a drastic decrease in MLG content (97% reduction in coleoptiles and virtually undetectable in other tissues). Immunodetection with an anti-MLG monoclonal antibody revealed that the coleoptiles and leaves retain trace amounts of MLG only in specific cell types such as sclerenchyma fibers. These results correlate with the absence of endogenous MLG synthase activity in mutant seedlings and 4-week-old sheaths. Mutant cell walls are weaker in mature stems but not seedlings, and more brittle in both stems and seedlings, compared to wild type. Mutants also display lesion mimic phenotypes in leaves, which correlates with enhanced defense-related gene expression and enhanced disease resistance. Taken together, our results underline a weaker role of MLG in cell expansion than previously thought, and highlight a structural role for MLG in nonexpanding, mature stem tissues in rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Pamela C. Ronald
- Joint BioEnergy Institute, Emeryville, California 94608 (M.E.V.-S., Y.V., U.C., X.C., V.S., P.V., M.J., S.S., M.A., H.V.S., P.C.R.); Divisions of Physical Biosciences (Y.V., U.C., V.S., H.V.S., P.C.R.) and Life Sciences (M.J., M.A.), Lawrence Berkeley National Laboratory, Berkeley, California 94720; Commonwealth Scientific and Industrial Research Organization Food Futures Flagship (S.A.J., M.T., R.G.W.) and Commonwealth Scientific and Industrial Research Organization Plant Industry (S.A.J.), Black Mountain Laboratories, Black Mountain, Australian Capital Territory 2601, Australia; Department of Plant Pathology (M.E.V.-S., X.C., P.C.R.) and The Genome Center (P.C.R.), University of California, Davis, California 95616; Biomass Science and Conversion Technologies Department, Sandia National Laboratories, Livermore, California 94551 (P.V., S.S.); and Department of Plant Molecular System Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 446–701, Korea (P.C.R.)
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