1
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Wang L, Xu F, Yu F. Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation. PLANT, CELL & ENVIRONMENT 2023; 46:718-732. [PMID: 36609800 DOI: 10.1111/pce.14537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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2
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Raveendran K, Freese NH, Kintali C, Tiwari S, Bole P, Dias C, Loraine AE. BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser. FRONTIERS IN BIOINFORMATICS 2022; 2:764619. [PMID: 36304269 PMCID: PMC9580933 DOI: 10.3389/fbinf.2022.764619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/28/2022] [Indexed: 11/19/2022] Open
Abstract
Genomics researchers do better work when they can interactively explore and visualize data. Due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and storage resources, but typically lack interactive visualization capability. In this paper, we present BioViz Connect, a middleware Web application that links CyVerse science gateway resources to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the user's personal computer. Using BioViz Connect, users can 1) stream data from the CyVerse data store into IGB for visualization, 2) improve the IGB user experience for themselves and others by adding IGB specific metadata to CyVerse data files, including genome version and track appearance, and 3) run compute-intensive visual analytics functions on CyVerse infrastructure to create new datasets for visualization in IGB or other applications. To demonstrate how BioViz Connect facilitates interactive data visualization, we describe an example RNA-Seq data analysis investigating how heat and desiccation stresses affect gene expression in the model plant Arabidopsis thaliana. The RNA-Seq use case illustrates how interactive visualization with IGB can help a user identify problematic experimental samples, sanity-check results using a positive control, and create new data files for interactive visualization in IGB (or other tools) using a Docker image deployed to CyVerse via the Terrain API. Lastly, we discuss limitations of the technologies used and suggest opportunities for future work. BioViz Connect is available from https://bioviz.org.
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Affiliation(s)
| | | | | | | | | | | | - Ann E. Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
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3
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Chen Y, Weng X, Zhou X, Gu J, Hu Q, Luo Q, Wen M, Li C, Wang ZY. Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153574. [PMID: 34890846 DOI: 10.1016/j.jplph.2021.153574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.
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Affiliation(s)
- Yanhang Chen
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Xun Weng
- College of Life Sciences, South China Agricultural University, Guangdong, 510642, China
| | - Xiaoxia Zhou
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Jinbao Gu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qing Hu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qingwen Luo
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Mingfu Wen
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Cong Li
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
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4
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Ma T, Gao H, Zhang D, Sun W, Yin Q, Wu L, Zhang T, Xu Z, Wei J, Su Y, Shi Y, Ding D, Yuan L, Dong G, Leng L, Xiang L, Chen S. Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L. FRONTIERS IN PLANT SCIENCE 2021; 12:733505. [PMID: 34659300 PMCID: PMC8511310 DOI: 10.3389/fpls.2021.733505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Artemisinin is currently the most effective ingredient in the treatment of malaria, which is thus of great significance to study the genetic regulation of Artemisia annua. Alternative splicing (AS) is a regulatory process that increases the complexity of transcriptome and proteome. The most common mechanism of alternative splicing (AS) in plant is intron retention (IR). However, little is known about whether the IR isoforms produced by light play roles in regulating biosynthetic pathways. In this work we would explore how the level of AS in A. annua responds to light regulation. We obtained a new dataset of AS by analyzing full-length transcripts using both Illumina- and single molecule real-time (SMRT)-based RNA-seq as well as analyzing AS on various tissues. A total of 5,854 IR isoforms were identified, with IR accounting for the highest proportion (48.48%), affirming that IR is the most common mechanism of AS. We found that the number of up-regulated IR isoforms (1534/1378, blue and red light, respectively) was more than twice that of down-regulated (636/682) after treatment of blue or red light. In the artemisinin biosynthetic pathway, 10 genes produced 16 differentially expressed IR isoforms. This work demonstrated that the differential expression of IR isoforms induced by light has the potential to regulate sesquiterpenoid biosynthesis. This study also provides high accuracy full-length transcripts, which can be a valuable genetic resource for further research of A. annua, including areas of development, breeding, and biosynthesis of active compounds.
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Affiliation(s)
- Tingyu Ma
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Han Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Dong Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qinggang Yin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianyuan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Yanyan Su
- Amway (China) Botanical R&D Center, Wuxi, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dandan Ding
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United States
| | | | - Liang Leng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United States
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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5
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Study of Triticum aestivum Resistome in Response to Wheat dwarf India Virus Infection. Life (Basel) 2021; 11:life11090955. [PMID: 34575104 PMCID: PMC8469153 DOI: 10.3390/life11090955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Susceptible and resistant germplasm respond differently to pathogenic attack, including virus infections. We compared the transcriptome changes between a resistant wheat cultivar, Sonalika, and a susceptible cultivar, WL711, to understand this process in wheat against wheat dwarf India virus (WDIV) infection. A total of 2760 and 1853 genes were differentially expressed in virus-infected and mock-inoculated Sonalika, respectively, compared to WL711. The overrepresentation of genes involved in signaling, hormone metabolism, enzymes, secondary metabolites, proteolysis, and transcription factors was documented, including the overexpression of multiple PR proteins. We hypothesize that the virus resistance in Sonalika is likely due to strong intracellular surveillance via the action of multiple PR proteins (PR1, RAR1, and RPM1) and ChiB. Other genes such as PIP1, LIP1, DnaJ, defensins, oxalate oxidase, ankyrin repeat protein, serine-threonine kinase, SR proteins, beta-1,3-glucanases, and O-methyltransferases had a significant differential expression and play roles in stress tolerance, may also be contributing towards the virus resistance in Sonalika. In addition, we identified putative genes with unknown functions, which are only expressed in response to WDIV infection in Sonalika. The role of these genes could be further validated and utilized in engineering resistance in wheat and other crops.
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Li Z, Tang J, Bassham DC, Howell SH. Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize. PLANT PHYSIOLOGY 2021; 186:1318-1335. [PMID: 33705553 PMCID: PMC8195531 DOI: 10.1093/plphys/kiab110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/18/2021] [Indexed: 05/04/2023]
Abstract
Elevated temperatures enhance alternative RNA splicing in maize (Zea mays) with the potential to expand the repertoire of plant responses to heat stress. Alternative RNA splicing generates multiple RNA isoforms for many maize genes, and here we observed changes in the pattern of RNA isoforms with temperature changes. Increases in maximum daily temperature elevated the frequency of the major modes of alternative splices (AS), in particular retained introns and skipped exons. The genes most frequently targeted by increased AS with temperature encode factors involved in RNA processing and plant development. Genes encoding regulators of alternative RNA splicing were themselves among the principal AS targets in maize. Under controlled environmental conditions, daily changes in temperature comparable to field conditions altered the abundance of different RNA isoforms, including the RNAs encoding the splicing regulator SR45a, a member of the SR45 gene family. We established an "in protoplast" RNA splicing assay to show that during the afternoon on simulated hot summer days, SR45a RNA isoforms were produced with the potential to encode proteins efficient in splicing model substrates. With the RNA splicing assay, we also defined the exonic splicing enhancers that the splicing-efficient SR45a forms utilize to aid in the splicing of model substrates. Hence, with rising temperatures on hot summer days, SR45a RNA isoforms in maize are produced with the capability to encode proteins with greater RNA splicing potential.
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Affiliation(s)
- Zhaoxia Li
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
| | - Jie Tang
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Diane C Bassham
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Stephen H. Howell
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
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7
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Muthusamy M, Yoon EK, Kim JA, Jeong MJ, Lee SI. Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes. Genes (Basel) 2020; 11:genes11020182. [PMID: 32050656 PMCID: PMC7074037 DOI: 10.3390/genes11020182] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/25/2020] [Accepted: 02/07/2020] [Indexed: 01/02/2023] Open
Abstract
The emerging evidence has shown that plant serine/arginine-rich (SR) proteins play a crucial role in abiotic stress responses by regulating the alternative splicing (AS) of key genes. Recently, we have shown that drought stress enhances the expression of SR45a (also known as SR-like 3) in Brassica rapa. Herein, we unraveled the hitherto unknown functions of BrSR45a in drought stress response by comparing the phenotypes, chlorophyll a fluorescence and splicing patterns of the drought-responsive genes of Arabidopsis BrSR45a overexpressors (OEs), homozygous mutants (SALK_052345), and controls (Col-0). Overexpression and loss of function did not result in aberrant phenotypes; however, the overexpression of BrSR45a was positively correlated with drought tolerance and the stress recovery rate in an expression-dependent manner. Moreover, OEs showed a higher drought tolerance index during seed germination (38.16%) than the control lines. Additionally, the overexpression of BrSR45a induced the expression of the drought stress-inducible genes RD29A, NCED3, and DREB2A under normal conditions. To further illustrate the molecular linkages between BrSR45a and drought tolerance, we investigated the AS patterns of key drought-tolerance and BrSR45a interacting genes in OEs, mutants, and controls under both normal and drought conditions. The splicing patterns of DCP5, RD29A, GOLS1, AKR, U2AF, and SDR were different between overexpressors and mutants under normal conditions. Furthermore, drought stress altered the splicing patterns of NCED2, SQE, UPF1, U4/U6-U5 tri-snRNP-associated protein, and UPF1 between OEs and mutants, indicating that both overexpression and loss of function differently influenced the splicing patterns of target genes. This study revealed that BrSR45a regulates the drought stress response via the alternative splicing of target genes in a concentration-dependent manner.
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Affiliation(s)
- Muthusamy Muthusamy
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea; (M.M.); (J.A.K.); (M.-J.J.)
| | - Eun Kyung Yoon
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore;
| | - Jin A Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea; (M.M.); (J.A.K.); (M.-J.J.)
| | - Mi-Jeong Jeong
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea; (M.M.); (J.A.K.); (M.-J.J.)
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea; (M.M.); (J.A.K.); (M.-J.J.)
- Correspondence: ; Tel.: +82-63-238-4618; Fax: +82-63-238-4604
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Kumar J, Gunapati S, Kianian SF, Singh SP. Comparative analysis of transcriptome in two wheat genotypes with contrasting levels of drought tolerance. PROTOPLASMA 2018; 255:1487-1504. [PMID: 29651660 DOI: 10.1007/s00709-018-1237-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/05/2018] [Indexed: 05/19/2023]
Abstract
Drought tolerance is a complex trait that is governed by multiple genes. The study presents differential transcriptome analysis between drought-tolerant (Triticum aestivum Cv. C306) and drought-sensitive (Triticum aestivum Cv. WL711) genotypes, using Affymetrix GeneChip® Wheat Genome Array. Both genotypes exhibited diverse global transcriptional responses under control and drought conditions. Pathway analysis suggested significant induction or repression of genes involved in secondary metabolism, nucleic acid synthesis, protein synthesis, and transport in C306, as compared to WL711. Significant up- and downregulation of transcripts for enzymes, hormone metabolism, and stress response pathways were observed in C306 under drought. The elevated expression of plasma membrane intrinsic protein 1 and downregulation of late embryogenesis abundant in the leaf tissues could play an important role in delayed wilting in C306. The other regulatory genes such as MT, FT, AP2, SKP1, ABA2, ARF6, WRKY6, AOS, and LOX2 are involved in defense response in C306 genotype. Additionally, transcripts with unknown functions were identified as differentially expressed, which could participate in drought responses.
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Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute, Mohali, India
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, USA
| | - Samatha Gunapati
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | - Sudhir P Singh
- National Agri-Food Biotechnology Institute, Mohali, India.
- Center of Innovative and Applied Bioprocessing, Mohali, India.
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9
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van Rooijen R, Harbinson J, Aarts MGM. Photosynthetic response to increased irradiance correlates to variation in transcriptional response of lipid-remodeling and heat-shock genes. PLANT DIRECT 2018; 2:e00069. [PMID: 31245733 PMCID: PMC6508758 DOI: 10.1002/pld3.69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/10/2018] [Accepted: 06/12/2018] [Indexed: 05/11/2023]
Abstract
Plants have evolved several mechanisms for sensing increased irradiance, involving signal perception by photoreceptors (cryptochromes), and subsequent biochemical (reactive oxygen species, ROS) and metabolic clues to transmit the signals. This results in the increased expression of heat-shock response genes and of the transcription factor LONG HYPOCOTYL 5 (HY5, mediated by the cryptochrome photoreceptor 1, CRY1). Here, we show the existence of another response pathway in Arabidopsis. This pathway evokes the SPX1-mediated expression activation of the transcription factor PHR1 and leads to the expression of several galactolipid biosynthesis genes. Gene expression analysis of accessions Col-0, Ga-0, and Ts-1, showed activated expression of the SPX1/PHR1-mediated gene expression activation pathway acting on galactolipids biosynthesis genes in both Ga-0 and Col-0, but not in Ts-1. The activation of the SPX1/PHR1-mediated response pathway can be associated with lower photosynthesis efficiency in Ts-1, compared to Col-0 and Ga-0. Besides the accession-associated activation of the SPX1/PHR1-mediated response pathway, comparing gene expression in the accessions showed stronger activation of several heat responsive genes in Ga-0, and the opposite in Ts-1, when compared to Col-0, in line with the differences in their efficiency of photosynthesis. We conclude that natural variation in activation of both heat responsive genes and of galactolipids biosynthesis genes contribute to the variation in photosynthesis efficiency in response to irradiance increase.
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Affiliation(s)
- Roxanne van Rooijen
- Laboratory of GeneticsWageningen University and ResearchWageningenThe Netherlands
- Horticulture and Product PhysiologyWageningen University and ResearchWageningenThe Netherlands
- Present address:
Cluster of Excellence on Plant ScienceHeinrich Heine UniversityDüsseldorfGermany
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchWageningenThe Netherlands
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10
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Zhang P, Meng X, Chen H, Liu Y, Xue J, Zhou Y, Chen M. PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:4718479. [PMID: 31725858 PMCID: PMC5727401 DOI: 10.1093/database/bax089] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022]
Abstract
Circular RNA (circRNA) is a novel type of endogenous noncoding RNA with covalently closed loop structures, which are widely expressed in various tissues and have functional implications in cellular processes. Acting as competing endogenous RNAs (ceRNAs), circRNAs are important regulators of miRNA activities. The identification of these circRNAs underlines the increasing complexity of ncRNA-mediated regulatory networks. However, more biological evidence is required to infer direct circRNA–miRNA associations while little attention has been paid to circRNAs in plants as compared to the abundant research in mammals. PlantCircNet is presented as an integrated database that provides visualized plant circRNA–miRNA–mRNA regulatory networks containing identified circRNAs in eight model plants. The bioinformatics integration of data from multiple sources reveals circRNA–miRNA–mRNA regulatory networks and helps identify mechanisms underlying metabolic effects of circRNAs. An enrichment analysis tool was implemented to detect significantly overrepresented Gene Ontology categories of miRNA targets. The genomic annotations, sequences and isoforms of circRNAs were also investigated. PlantCircNet provides a user-friendly interface for querying detailed information of specific plant circRNAs. The database may serve as a resource to facilitate plant circRNA research. Several circRNAs were identified to play potential regulatory roles in flower development and response to environmental stress from regulatory networks related with miR156a and AT5G59720, respectively. This present research indicated that circRNAs could be involved in diverse biological processes. Database URL: http://bis.zju.edu.cn/plantcircnet/index.php
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Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongjun Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongjing Liu
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jitong Xue
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yincong Zhou
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
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11
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Zhang H, Lin C, Gu L. Light Regulation of Alternative Pre-mRNA Splicing in Plants. Photochem Photobiol 2017; 93:159-165. [PMID: 27925216 DOI: 10.1111/php.12680] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/20/2016] [Indexed: 02/03/2023]
Abstract
Alternative splicing (AS) is a major post-transcriptional mechanism to enhance the diversity of proteome in response to environmental signals. Among the numerous external signals perceived by plants, light is the most crucial one. Plants utilize complex photoreceptor signaling networks to sense different light conditions and adjust their growth and development accordingly. Although light-mediated gene expression has been widely investigated, little is known regarding the mechanism of light affecting AS to modulate mRNA at the post-transcriptional level. In this minireview, we summarize current progresses on how light affects AS, and how sensory photoreceptors and retrograde signaling pathways may coordinately regulate AS of pre-mRNAs. In addition, we also discuss the possibility that AS of the mRNAs encoding photoreceptors may be involved in feedback control of AS. We hypothesize that light regulation of the expression and activity of splicing factors would be a major mechanism of light-mediated AS. The combination of genetic study and high-throughput analyses of AS and splicing complexes in response to light is likely to further advance our understanding of the molecular mechanisms underlying light control of AS and plant development.
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Affiliation(s)
- Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
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Srinivasan A, Jiménez-Gómez JM, Fornara F, Soppe WJJ, Brambilla V. Alternative splicing enhances transcriptome complexity in desiccating seeds. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:947-958. [PMID: 27121908 DOI: 10.1111/jipb.12482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/20/2016] [Indexed: 05/22/2023]
Abstract
Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are established during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing (AS). However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 34% of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.
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Affiliation(s)
- Arunkumar Srinivasan
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Open Analytics, Antwerp, Belgium
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Versailles, France
| | - Fabio Fornara
- University of Milan, Department of Biosciences, Milano 20133, Italy
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vittoria Brambilla
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- University of Milan, Department of Biosciences, Milano 20133, Italy
- University of Milan, Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milano, Italy
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Abscisic acid (ABA) regulation of Arabidopsis SR protein gene expression. Int J Mol Sci 2014; 15:17541-64. [PMID: 25268622 PMCID: PMC4227177 DOI: 10.3390/ijms151017541] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/13/2014] [Accepted: 09/23/2014] [Indexed: 11/21/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are major modulators of alternative splicing, a key generator of proteomic diversity and flexible means of regulating gene expression likely to be crucial in plant environmental responses. Indeed, mounting evidence implicates splicing factors in signal transduction of the abscisic acid (ABA) phytohormone, which plays pivotal roles in the response to various abiotic stresses. Using real-time RT-qPCR, we analyzed total steady-state transcript levels of the 18 SR and two SR-like genes from Arabidopsis thaliana in seedlings treated with ABA and in genetic backgrounds with altered expression of the ABA-biosynthesis ABA2 and the ABA-signaling ABI1 and ABI4 genes. We also searched for ABA-responsive cis elements in the upstream regions of the 20 genes. We found that members of the plant-specific SC35-Like (SCL) Arabidopsis SR protein subfamily are distinctively responsive to exogenous ABA, while the expression of seven SR and SR-related genes is affected by alterations in key components of the ABA pathway. Finally, despite pervasiveness of established ABA-responsive promoter elements in Arabidopsis SR and SR-like genes, their expression is likely governed by additional, yet unidentified cis-acting elements. Overall, this study pinpoints SR34, SR34b, SCL30a, SCL28, SCL33, RS40, SR45 and SR45a as promising candidates for involvement in ABA-mediated stress responses.
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Analysis of gene expression profiles of soft tissue sarcoma using a combination of knowledge-based filtering with integration of multiple statistics. PLoS One 2014; 9:e106801. [PMID: 25188299 PMCID: PMC4154757 DOI: 10.1371/journal.pone.0106801] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 08/01/2014] [Indexed: 12/21/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STS) have been difficult. Of the diverse histological subtypes, undifferentiated pleomorphic sarcoma (UPS) is particularly difficult to diagnose accurately, and its classification per se is still controversial. Recent advances in genomic technologies provide an excellent way to address such problems. However, it is often difficult, if not impossible, to identify definitive disease-associated genes using genome-wide analysis alone, primarily because of multiple testing problems. In the present study, we analyzed microarray data from 88 STS patients using a combination method that used knowledge-based filtering and a simulation based on the integration of multiple statistics to reduce multiple testing problems. We identified 25 genes, including hypoxia-related genes (e.g., MIF, SCD1, P4HA1, ENO1, and STAT1) and cell cycle- and DNA repair-related genes (e.g., TACC3, PRDX1, PRKDC, and H2AFY). These genes showed significant differential expression among histological subtypes, including UPS, and showed associations with overall survival. STAT1 showed a strong association with overall survival in UPS patients (logrank p = 1.84 × 10(-6) and adjusted p value 2.99 × 10(-3) after the permutation test). According to the literature, the 25 genes selected are useful not only as markers of differential diagnosis but also as prognostic/predictive markers and/or therapeutic targets for STS. Our combination method can identify genes that are potential prognostic/predictive factors and/or therapeutic targets in STS and possibly in other cancers. These disease-associated genes deserve further preclinical and clinical validation.
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15
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Takahashi H, Sai K, Saito Y, Kaniwa N, Matsumura Y, Hamaguchi T, Shimada Y, Ohtsu A, Yoshino T, Doi T, Okuda H, Ichinohe R, Takahashi A, Doi A, Odaka Y, Okuyama M, Saijo N, Sawada JI, Sakamoto H, Yoshida T. Application of a combination of a knowledge-based algorithm and 2-stage screening to hypothesis-free genomic data on irinotecan-treated patients for identification of a candidate single nucleotide polymorphism related to an adverse effect. PLoS One 2014; 9:e105160. [PMID: 25127363 PMCID: PMC4134257 DOI: 10.1371/journal.pone.0105160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 07/17/2014] [Indexed: 01/27/2023] Open
Abstract
Interindividual variation in a drug response among patients is known to cause serious problems in medicine. Genomic information has been proposed as the basis for “personalized” health care. The genome-wide association study (GWAS) is a powerful technique for examining single nucleotide polymorphisms (SNPs) and their relationship with drug response variation; however, when using only GWAS, it often happens that no useful SNPs are identified due to multiple testing problems. Therefore, in a previous study, we proposed a combined method consisting of a knowledge-based algorithm, 2 stages of screening, and a permutation test for identifying SNPs. In the present study, we applied this method to a pharmacogenomics study where 109,365 SNPs were genotyped using Illumina Human-1 BeadChip in 168 cancer patients treated with irinotecan chemotherapy. We identified the SNP rs9351963 in potassium voltage-gated channel subfamily KQT member 5 (KCNQ5) as a candidate factor related to incidence of irinotecan-induced diarrhea. The p value for rs9351963 was 3.31×10−5 in Fisher's exact test and 0.0289 in the permutation test (when multiple testing problems were corrected). Additionally, rs9351963 was clearly superior to the clinical parameters and the model involving rs9351963 showed sensitivity of 77.8% and specificity of 57.6% in the evaluation by means of logistic regression. Recent studies showed that KCNQ4 and KCNQ5 genes encode members of the M channel expressed in gastrointestinal smooth muscle and suggested that these genes are associated with irritable bowel syndrome and similar peristalsis diseases. These results suggest that rs9351963 in KCNQ5 is a possible predictive factor of incidence of diarrhea in cancer patients treated with irinotecan chemotherapy and for selecting chemotherapy regimens, such as irinotecan alone or a combination of irinotecan with a KCNQ5 opener. Nonetheless, clinical importance of rs9351963 should be further elucidated.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Kimie Sai
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Tetsuya Hamaguchi
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuhiro Shimada
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Ohtsu
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Toshihiko Doi
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Haruhiro Okuda
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Risa Ichinohe
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Ayano Doi
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Yoko Odaka
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Misuzu Okuyama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nagahiro Saijo
- National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Jun-ichi Sawada
- Division of Functional Biochemistry and Genomics, National Institute of Health Sciences, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
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16
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Kianianmomeni A. More light behind gene expression. TRENDS IN PLANT SCIENCE 2014; 19:488-90. [PMID: 24928178 DOI: 10.1016/j.tplants.2014.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/02/2014] [Accepted: 05/23/2014] [Indexed: 05/20/2023]
Abstract
Light-regulated gene expression, mediated by photoreceptors, acts as a multifaceted regulator to control the abundance of functional genes at different levels. Two recent genome-wide studies by Wu et al. and Liu et al. show that light controls gene expression at post-transcriptional and translational level through alternative splicing and translational regulation, respectively.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany.
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17
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Yu E, Fan C, Yang Q, Li X, Wan B, Dong Y, Wang X, Zhou Y. Identification of heat responsive genes in Brassica napus siliques at the seed-filling stage through transcriptional profiling. PLoS One 2014; 9:e101914. [PMID: 25013950 PMCID: PMC4094393 DOI: 10.1371/journal.pone.0101914] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022] Open
Abstract
High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, global transcription profiles of 20 d-old siliques of B. napus were analyzed after heat stress using a Brassica 95k EST microarray. The up-regulated genes included many HSF/HSP transcripts and other heat-related marker genes, such as ROF2, DREB2a, MBF1c and Hsa32, reflecting the conservation of key heat resistance factors among plants. Other up-regulated genes were preferentially expressed in heat-stressed silique walls or seeds, including some transcription factors and potential developmental regulators. In contrast, down-regulated genes differed between the silique wall and seeds and were largely tied to the biological functions of each tissue, such as glucosinolate metabolism in the silique wall and flavonoid synthesis in seeds. Additionally, a large proportion (one-third) of these differentially expressed genes had unknown functions. Based on these gene expression profiles, Arabidopsis mutants for eight heat-induced Brassica homologous genes were treated with different heat stress methods, and thermotolerance varied with each mutation, heat stress regimen and plant development stage. At least two of the eight mutants exhibited sensitivity to the heat treatments, suggesting the importance of the respective genes in responding to heat stress. In summary, this study elucidated the molecular bases of the heat responses in siliques during later reproductive stages and provides valuable information and gene resources for the genetic improvement of heat tolerance in oilseed rape breeding.
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Affiliation(s)
- Erru Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaodong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Bingxi Wan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanni Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, Saint Louis, Missouri, United States of America
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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18
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Wu HP, Su YS, Chen HC, Chen YR, Wu CC, Lin WD, Tu SL. Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol 2014; 15:R10. [PMID: 24398233 PMCID: PMC4054894 DOI: 10.1186/gb-2014-15-1-r10] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/07/2014] [Indexed: 12/22/2022] Open
Abstract
Background Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of gene expression are modulated by photoreceptors, regulation at the mRNA splicing step remains unclear. Results We performed high-throughput mRNA sequencing to analyze light-responsive changes in alternative splicing in the moss Physcomitrella patens, and found that a large number of alternative splicing events were induced by light in the moss protonema. Light-responsive intron retention preferentially occurred in transcripts involved in photosynthesis and translation. Many of the alternatively spliced transcripts were expressed from genes with a function relating to splicing or light signaling, suggesting a potential impact on pre-mRNA splicing and photomorphogenic gene regulation in response to light. Moreover, most light-regulated intron retention was induced immediately upon light exposure, while motif analysis identified a repetitive GAA motif that may function as an exonic regulatory cis element in light-mediated alternative splicing. Further analysis in gene-disrupted mutants was consistent with a function for multiple red-light photoreceptors in the upstream regulation of light-responsive alternative splicing. Conclusions Our results indicate that intensive alternative splicing occurs in non-vascular plants and that, during photomorphogenesis, light regulates alternative splicing with transcript selectivity. We further suggest that alternative splicing is rapidly fine-tuned by light to modulate gene expression and reorganize metabolic processes, and that pre-mRNA cis elements are involved in photoreceptor-mediated splicing regulation.
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19
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Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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20
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Takahashi H, Nakayama R, Hayashi S, Nemoto T, Murase Y, Nomura K, Takahashi T, Kubo K, Marui S, Yasuhara K, Nakamura T, Sueo T, Takahashi A, Tsutsumiuchi K, Ohta T, Kawai A, Sugita S, Yamamoto S, Kobayashi T, Honda H, Yoshida T, Hasegawa T. Macrophage migration inhibitory factor and stearoyl-CoA desaturase 1: potential prognostic markers for soft tissue sarcomas based on bioinformatics analyses. PLoS One 2013; 8:e78250. [PMID: 24167613 PMCID: PMC3805525 DOI: 10.1371/journal.pone.0078250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STSs) has been particularly difficult, because STSs are a group of highly heterogeneous tumors in terms of histopathology, histological grade, and primary site. Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis, treatment selection, and investigation of therapeutic targets. We had previously developed a novel bioinformatics method for marker gene selection and applied this method to gene expression data from STS patients. This previous analysis revealed that the extracted gene combination of macrophage migration inhibitory factor (MIF) and stearoyl-CoA desaturase 1 (SCD1) is an effective diagnostic marker to discriminate between subtypes of STSs with highly different outcomes. In the present study, we hypothesize that the combination of MIF and SCD1 is also a prognostic marker for the overall outcome of STSs. To prove this hypothesis, we first analyzed microarray data from 88 STS patients and their outcomes. Our results show that the survival rates for MIF- and SCD1-positive groups were lower than those for negative groups, and the p values of the log-rank test are 0.0146 and 0.00606, respectively. In addition, survival rates are more significantly different (p = 0.000116) between groups that are double-positive and double-negative for MIF and SCD1. Furthermore, in vitro cell growth inhibition experiments by MIF and SCD1 inhibitors support the hypothesis. These results suggest that the gene set is useful as a prognostic marker associated with tumor progression.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Robert Nakayama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Transcriptome Project, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Hayashi
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Nemoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Dermatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuyuki Murase
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Koji Nomura
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruyoshi Takahashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Kenji Kubo
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Shigetaka Marui
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Koji Yasuhara
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tetsuro Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Takuya Sueo
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Kaname Tsutsumiuchi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tsutomu Ohta
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Kawai
- Orthopedics Division, National Cancer Center Hospital, Tokyo, Japan
| | - Shintaro Sugita
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Shinjiro Yamamoto
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Kobayashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
- Pathology Division, National Cancer Center Hospital, Tokyo, Japan,
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21
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Takahashi H, Kaniwa N, Saito Y, Sai K, Hamaguchi T, Shirao K, Shimada Y, Matsumura Y, Ohtsu A, Yoshino T, Takahashi A, Odaka Y, Okuyama M, Sawada JI, Sakamoto H, Yoshida T. Identification of a candidate single-nucleotide polymorphism related to chemotherapeutic response through a combination of knowledge-based algorithm and hypothesis-free genomic data. J Biosci Bioeng 2013; 116:768-73. [PMID: 23816762 DOI: 10.1016/j.jbiosc.2013.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/02/2013] [Accepted: 05/13/2013] [Indexed: 01/06/2023]
Abstract
Inter-individual variations in drug responses among patients are known to cause serious problems in medicine. Genome-wide association study (GWAS) is powerful for examining single-nucleotide polymorphisms (SNPs) and their relationships with drug response variations. However, no significant SNP has been identified using GWAS due to multiple testing problems. Therefore, we propose a combination method consisting of knowledge-based algorithm, two stages of screening, and permutation test for identifying SNPs in the present study. We applied this method to a genome-wide pharmacogenomics study for which 109,365 SNPs had been genotyped using Illumina Human-1 BeadChip for 119 gastric cancer patients treated with fluoropyrimidine. We identified rs2293347 in epidermal growth factor receptor (EGFR) is as a candidate SNP related to chemotherapeutic response. The p value for the rs2293347 was 2.19 × 10(-5) for Fisher's exact test, and the p value was 0.00360 for the permutation test (multiple testing problems are corrected). Additionally, rs2293347 was clearly superior to clinical parameters and showed a sensitivity value of 55.0% and specificity value of 94.4% in the evaluation by using multiple regression models. Recent studies have shown that combination chemotherapy of fluoropyrimidine and EGFR-targeting agents is effective for gastric cancer patients highly expressing EGFR. These results suggest that rs2293347 is a potential predictive factor for selecting chemotherapies, such as fluoropyrimidine alone or combination chemotherapies.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan; Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi 487-8501, Japan; Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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22
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Takahashi H, Iwakawa H, Ishibashi N, Kojima S, Matsumura Y, Prananingrum P, Iwasaki M, Takahashi A, Ikezaki M, Luo L, Kobayashi T, Machida Y, Machida C. Meta-analyses of microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and their modifying mutants reveal a critical role for the ETT pathway in stabilization of adaxial-abaxial patterning and cell division during leaf development. PLANT & CELL PHYSIOLOGY 2013; 54:418-31. [PMID: 23396601 PMCID: PMC3589830 DOI: 10.1093/pcp/pct027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/01/2013] [Indexed: 05/22/2023]
Abstract
It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial-abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1-AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1-AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1-AS2-ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba, 271-8510 Japan
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
| | - Hidekazu Iwakawa
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
- Present address: Department of Biological Sciences, Purdue University, West, Lafayette, IN 47907-1392, USA
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- These authors contributed equally to this work
| | - Shoko Kojima
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Pratiwi Prananingrum
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Mayumi Iwasaki
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Present address: Department of Plant Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Masaya Ikezaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Takeshi Kobayashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
| | - Chiyoko Machida
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
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Funck D, Clauß K, Frommer WB, Hellmann HA. The Arabidopsis CstF64-Like RSR1/ESP1 Protein Participates in Glucose Signaling and Flowering Time Control. FRONTIERS IN PLANT SCIENCE 2012; 3:80. [PMID: 22629280 PMCID: PMC3355569 DOI: 10.3389/fpls.2012.00080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 04/10/2012] [Indexed: 05/03/2023]
Abstract
Mechanisms for sensing and regulating metabolic processes at the cellular level are critical for the general physiology and development of living organisms. In higher plants, sugar signaling is crucial for adequate regulation of carbon and energy metabolism and affects virtually every aspect of development. Although many genes are regulated by sugar levels, little is known on how sugar levels are measured by plants. Several components of the sugar signaling network have been unraveled and demonstrated to have extensive overlap with hormone signaling networks. Here we describe the reduced sugar response1-1 (rsr1-1) mutant as a new early flowering mutant that displays decreased sensitivity to abscisic acid. Both hexokinase1 (HXK1)-dependent and glucose phosphorylation-independent signaling is reduced in rsr1-1. Map-based identification of the affected locus demonstrated that rsr1-1 carries a premature stop codon in the gene for a CstF64-like putative RNA processing factor, ESP1, which is involved in mRNA 3'-end formation. The identification of RSR1/ESP1 as a nuclear protein with a potential threonine phosphorylation site may explain the impact of protein phosphorylation cascades on sugar-dependent signal transduction. Additionally, RSR1/ESP1 may be a crucial factor in linking sugar signaling to the control of flowering time.
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Affiliation(s)
- Dietmar Funck
- Department of Plant Physiology and Biochemistry, University KonstanzKonstanz, Germany
| | - Karen Clauß
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
- *Correspondence: Wolf B. Frommer, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94306, USA. e-mail:
| | - Hanjo A. Hellmann
- School of Biological Sciences, Washington State UniversityPullman, WA, USA
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