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Lin D, Zhang L, Mei J, Chen J, Piao Z, Lee G, Dong Y. Mutation of the rice TCM12 gene encoding 2,3-bisphosphoglycerate-independent phosphoglycerate mutase affects chlorophyll synthesis, photosynthesis and chloroplast development at seedling stage at low temperatures. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:585-594. [PMID: 30803106 DOI: 10.1111/plb.12978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Glycolysis is a central metabolic pathway that provides energy and products of primary metabolites. 2,3-Biphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is a key enzyme that catalyses the reversible interconversion of 3-phosphoglycerate (3-PGA) to 2-phosphoglycerate (2-PGA) in glycolysis. Low temperature is a common abiotic stress in rice production. However, the mechanism for rice iPGAM genes is not fully understood at low temperature. In this study, the rice mutant tcm12, with chlorosis, malformed chloroplasts and impaired photosynthesis, was grown at a low temperature (<20 °C) to the three-leaf stage, while the normal phenotype at 32 °C was used. Chlorophyll fluorescence analysis and transmission electron microscopy were used to examine features of the tcm12 mutant. The inheritance behaviour and function of TCM12 were then analysed thorough map-based cloning, transgenic complementation and subcellular localisation. The thermo-sensitive chlorosis phenotype was caused by a single nucleotide mutation (T→C) on the fifth exon of TCM12 (LOC_Os12g35040) encoding iPGAM, localised to both nucleus and membranes. In addition, TCM12 was constitutively expressed, and its disruption resulted in down-regulation of some genes associated with chlorophyll biosynthesis and photosynthesis at low temperatures (20 °C). This is the first report of the involvement of rice iPGAM gene in chlorophyll synthesis, photosynthesis and chloroplast development, providing new insights into the mechanisms underlying early growth of rice at low temperatures.
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Affiliation(s)
- D Lin
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - L Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - J Mei
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - J Chen
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Z Piao
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Fengxian District, Shanghai 3, China
| | - G Lee
- National Institute of Agricultural Science, Jeon Ju, Korea
| | - Y Dong
- College of Life Sciences, Shanghai Normal University, Shanghai, China
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Elmarakeby H, Arefiyan M, Myers E, Li S, Grene R, Heath LS. Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language. J Comput Biol 2017; 24:1226-1229. [PMID: 28846457 DOI: 10.1089/cmb.2017.0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.
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Affiliation(s)
| | - Mostafa Arefiyan
- 2 Bradley Department of Electrical and Computer Engineering, Virginia Tech , Blacksburg, Virginia
| | - Elijah Myers
- 3 Genetics, Bioinformatics and Computational Biology Program, Virginia Tech , Blacksburg, Virginia
| | - Song Li
- 4 Department of Crop and Soil Environmental Sciences, Virginia Tech , Blacksburg, Virginia
| | - Ruth Grene
- 5 Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech , Blacksburg, Virginia
| | - Lenwood S Heath
- 1 Department of Computer Science, Virginia Tech , Blacksburg, Virginia
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Samynathan R, Perisamy SK, Gandhi S, Anitha J, Sanmugam G, Padmanabhan M, Velliyur Kanniappan G. Biochemical and molecular analysis of Camellia sinensis (L.) O. Kuntze tea from the selected P/11/15 clone. J Genet Eng Biotechnol 2016; 14:69-75. [PMID: 30647599 PMCID: PMC6299898 DOI: 10.1016/j.jgeb.2015.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/12/2015] [Accepted: 12/24/2015] [Indexed: 11/28/2022]
Abstract
Green tea is one of the most important beverages consumed across the world and it possesses various phytotherapeutics. Polyphenol oxidase (PPO) activity, total polyphenols, catechins, amino acid content and enzymatic antioxidants are considered to be potential parameters in tea characterization. P/11/15 clone (Camellia sinensis (L) O. Kuntze) was chosen to analyze the biochemical characterization and to analyze the gene expression pattern. The selected P/11/15 clone (C. sinensis (L) O. Kuntze) possess potent Polyphenol oxidase (49.62 U/mg of protein), sufficient catechin (20.75%), Polyphenol (20.01%), Peroxidase (450.08 μM of O2 formed min-1 g-1 dry weight), Catalase (1.20 μM H2O2 reduced min-1 mg-1 protein) and Super Oxide Dismutase (45.11 U/mg proteins). Flavonoid gene expression reveals ANR (1.66%) and F3H (1.02%) were up regulated in the selected P/11/15 clone. The results obtained suggest that P/11/15 clone showed adequate enzyme levels, thus an increased antioxidant activity.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Biochemistry and Bioinformatics, Karpagam University, Coimbatore 641021, TN, India
| | - Suresh kumar Perisamy
- Department of Biotechnology, Anna University, BIT Campus, Tiruchirappalli, TN 620024, India
| | - Sudhakar Gandhi
- Department of Biotechnology, Anna University, BIT Campus, Tiruchirappalli, TN 620024, India
| | - J. Anitha
- Department of Biochemistry and Bioinformatics, Karpagam University, Coimbatore 641021, TN, India
| | - Geetha Sanmugam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology, TNAU, Coimbatore 641003, India
| | - Mohankumar Padmanabhan
- UPASI Tea Research Foundation, UPASI Tea Research Institute, Valparai 642 127, Coimbatore District, TN, India
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Cañas RA, Feito I, Fuente-Maqueda JF, Ávila C, Majada J, Cánovas FM. Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats. BMC Genomics 2015; 16:909. [PMID: 26545587 PMCID: PMC4636790 DOI: 10.1186/s12864-015-2177-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/31/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. RESULTS An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95% of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5% for PINARRAY3 and 5.7% for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. CONCLUSIONS Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds.
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Affiliation(s)
- Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto Andaluz de Biotecnología, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain.
| | - Isabel Feito
- Sección Forestal, SERIDA, Finca Experimental La Mata, 33825, Grado, Principado de Asturias, Spain.
| | | | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto Andaluz de Biotecnología, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain.
| | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental La Mata, 33825, Grado, Principado de Asturias, Spain.
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto Andaluz de Biotecnología, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain.
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Cañas RA, Canales J, Muñoz-Hernández C, Granados JM, Ávila C, García-Martín ML, Cánovas FM. Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3113-27. [PMID: 25873654 PMCID: PMC4449534 DOI: 10.1093/jxb/erv118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into these responses, we examined metabolite and transcriptomic profiles of needles from naturally growing 25-year-old maritime pine (Pinus pinaster L. Aiton) trees over a year. The effect of environmental parameters such as temperature and rain on needle development were studied. Our results show that seasonal changes in the metabolite profiles were mainly affected by the needles' age and acclimation for winter, but changes in transcript profiles were mainly dependent on climatic factors. The relative abundance of most transcripts correlated well with temperature, particularly for genes involved in photosynthesis or winter acclimation. Gene network analysis revealed relationships between 14 co-expressed gene modules and development and adaptation to environmental stimuli. Novel Myb transcription factors were identified as candidate regulators during needle development. Our systems-based analysis provides integrated data of the seasonal regulation of maritime pine growth, opening new perspectives for understanding the complex regulatory mechanisms underlying conifers' adaptive responses. Taken together, our results suggest that the environment regulates the transcriptome for fine tuning of the metabolome during development.
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Affiliation(s)
- Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - Javier Canales
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - Carmen Muñoz-Hernández
- Unidad de Nanoimagen, Centro Andaluz de Nanomedicina y Biotecnología (BIONAND), Parque Tecnológico de Andalucía, C/ Severo Ochoa 35, 29590 Campanillas (Málaga), Spain
| | - Jose M Granados
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
| | - María L García-Martín
- Unidad de Nanoimagen, Centro Andaluz de Nanomedicina y Biotecnología (BIONAND), Parque Tecnológico de Andalucía, C/ Severo Ochoa 35, 29590 Campanillas (Málaga), Spain
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071 Málaga, Spain
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Schöttler MA, Tóth SZ. Photosynthetic complex stoichiometry dynamics in higher plants: environmental acclimation and photosynthetic flux control. FRONTIERS IN PLANT SCIENCE 2014; 5:188. [PMID: 24860580 PMCID: PMC4026699 DOI: 10.3389/fpls.2014.00188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/22/2014] [Indexed: 05/02/2023]
Abstract
The composition of the photosynthetic apparatus of higher plants is dynamically adjusted to long-term changes in environmental conditions such as growth light intensity and light quality, and to changing metabolic demands for ATP and NADPH imposed by stresses and leaf aging. By changing photosynthetic complex stoichiometry, a long-term imbalance between the photosynthetic production of ATP and NADPH and their metabolic consumption is avoided, and cytotoxic side reactions are minimized. Otherwise, an excess capacity of the light reactions, relative to the demands of primary metabolism, could result in a disturbance of cellular redox homeostasis and an increased production of reactive oxygen species, leading to the destruction of the photosynthetic apparatus and the initiation of cell death programs. In this review, changes of the abundances of the different constituents of the photosynthetic apparatus in response to environmental conditions and during leaf ontogenesis are summarized. The contributions of the different photosynthetic complexes to photosynthetic flux control and the regulation of electron transport are discussed.
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Affiliation(s)
- Mark A. Schöttler
- Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
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