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Razi K, Muneer S. Grafting enhances drought tolerance by regulating and mobilizing proteome, transcriptome and molecular physiology in okra genotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1178935. [PMID: 37251756 PMCID: PMC10214962 DOI: 10.3389/fpls.2023.1178935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/06/2023] [Indexed: 05/31/2023]
Abstract
Drought stress poses a serious concern to the growth, development, and quality of the okra crop due to factors including decreased yield, inadequate development of dietary fibre, increased mite infestation, and decreased seed viability. Grafting is one of the strategies that have been developed to increase the drought stress tolerance of crops. We conducted proteomics, transcriptomics and integrated it with molecular physiology to assess the response of sensitive okra genotypes; NS7772 (G1), Green gold (G2) and OH3312 (G3) (scion) grafted to NS7774 (rootstock). In our studies we observed that sensitive okra genotypes grafted to tolerant genotypes mitigated the deleterious effects of drought stress through an increase in physiochemical parameters, and lowered reactive oxygen species. A comparative proteomic analysis showed a stress responsive proteins related to Photosynthesis, energy and metabolism, defence response, protein and nucleic acid biosynthesis. A proteomic investigation demonstrated that scions grafted onto okra rootstocks increased more photosynthesis-related proteins during drought stress, indicating an increase in photosynthetic activity when plants were subjected to drought stress. Furthermore, transcriptome of RD2, PP2C, HAT22, WRKY and DREB increased significantly, specifically for grafted NS7772 genotype. Furthermore, our study also indicated that grafting improved the yield components such as number of pods and seeds per plant, maximum fruit diameter, and maximum plant height in all genotypes which directly contributed towards their high resistance towards drought stress.
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Affiliation(s)
- Kaukab Razi
- Horticulture and Molecular Physiology Lab, Department of Horticulture and Food Science, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil Nadu, Vellore, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, Department of Horticulture and Food Science, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil Nadu, Vellore, India
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2
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Le XH, Millar AH. The diversity of substrates for plant respiration and how to optimize their use. PLANT PHYSIOLOGY 2023; 191:2133-2149. [PMID: 36573332 PMCID: PMC10069909 DOI: 10.1093/plphys/kiac599] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Plant respiration is a foundational biological process with the potential to be optimized to improve crop yield. To understand and manipulate the outputs of respiration, the inputs of respiration-respiratory substrates-need to be probed in detail. Mitochondria house substrate catabolic pathways and respiratory machinery, so transport into and out of these organelles plays an important role in committing substrates to respiration. The large number of mitochondrial carriers and catabolic pathways that remain unidentified hinder this process and lead to confusion about the identity of direct and indirect respiratory substrates in plants. The sources and usage of respiratory substrates vary and are increasing found to be highly regulated based on cellular processes and environmental factors. This review covers the use of direct respiratory substrates following transport through mitochondrial carriers and catabolism under normal and stressed conditions. We suggest the introduction of enzymes not currently found in plant mitochondria to enable serine and acetate to be direct respiratory substrates in plants. We also compare respiratory substrates by assessing energetic yields, availability in cells, and their full or partial oxidation during cell catabolism. This information can assist in decisions to use synthetic biology approaches to alter the range of respiratory substrates in plants. As a result, respiration could be optimized by introducing, improving, or controlling specific mitochondrial transporters and mitochondrial catabolic pathways.
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Affiliation(s)
- Xuyen H Le
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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3
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Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
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Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
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Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
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Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
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de Souza LP, Borghi M, Fernie A. Plant Single-Cell Metabolomics-Challenges and Perspectives. Int J Mol Sci 2020; 21:E8987. [PMID: 33256100 PMCID: PMC7730874 DOI: 10.3390/ijms21238987] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a similar trend as the original development of these techniques, proteomics alternatives for single-cell exploration have become more accessible and reliable, whilst metabolomics lag behind the rest. This review summarizes state-of-the-art technologies for spatially resolved metabolomics analysis, as well as the challenges hindering the achievement of sensu stricto metabolome coverage at the single-cell level. Furthermore, we discuss several essential contributions to understanding plant single-cell metabolism, finishing with our opinion on near-future developments and relevant scientific questions that will hopefully be tackled by incorporating these new exciting technologies.
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Affiliation(s)
- Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
| | - Monica Borghi
- Department of Biology, Utah State University, 1435 Old Main Hill, Logan, UT 84322, USA;
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
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Lee SK, Jeon JS. Review: Crucial role of inorganic pyrophosphate in integrating carbon metabolism from sucrose breakdown to starch synthesis in rice endosperm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110572. [PMID: 32771173 DOI: 10.1016/j.plantsci.2020.110572] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/28/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
The endosperm is a primary constituent of mature seeds in rice as well as in other cereal crops, serving as the major storage reserve of starch. Observations indicate that the central part of the endosperm is subject to hypoxic conditions, which require a switch of energy metabolism owing to limited mitochondrial respiration. Uniquely, this endosperm generates a large source of inorganic pyrophosphate (PPi) as a byproduct of the reaction of ADP glucose pyrophosphorylase in the cytosol. Recent results derived from examination of the mutants of cereal crops, especially rice, for PPi-utilizing enzymes clearly suggest an important role of PPi as an alternative energy currency for integrating carbon metabolism from sucrose breakdown to starch synthesis in the endosperm. Thus, the present review provides an outline of the interlaced PPi-dependent metabolic pathways, which are critical for starch synthesis in the endosperm in terms of energy metabolism, along with its application to enhance yield potential.
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Affiliation(s)
- Sang-Kyu Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, South Korea.
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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8
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Impe D, Reitz J, Köpnick C, Rolletschek H, Börner A, Senula A, Nagel M. Assessment of Pollen Viability for Wheat. FRONTIERS IN PLANT SCIENCE 2020; 10:1588. [PMID: 32038666 PMCID: PMC6987437 DOI: 10.3389/fpls.2019.01588] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/12/2019] [Indexed: 05/15/2023]
Abstract
Wheat sheds tricellular short-lived pollen at maturity. The identification of viable pollen required for high seed set is important for breeders and conservators. The present study aims to evaluate and improve pollen viability tests and to identify factors influencing viability of pollen. In fresh wheat pollen, sucrose was the most abundant soluble sugar (90%). Raffinose was present in minor amounts. However, the analyses of pollen tube growth on 112 liquid and 45 solid media revealed that solid medium with 594 mM raffinose, 0.81 mM H3BO3, 2.04 mM CaCl2 at pH5.8 showed highest pollen germination. Partly or complete substitution of raffinose by sucrose, maltose, or sorbitol reduced in vitro germination of the pollen assuming a higher metabolic efficiency or antioxidant activity of raffinose. In vitro pollen germination varied between 26 lines (P < 0.001); between winter (15.3 ± 8.5%) and spring types (30.2 ± 13.3%) and was highest for the spring wheat TRI 2443 (50.1 ± 20.0%). Alexander staining failed to discriminate between viable, fresh pollen, and non-viable pollen inactivated by ambient storage for >60 min. Viability of fresh wheat pollen assessed by fluorescein diacetate (FDA) staining and impedance flow (IF) cytometry was 79.2 ± 4.2% and 88.1 ± 2.7%, respectively; and, when non-viable, stored pollen was additionally tested, it correlated at r = 0.54 (P < 0.05) and r = 0.67 (P < 0.001) with in vitro germination, respectively. When fresh pollen was used to assess the pollen viability of 19 wheat, 25 rye, 11 barley, and 4 maize lines, correlations were absent and in vitro germination was lower for rye (11.7 ± 8.5%), barley (6.8 ± 4.3%), and maize (2.1 ± 1.8%) pollen compared to wheat. Concluding, FDA staining and IF cytometry are used for a range of pollen species, whereas media for in vitro pollen germination require specific adaptations; in wheat, a solid medium with raffinose was chosen. On adapted media, the pollen tube growth can be exactly analyzed whereas results achieved by FDA staining and IF cytometry are higher and may overestimate pollen tube growth. Hence, as the exact viability and fertilization potential of a larger pollen batch remains elusive, a combination of pollen viability tests may provide reasonable indications of the ability of pollen to germinate and grow.
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Affiliation(s)
- Daniela Impe
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Janka Reitz
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Claudia Köpnick
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Angelika Senula
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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You X, Zhang W, Hu J, Jing R, Cai Y, Feng Z, Kong F, Zhang J, Yan H, Chen W, Chen X, Ma J, Tang X, Wang P, Zhu S, Liu L, Jiang L, Wan J. FLOURY ENDOSPERM15 encodes a glyoxalase I involved in compound granule formation and starch synthesis in rice endosperm. PLANT CELL REPORTS 2019; 38:345-359. [PMID: 30649573 DOI: 10.1007/s00299-019-02370-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/02/2019] [Indexed: 05/06/2023]
Abstract
FLO15encodes a plastidic glyoxalase I protein, OsGLYI7, which affects compound starch granule formation and starch synthesis in rice endosperm. Starch synthesis in rice (Oryza sativa) endosperm is a sophisticated process, and its underlying molecular machinery still remains to be elucidated. Here, we identified and characterized two allelic rice floury endosperm 15 (flo15) mutants, both with a white-core endosperm. The flo15 grains were characterized by defects in compound starch granule development, along with decreased starch content. Map-based cloning of the flo15 mutants identified mutations in OsGLYI7, which encodes a glyoxalase I (GLYI) involved in methylglyoxal (MG) detoxification. The mutations of FLO15/OsGLYI7 resulted in increased MG content in flo15 developing endosperms. FLO15/OsGLYI7 localizes to the plastids, and the in vitro GLYI activity derived from flo15 was significantly decreased relative to the wild type. Moreover, the expression of starch synthesis-related genes was obviously altered in the flo15 mutants. These findings suggest that FLO15 plays an important role in compound starch granule formation and starch synthesis in rice endosperm.
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Affiliation(s)
- Xiaoman You
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinlong Hu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruonan Jing
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiming Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Kong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Xingang Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojie Tang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China.
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Guendel A, Rolletschek H, Wagner S, Muszynska A, Borisjuk L. Micro Imaging Displays the Sucrose Landscape within and along Its Allocation Pathways. PLANT PHYSIOLOGY 2018; 178:1448-1460. [PMID: 30275056 PMCID: PMC6288747 DOI: 10.1104/pp.18.00947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/18/2018] [Indexed: 05/05/2023]
Abstract
Sucrose (Suc) is the major transport sugar in plants and plays a primary role as an energy source and signal in adaptive and stress responses. An ability to quantify Suc over time and space would serve to advance our understanding of these important processes. Current technologies used for Suc mapping are unable to quantitatively visualize its distribution within tissues. Here, we present an infrared-based microspectroscopic method that allows for the quantitative visualization of Suc at a microscopic level of resolution (∼12 µm). This method can successfully model the sugar concentration in individual vascular bundles and within a complex organ such as the stem, leaf, or seed. The sensitivity of the assay ranges from 20 to 1,000 mm We applied this method to the cereal crop barley (Hordeum vulgare) and the model plant Arabidopsis (Arabidopsis thaliana) to highlight the potential of the procedure for resolving the spatial distribution of metabolites. We also discuss the relevance of the method for studies on carbon allocation and storage in the context of crop improvement.
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Affiliation(s)
- André Guendel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Steffen Wagner
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Aleksandra Muszynska
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
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Ishibashi Y, Yuasa T, Iwaya-Inoue M. Mechanisms of Maturation and Germination in Crop Seeds Exposed to Environmental Stresses with a Focus on Nutrients, Water Status, and Reactive Oxygen Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:233-257. [DOI: 10.1007/978-981-13-1244-1_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Lu J, Magnani E. Seed tissue and nutrient partitioning, a case for the nucellus. PLANT REPRODUCTION 2018; 31:309-317. [PMID: 29869727 PMCID: PMC6105262 DOI: 10.1007/s00497-018-0338-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Flowering plants display a large spectrum of seed architectures. The volume ratio of maternal versus zygotic seed tissues changes considerably among species and underlies different nutrient-storing strategies. Such diversity arose through the evolution of cell elimination programs that regulate the relative growth of one tissue over another to become the major storage compartment. The elimination of the nucellus maternal tissue is regulated by developmental programs that marked the origin of angiosperms and outlined the most ancient seed architectures. This review focuses on such a defining mechanism for seed evolution and discusses the role of nucellus development in seed tissues and nutrient partitioning at the light of novel discoveries on its molecular regulation.
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Affiliation(s)
- Jing Lu
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026, Versailles Cedex, France
- Ecole Doctorale 567 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, Bat 360, 91405, Orsay Cedex, France
| | - Enrico Magnani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026, Versailles Cedex, France.
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13
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Goh HH. Integrative Multi-Omics Through Bioinformatics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1102:69-80. [DOI: 10.1007/978-3-319-98758-3_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Xu Y, Yuan Y, Du N, Wang Y, Shu S, Sun J, Guo S. Proteomic analysis of heat stress resistance of cucumber leaves when grafted onto Momordica rootstock. HORTICULTURE RESEARCH 2018; 5:53. [PMID: 30302257 PMCID: PMC6165847 DOI: 10.1038/s41438-018-0060-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/09/2018] [Accepted: 05/21/2018] [Indexed: 05/22/2023]
Abstract
Various biotic and abiotic stresses threaten the cultivation of future agricultural crops. Among these stresses, heat stress is a major abiotic stress that substantially reduces agricultural productivity. Many strategies to enhance heat stress tolerance of crops have been developed, among which is grafting. Here, we show that Momordica-grafted cucumber scions have intrinsically enhanced chlorophyll content, leaf area, and net photosynthetic rate under heat stress compared to plants grafted onto cucumber rootstock. To investigate the mechanisms by which Momordica rootstock enhanced cucumber scions heat stress tolerance, comparative proteomic analysis of cucumber leaves in response to rootstock-grafting and/or heat stress was conducted. Seventy-seven differentially accumulated proteins involved in diverse biological processes were identified by two-dimensional electrophoresis (2-DE) in conjunction with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS). The following four main categories of proteins were involved: photosynthesis (42.8%), energy and metabolism (18.2%), defense response (14.3%), and protein and nucleic acid biosynthesis (11.7%). Proteomic analysis revealed that scions grafted onto Momordica rootstocks upregulated more proteins involved in photosynthesis compared to scions grafted onto cucumber rootstocks under heat stress and indicated enhanced photosynthetic capacity when seedlings were exposed to heat stress. Furthermore, the expression of photosynthesis-related genes in plants grafted onto Momordica rootstocks significantly increased in response to heat stress. In addition, increased high-temperature tolerance of plants grafted onto Momordica rootstock was associated with the accumulation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and oxygen-evolving enhancer protein 1 (OEE1). Taken together, the data indicated that Momordica rootstock might alleviate growth inhibition caused by heat stress by improving photosynthesis, providing valuable insight into enhancing heat stress tolerance in the global warming epoch.
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Affiliation(s)
- Ye Xu
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yinghui Yuan
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Nanshan Du
- Department of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Yu Wang
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sheng Shu
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, China
| | - Jin Sun
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, China
| | - Shirong Guo
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, China
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Abstract
The starch-rich endosperms of the Poaceae, which includes wild grasses and their domesticated descendents the cereals, have provided humankind and their livestock with the bulk of their daily calories since the dawn of civilization up to the present day. There are currently unprecedented pressures on global food supplies, largely resulting from population growth, loss of agricultural land that is linked to increased urbanization, and climate change. Since cereal yields essentially underpin world food and feed supply, it is critical that we understand the biological factors contributing to crop yields. In particular, it is important to understand the biochemical pathway that is involved in starch biosynthesis, since this pathway is the major yield determinant in the seeds of six out of the top seven crops grown worldwide. This review outlines the critical stages of growth and development of the endosperm tissue in the Poaceae, including discussion of carbon provision to the growing sink tissue. The main body of the review presents a current view of our understanding of storage starch biosynthesis, which occurs inside the amyloplasts of developing endosperms.
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Salon C, Avice JC, Colombié S, Dieuaide-Noubhani M, Gallardo K, Jeudy C, Ourry A, Prudent M, Voisin AS, Rolin D. Fluxomics links cellular functional analyses to whole-plant phenotyping. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2083-2098. [PMID: 28444347 DOI: 10.1093/jxb/erx126] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding.
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Affiliation(s)
- Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Jean-Christophe Avice
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Sophie Colombié
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Martine Dieuaide-Noubhani
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Alain Ourry
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Anne-Sophie Voisin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Dominique Rolin
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
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17
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Galland M, He D, Lounifi I, Arc E, Clément G, Balzergue S, Huguet S, Cueff G, Godin B, Collet B, Granier F, Morin H, Tran J, Valot B, Rajjou L. An Integrated "Multi-Omics" Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality. FRONTIERS IN PLANT SCIENCE 2017; 8:1984. [PMID: 29213276 PMCID: PMC5702907 DOI: 10.3389/fpls.2017.01984] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 11/03/2017] [Indexed: 05/20/2023]
Abstract
Although rice is a key crop species, few studies have addressed both rice seed physiological and nutritional quality, especially at the tissue level. In this study, an exhaustive "multi-omics" dataset on the mature rice seed was obtained by combining transcriptomics, label-free shotgun proteomics and metabolomics from embryo and endosperm, independently. These high-throughput analyses provide a new insight on the tissue-specificity related to rice seed quality. Foremost, we pinpointed that extensive post-transcriptional regulations occur at the end of rice seed development such that the embryo proteome becomes much more diversified than the endosperm proteome. Secondly, we observed that survival in the dry state in each seed compartment depends on contrasted metabolic and enzymatic apparatus in the embryo and the endosperm, respectively. Thirdly, it was remarkable to identify two different sets of starch biosynthesis enzymes as well as seed storage proteins (glutelins) in both embryo and endosperm consistently with the supernumerary embryo hypothesis origin of the endosperm. The presence of a putative new glutelin with a possible embryonic favored abundance is described here for the first time. Finally, we quantified the rate of mRNA translation into proteins. Consistently, the embryonic panel of protein translation initiation factors is much more diverse than that of the endosperm. This work emphasizes the value of tissue-specificity-centered "multi-omics" study in the seed to highlight new features even from well-characterized pathways. It paves the way for future studies of critical genetic determinants of rice seed physiological and nutritional quality.
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Affiliation(s)
- Marc Galland
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Dongli He
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Imen Lounifi
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Erwann Arc
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Gilles Clément
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Sandrine Balzergue
- IPS2, Institute of Plant Sciences Paris-Saclay (INRA, CNRS, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay), POPS-Transcriptomic Platform, Saclay Plant Sciences (SPS), Orsay, France
| | - Stéphanie Huguet
- IPS2, Institute of Plant Sciences Paris-Saclay (INRA, CNRS, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay), POPS-Transcriptomic Platform, Saclay Plant Sciences (SPS), Orsay, France
| | - Gwendal Cueff
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Béatrice Godin
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Boris Collet
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Fabienne Granier
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Halima Morin
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Joseph Tran
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
| | - Benoit Valot
- GQE-Le Moulon, Génétique Quantitative et Evolution (INRA Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay), PAPPSO-Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Saclay Plant Sciences (SPS), Gif-sur-Yvette, France
| | - Loïc Rajjou
- IJPB, Institut Jean-Pierre Bourgin (INRA, AgroParisTech, CNRS, Université Paris-Saclay), Saclay Plant Sciences (SPS), Versailles, France
- *Correspondence: Loïc Rajjou
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Lee SK, Eom JS, Hwang SK, Shin D, An G, Okita TW, Jeon JS. Plastidic phosphoglucomutase and ADP-glucose pyrophosphorylase mutants impair starch synthesis in rice pollen grains and cause male sterility. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5557-5569. [PMID: 27588462 PMCID: PMC5049399 DOI: 10.1093/jxb/erw324] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To elucidate the starch synthesis pathway and the role of this reserve in rice pollen, we characterized mutations in the plastidic phosphoglucomutase, OspPGM, and the plastidic large subunit of ADP-glucose (ADP-Glc) pyrophosphorylase, OsAGPL4 Both genes were up-regulated in maturing pollen, a stage when starch begins to accumulate. Progeny analysis of self-pollinated heterozygous lines carrying the OspPGM mutant alleles, osppgm-1 and osppgm-2, or the OsAGPL4 mutant allele, osagpl4-1, as well as reciprocal crosses between the wild type (WT) and heterozygotes revealed that loss of OspPGM or OsAGPL4 caused male sterility, with the former condition rescued by the introduction of the WT OspPGM gene. While iodine staining and transmission electron microscopy analyses of pollen grains from homozygous osppgm-1 lines produced by anther culture confirmed the starch null phenotype, pollen from homozygous osagpl4 mutant lines, osagpl4-2 and osagpl4-3, generated by the CRISPR/Cas system, accumulated small amounts of starch which were sufficient to produce viable seed. Such osagpl4 mutant pollen, however, was unable to compete against WT pollen successfully, validating the important role of this reserve in fertilization. Our results demonstrate that starch is mainly polymerized from ADP-Glc synthesized from plastidic hexose phosphates in rice pollen and that starch is an essential requirement for successful fertilization in rice.
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Affiliation(s)
- Sang-Kyu Lee
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Joon-Seob Eom
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Dongjin Shin
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Milyang 50424, Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Jong-Seong Jeon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
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19
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Imam J, Singh PK, Shukla P. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications. Front Microbiol 2016; 7:1488. [PMID: 27725809 PMCID: PMC5035750 DOI: 10.3389/fmicb.2016.01488] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023] Open
Abstract
Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.
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Affiliation(s)
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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20
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Label-free proteome profiling reveals developmental-dependent patterns in young barley grains. J Proteomics 2016; 143:106-121. [DOI: 10.1016/j.jprot.2016.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/16/2016] [Accepted: 04/11/2016] [Indexed: 12/17/2022]
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21
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Allen DK. Assessing compartmentalized flux in lipid metabolism with isotopes. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1226-1242. [PMID: 27003250 DOI: 10.1016/j.bbalip.2016.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/13/2016] [Accepted: 03/14/2016] [Indexed: 12/28/2022]
Abstract
Metabolism in plants takes place across multiple cell types and within distinct organelles. The distributions equate to spatial heterogeneity; though the limited means to experimentally assess metabolism frequently involve homogenizing tissues and mixing metabolites from different locations. Most current isotope investigations of metabolism therefore lack the ability to resolve spatially distinct events. Recognition of this limitation has resulted in inspired efforts to advance metabolic flux analysis and isotopic labeling techniques. Though a number of these efforts have been applied to studies in central metabolism; recent advances in instrumentation and techniques present an untapped opportunity to make similar progress in lipid metabolism where the use of stable isotopes has been more limited. These efforts will benefit from sophisticated radiolabeling reports that continue to enrich our knowledge on lipid biosynthetic pathways and provide some direction for stable isotope experimental design and extension of MFA. Evidence for this assertion is presented through the review of several elegant stable isotope studies and by taking stock of what has been learned from radioisotope investigations when spatial aspects of metabolism were considered. The studies emphasize that glycerolipid production occurs across several locations with assembly of lipids in the ER or plastid, fatty acid biosynthesis occurring in the plastid, and the generation of acetyl-CoA and glycerol-3-phosphate taking place at multiple sites. Considering metabolism in this context underscores the cellular and subcellular organization that is important to enhanced production of glycerolipids in plants. An attempt is made to unify salient features from a number of reports into a diagrammatic model of lipid metabolism and propose where stable isotope labeling experiments and further flux analysis may help address questions in the field. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
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22
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Dersch LM, Beckers V, Wittmann C. Green pathways: Metabolic network analysis of plant systems. Metab Eng 2016; 34:1-24. [DOI: 10.1016/j.ymben.2015.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
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23
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Shi H, Schwender J. Mathematical models of plant metabolism. Curr Opin Biotechnol 2015; 37:143-152. [PMID: 26723012 DOI: 10.1016/j.copbio.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 11/24/2022]
Abstract
Among various modeling approaches in plant metabolic research, applications of Constraint-Based modeling are fast increasing in recent years, apparently driven by current advances in genomics and genome sequencing. Constraint-Based modeling, the functional analysis of metabolic networks at the whole cell or genome scale, is more difficult to apply to plants than to microbes. Here we discuss recent developments in Constraint-Based modeling in plants with focus on issues of model reconstruction and flux prediction. Another topic is the emerging application of integration of Constraint-Based modeling with omics data to increase predictive power. Furthermore, advances in experimental measurements of cellular fluxes by (13)C-Metabolic Flux Analysis are highlighted, including instationary (13)C-MFA used to probe autotrophic metabolism in photosynthetic tissue in the light.
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Affiliation(s)
- Hai Shi
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Jörg Schwender
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States.
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24
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Etalo DW, De Vos RCH, Joosten MHAJ, Hall RD. Spatially Resolved Plant Metabolomics: Some Potentials and Limitations of Laser-Ablation Electrospray Ionization Mass Spectrometry Metabolite Imaging. PLANT PHYSIOLOGY 2015; 169:1424-35. [PMID: 26392264 PMCID: PMC4634093 DOI: 10.1104/pp.15.01176] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/20/2015] [Indexed: 05/19/2023]
Abstract
Laser-ablation electrospray ionization (LAESI)-mass spectrometry imaging has been applied to contrasting plant organs to assess its potential as a procedure for performing in vivo metabolomics in plants. In a proof-of-concept experiment, purple/white segmented Phalaenopsis spp. petals were first analyzed using standard liquid chromatography-mass spectrometry analyses of separate extracts made specifically from the purple and white regions. Discriminatory compounds were defined and putatively annotated. LAESI analyses were then performed on living tissues, and these metabolites were then relocalized within the LAESI-generated data sets of similar tissues. Maps were made to illustrate their locations across the petals. Results revealed that, as expected, anthocyanins always mapped to the purple regions. Certain other (nonvisible) polyphenols were observed to colocalize with the anthocyanins, whereas others were found specifically within the white tissues. In a contrasting example, control and Cladosporium fulvum-infected tomato (Solanum lycopersicum) leaves were subjected to the same procedures, and it could be observed that the alkaloid tomatine has clear heterogeneous distribution across the tomato leaf lamina. Furthermore, LAESI analyses revealed perturbations in alkaloid content following pathogen infection. These results show the clear potential of LAESI-based imaging approaches as a convenient and rapid way to perform metabolomics analyses on living tissues. However, a range of limitations and factors have also been identified that must be taken into consideration when interpreting LAESI-derived data. Such aspects deserve further evaluation before this approach can be applied in a routine manner.
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Affiliation(s)
- Desalegn W Etalo
- Laboratory of Plant Physiology (D.W.E., R.D.H.), Plant Research International Bioscience (D.W.E., R.C.H.D.V., R.D.H.), and Laboratory of Phytopathology (M.H.A.J.J.), Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Ric C H De Vos
- Laboratory of Plant Physiology (D.W.E., R.D.H.), Plant Research International Bioscience (D.W.E., R.C.H.D.V., R.D.H.), and Laboratory of Phytopathology (M.H.A.J.J.), Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Matthieu H A J Joosten
- Laboratory of Plant Physiology (D.W.E., R.D.H.), Plant Research International Bioscience (D.W.E., R.C.H.D.V., R.D.H.), and Laboratory of Phytopathology (M.H.A.J.J.), Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Robert D Hall
- Laboratory of Plant Physiology (D.W.E., R.D.H.), Plant Research International Bioscience (D.W.E., R.C.H.D.V., R.D.H.), and Laboratory of Phytopathology (M.H.A.J.J.), Wageningen University, 6708 PB, Wageningen, The Netherlands
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25
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Yang J, Kim SR, Lee SK, Choi H, Jeon JS, An G. Alanine aminotransferase 1 (OsAlaAT1) plays an essential role in the regulation of starch storage in rice endosperm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:79-89. [PMID: 26475189 DOI: 10.1016/j.plantsci.2015.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
Alteration of storage substances, in particular the major storage form starch, leads to floury endosperm. Because floury mutants have physical attributes for milling processes, identification and characterization of those mutants are valuable. In this study we identified a floury endosperm mutant caused by a T-DNA insertion in Oryza sativa alanine-aminotransferase1 (OsAlaAT1). OsAlaAT1 is localized in the cytosol and has aminotransferase enzyme activity. The osalaat1 mutant has less amylose and its amylopectin is structurally altered. OsAlaAT1 is predominantly expressed in developing seeds during active starch synthesis. AlaAT catalyzes the interconversion of pyruvate to alanine, and this pathway is activated under low-oxygen conditions. Consistently, OsAlaAT1 is induced by such conditions. Expression of the starch synthesis genes AGPases, OsSSI, OsSSIIa, and OsPPDKB is decreased in the mutant. Thus, our observations suggest that OsAlaAT1 plays an essential role in starch synthesis in developing seeds that are exposed to low concentrations of oxygen.
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Affiliation(s)
- Jungil Yang
- Crop Biotech Institute & Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Sung-Ryul Kim
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Sang-Kyu Lee
- Crop Biotech Institute & Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Heebak Choi
- Crop Biotech Institute & Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Jong-Seong Jeon
- Crop Biotech Institute & Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Gynheung An
- Crop Biotech Institute & Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Republic of Korea.
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Rolletschek H, Grafahrend-Belau E, Munz E, Radchuk V, Kartäusch R, Tschiersch H, Melkus G, Schreiber F, Jakob PM, Borisjuk L. Metabolic Architecture of the Cereal Grain and Its Relevance to Maximize Carbon Use Efficiency. PLANT PHYSIOLOGY 2015; 169:1698-713. [PMID: 26395842 PMCID: PMC4634074 DOI: 10.1104/pp.15.00981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/20/2015] [Indexed: 05/20/2023]
Abstract
Here, we have characterized the spatial heterogeneity of the cereal grain's metabolism and demonstrated how, by integrating a distinct set of metabolic strategies, the grain has evolved to become an almost perfect entity for carbon storage. In vivo imaging revealed light-induced cycles in assimilate supply toward the ear/grain of barley (Hordeum vulgare) and wheat (Triticum aestivum). In silico modeling predicted that, in the two grain storage organs (the endosperm and embryo), the light-induced shift in solute influx does cause adjustment in metabolic flux without changes in pathway utilization patterns. The enveloping, leaf-like pericarp, in contrast, shows major shifts in flux distribution (starch metabolism, photosynthesis, remobilization, and tricarboxylic acid cycle activity) allow to refix 79% of the CO2 released by the endosperm and embryo, allowing the grain to achieve an extraordinary high carbon conversion efficiency of 95%. Shading experiments demonstrated that ears are autonomously able to raise the influx of solutes in response to light, but with little effect on the steady-state levels of metabolites or transcripts or on the pattern of sugar distribution within the grain. The finding suggests the presence of a mechanism(s) able to ensure metabolic homeostasis in the face of short-term environmental fluctuation. The proposed multicomponent modeling approach is informative for predicting the metabolic effects of either an altered level of incident light or a momentary change in the supply of sucrose. It is therefore of potential value for assessing the impact of either breeding and/or biotechnological interventions aimed at increasing grain yield.
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Affiliation(s)
- Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Eva Grafahrend-Belau
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Eberhard Munz
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Volodymyr Radchuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Ralf Kartäusch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Henning Tschiersch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Gerd Melkus
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Falk Schreiber
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Peter M Jakob
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (H.R., E.M., V.R., H.T., L.B.);Institut für Pharmazie, Martin-Luther-University of Halle, 06120 Halle, Germany (E.G.-B.);Institute of Experimental Physics 5, University of Würzburg, 97074 Würzburg, Germany (E.M., P.M.J.);Research Center Magnetic Resonance Bavaria, 97074 Wurzburg, Germany (R.K., P.M.J.);Department of Medical Imaging, University of Ottawa, Ottawa, Ontario, Canada K1Y 4E9 (G.M.); andClayton School of IT, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
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Winkelmann T, Ratjens S, Bartsch M, Rode C, Niehaus K, Bednarz H. Metabolite profiling of somatic embryos of Cyclamen persicum in comparison to zygotic embryos, endosperm, and testa. FRONTIERS IN PLANT SCIENCE 2015; 6:597. [PMID: 26300898 PMCID: PMC4523879 DOI: 10.3389/fpls.2015.00597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/20/2015] [Indexed: 05/29/2023]
Abstract
Somatic embryogenesis has been shown to be an efficient in vitro plant regeneration system for many crops such as the important ornamental plant Cyclamen persicum, for which this regeneration pathway of somatic embryogenesis is of interest for the vegetative propagation of parental lines as well as elite plants. However, somatic embryogenesis is not commercially used in many crops due to several unsolved problems, such as malformations, asynchronous development, deficiencies in maturation and germination of somatic embryos. In contrast, zygotic embryos in seeds develop and germinate without abnormalities in most cases. Instead of time-consuming and labor-intensive experiments involving tests of different in vitro culture conditions and plant growth regulator supplements, we follow a more directed approach. Zygotic embryos served as a reference and were compared to somatic embryos in metabolomic analyses allowing the future optimization of the in vitro system. The aims of this study were to detect differences in the metabolite profiles of torpedo stage somatic and zygotic embryos of C. persicum. Moreover, major metabolites in endosperm and testa were identified and quantified. Two sets of extracts of two to four biological replicates each were analyzed. In total 52 metabolites were identified and quantified in the different tissues. One of the most significant differences between somatic and zygotic embryos was that the proline concentration in the zygotic embryos was about 40 times higher than that found in somatic embryos. Epicatechin, a scavenger for reactive oxygen species, was found in highest abundance in the testa. Sucrose, the most abundant metabolite was detected in significantly higher concentrations in zygotic embryos. Also, a yet unknown trisaccharide, was significantly enriched in zygotic embryos.
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Affiliation(s)
- Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Svenja Ratjens
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Melanie Bartsch
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Christina Rode
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Karsten Niehaus
- Faculty of Biology, Bio 27, Proteome and Metabolome Research, Bielefeld UniversityBielefeld, Germany
| | - Hanna Bednarz
- Faculty of Biology, Bio 27, Proteome and Metabolome Research, Bielefeld UniversityBielefeld, Germany
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Schwender J, Hebbelmann I, Heinzel N, Hildebrandt T, Rogers A, Naik D, Klapperstück M, Braun HP, Schreiber F, Denolf P, Borisjuk L, Rolletschek H. Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture. PLANT PHYSIOLOGY 2015; 168:828-48. [PMID: 25944824 PMCID: PMC4741336 DOI: 10.1104/pp.15.00385] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/04/2015] [Indexed: 05/05/2023]
Abstract
Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 3',5'-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism.
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Affiliation(s)
- Jörg Schwender
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Inga Hebbelmann
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Nicolas Heinzel
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Tatjana Hildebrandt
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Alistair Rogers
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Dhiraj Naik
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Matthias Klapperstück
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Hans-Peter Braun
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Falk Schreiber
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Peter Denolf
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Ljudmilla Borisjuk
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Hardy Rolletschek
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
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Tsogtbaatar E, Cocuron JC, Sonera MC, Alonso AP. Metabolite fingerprinting of pennycress (Thlaspi arvense L.) embryos to assess active pathways during oil synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4267-77. [PMID: 25711705 PMCID: PMC4493779 DOI: 10.1093/jxb/erv020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pennycress (Thlaspi arvense L.), a plant naturalized to North America, accumulates high levels of erucic acid in its seeds, which makes it a promising biodiesel and industrial crop. The main carbon sinks in pennycress embryos were found to be proteins, fatty acids, and cell wall, which respectively represented 38.5, 33.2, and 27.0% of the biomass at 21 days after pollination. Erucic acid reached a maximum of 36% of the total fatty acids. Together these results indicate that total oil and erucic acid contents could be increased to boost the economic competitiveness of this crop. Understanding the biochemical basis of oil synthesis in pennycress embryos is therefore timely and relevant to guide future breeding and/or metabolic engineering efforts. For this purpose, a combination of metabolomics approaches was conducted to assess the active biochemical pathways during oil synthesis. First, gas chromatography-mass spectrometry (GC-MS) profiling of intracellular metabolites highlighted three main families of compounds: organic acids, amino acids, and sugars/sugar alcohols. Secondly, these intermediates were quantified in developing pennycress embryos by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring mode. Finally, partitional clustering analysis grouped the intracellular metabolites that shared a similar pattern of accumulation over time into eight clusters. This study underlined that: (i) sucrose might be stored rather than cleaved into hexoses; (ii) glucose and glutamine would be the main sources of carbon and nitrogen, respectively; and (iii) glycolysis, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and the Calvin cycle were active in developing pennycress embryos.
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Affiliation(s)
- Enkhtuul Tsogtbaatar
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA
| | - Jean-Christophe Cocuron
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA The Ohio State University, Center for Applied Plant Sciences, Columbus, OH 43210, USA
| | - Marcos Corchado Sonera
- University of Puerto Rico, Mechanical Engineering Department, Mayagüez, 00681-9000, Puerto Rico
| | - Ana Paula Alonso
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA
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Subbarayan K, Rolletschek H, Senula A, Ulagappan K, Hajirezaei MR, Keller ERJ. Influence of oxygen deficiency and the role of specific amino acids in cryopreservation of garlic shoot tips. BMC Biotechnol 2015; 15:40. [PMID: 26016569 PMCID: PMC4446907 DOI: 10.1186/s12896-015-0171-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Garlic has lost its ability to form seeds in the course of its domestication. Therefore, the germplasm storage via cryopreservation is increasingly applied. The progression of the various steps within the cryopreservation procedure is accompanied by declining survival rates of the explants. Much of the recent work on cryo-stress has been focussed on osmotic and cold stress components. However, two decades after invention of garlic cryopreservation, the function of metabolites and oxygen in and around the cryopreserved tissues is still largely obscure. METHODS In this study, hypoxia was characterized in cryopreservation of garlic with oxygen sensors and amino acid metabolism. Furthermore, malondialdehyde, soluble sugars and ammonium were quantified to demonstrate the influence of cryo-stress in declining survival rates. RESULTS To better understand the possible reasons for a reduction in the survival rate at the subsequent steps of cryopreservation, the concentration of amino acids, ammonium, γ-aminobutyric acid (GABA), soluble sugars, malondialdehyde (MDA), and oxygen were measured in garlic shoot tips undergoing cryopreservation. Using microsensors, a very low oxygen concentration (<0.1 μM) was detected within the central meristem region of the shoot apex. When apices were immersed in cryoprotectant solution, the well-oxygenated peripheral regions (foliage leaf bases) became likewise hypoxic within a few minutes, probably resulting from strongly restricted gaseous diffusion. CONCLUSIONS Tissue level oxygen measurements supported the occurrence of hypoxia while biochemical analysis indicated adaptive responses, in particular the modulation in alanine and glutamate metabolism. The possible role of serine and glycine metabolism during cryopreservation is also discussed.
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Affiliation(s)
- Karthikeyan Subbarayan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Gatersleben, Germany.
| | - Hardy Rolletschek
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Gatersleben, Germany.
| | - Angelika Senula
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Gatersleben, Germany.
| | - Kamatchi Ulagappan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Gatersleben, Germany.
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Gatersleben, Germany.
| | - E R Joachim Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Gatersleben, Germany.
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Fuchs J, Melkus G, Borisjuk L, Jakob P. Tracking metabolite dynamics in plants via indirect 13C chemical shift imaging with an interleaved variable density acquisition weighted sampling pattern. MAGMA (NEW YORK, N.Y.) 2015; 28:127-134. [PMID: 24952645 DOI: 10.1007/s10334-014-0453-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/16/2014] [Accepted: 06/03/2014] [Indexed: 06/03/2023]
Abstract
OBJECTIVE Developing and evaluating an improved sampling pattern to track the dynamics of labeled substances in plants using indirect (13)C chemical shift imaging. MATERIALS AND METHODS An algorithm to split an acquisition weighted sampling pattern into several undersampled sub-images is presented. The sampling patterns are used in CSI moving phantom experiments as well as in in vivo POCE-CSI experiments on barley stem and grain. Reconstruction is performed traditionally or by compressed sensing. RESULTS The moving phantom experiments show that the sampling pattern can reduce motion artifacts at the cost of an increased overall noise. The in vivo experiments demonstrate the feasibility of extracting a time series from a single imaging experiment. CONCLUSION The sampling pattern is suitable for tracking the uptake of label substances into plant material. The use of compressed sensing allows an increased spatial and temporal resolution.
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Affiliation(s)
- Johannes Fuchs
- Department of Experimental Physics 5 (Biophysics), University of Würzburg, Würzburg, Germany,
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Allen DK, Bates PD, Tjellström H. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Prog Lipid Res 2015; 58:97-120. [PMID: 25773881 DOI: 10.1016/j.plipres.2015.02.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Philip D Bates
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, United States
| | - Henrik Tjellström
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, United States
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Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. FRONTIERS IN PLANT SCIENCE 2015; 6:142. [PMID: 25806041 PMCID: PMC4354304 DOI: 10.3389/fpls.2015.00142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/22/2015] [Indexed: 05/08/2023]
Abstract
There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.
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Affiliation(s)
- Samuel M. D. Seaver
- Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA
- Computation Institute, The University of ChicagoChicago, IL, USA
| | - Louis M. T. Bradbury
- Horticultural Sciences Department, University of FloridaGainesville, FL, USA
- Department of Biology, York College, City University of New YorkNew York, NY, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of FloridaGainesville, FL, USA
| | - Raphy Zarecki
- Sackler Faculty of Medicine, Tel Aviv UniversityTel Aviv, Israel
| | - Eytan Ruppin
- Sackler Faculty of Medicine, Tel Aviv UniversityTel Aviv, Israel
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of FloridaGainesville, FL, USA
| | - Christopher S. Henry
- Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA
- Computation Institute, The University of ChicagoChicago, IL, USA
- *Correspondence: Christopher S. Henry, Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
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Metabolic engineering of higher plants and algae for isoprenoid production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:161-99. [PMID: 25636485 DOI: 10.1007/10_2014_290] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Isoprenoids are a class of compounds derived from the five carbon precursors, dimethylallyl diphosphate, and isopentenyl diphosphate. These molecules present incredible natural chemical diversity, which can be valuable for humans in many aspects such as cosmetics, agriculture, and medicine. However, many terpenoids are only produced in small quantities by their natural hosts and can be difficult to generate synthetically. Therefore, much interest and effort has been directed toward capturing the genetic blueprint for their biochemistry and engineering it into alternative hosts such as plants and algae. These autotrophic organisms are attractive when compared to traditional microbial platforms because of their ability to utilize atmospheric CO2 as a carbon substrate instead of supplied carbon sources like glucose. This chapter will summarize important techniques and strategies for engineering the accumulation of isoprenoid metabolites into higher plants and algae by choosing the correct host, avoiding endogenous regulatory mechanisms, and optimizing potential flux into the target compound. Future endeavors will build on these efforts by fine-tuning product accumulation levels via the vast amount of available "-omic" data and devising metabolic engineering schemes that integrate this into a whole-organism approach. With the development of high-throughput transformation protocols and synthetic biology molecular tools, we have only begun to harness the power and utility of plant and algae metabolic engineering.
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Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME, Lawrence CJ, Bass HW. G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. J Genet Genomics 2014; 41:627-47. [DOI: 10.1016/j.jgg.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/16/2014] [Accepted: 10/24/2014] [Indexed: 02/07/2023]
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Multi-Spectroscopic Analysis of Seed Quality and 13C-Stable-Iotopologue Monitoring in Initial Growth Metabolism of Jatropha curcas L. Metabolites 2014; 4:1018-33. [PMID: 25401292 PMCID: PMC4279157 DOI: 10.3390/metabo4041018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/10/2014] [Accepted: 11/05/2014] [Indexed: 12/20/2022] Open
Abstract
In the present study, we applied nuclear magnetic resonance (NMR), as well as near-infrared (NIR) spectroscopy, to Jatropha curcas to fulfill two objectives: (1) to qualitatively examine the seeds stored at different conditions, and (2) to monitor the metabolism of J. curcas during its initial growth stage under stable-isotope-labeling condition (until 15 days after seeding). NIR spectra could non-invasively distinguish differences in storage conditions. NMR metabolic analysis of water-soluble metabolites identified sucrose and raffinose family oligosaccharides as positive markers and gluconic acid as a negative marker of seed germination. Isotopic labeling patteren of metabolites in germinated seedlings cultured in agar-plate containg 13C-glucose and 15N-nitrate was analyzed by zero-quantum-filtered-total correlation spectroscopy (ZQF-TOCSY) and 13C-detected 1H-13C heteronuclear correlation spectroscopy (HETCOR). 13C-detected HETOCR with 13C-optimized cryogenic probe provided high-resolution 13C-NMR spectra of each metabolite in molecular crowd. The 13C-13C/12C bondmer estimated from 1H-13C HETCOR spectra indicated that glutamine and arginine were the major organic compounds for nitrogen and carbon transfer from roots to leaves.
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Radchuk V, Borisjuk L. Physical, metabolic and developmental functions of the seed coat. FRONTIERS IN PLANT SCIENCE 2014; 5:510. [PMID: 25346737 PMCID: PMC4193196 DOI: 10.3389/fpls.2014.00510] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/11/2014] [Indexed: 05/04/2023]
Abstract
The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction.
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Affiliation(s)
| | - Ljudmilla Borisjuk
- Heterosis, Molecular Genetics, Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
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38
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Peukert M, Thiel J, Peshev D, Weschke W, Van den Ende W, Mock HP, Matros A. Spatio-temporal dynamics of fructan metabolism in developing barley grains. THE PLANT CELL 2014; 26:3728-44. [PMID: 25271242 PMCID: PMC4213166 DOI: 10.1105/tpc.114.130211] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/26/2014] [Accepted: 09/08/2014] [Indexed: 05/19/2023]
Abstract
Barley (Hordeum vulgare) grain development follows a series of defined morphological and physiological stages and depends on the supply of assimilates (mainly sucrose) from the mother plant. Here, spatio-temporal patterns of sugar distributions were investigated by mass spectrometric imaging, targeted metabolite analyses, and transcript profiling of microdissected grain tissues. Distinct spatio-temporal sugar balances were observed, which may relate to differentiation and grain filling processes. Notably, various types of oligofructans showed specific distribution patterns. Levan- and graminan-type oligofructans were synthesized in the cellularized endosperm prior to the commencement of starch biosynthesis, while during the storage phase, inulin-type oligofructans accumulated to a high concentration in and around the nascent endosperm cavity. In the shrunken endosperm mutant seg8, with a decreased sucrose flux toward the endosperm, fructan accumulation was impaired. The tight partitioning of oligofructan biosynthesis hints at distinct functions of the various fructan types in the young endosperm prior to starch accumulation and in the endosperm transfer cells that accomplish the assimilate supply toward the endosperm at the storage phase.
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Affiliation(s)
- Manuela Peukert
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Stadt Seeland, OT Gatersleben, Germany
| | - Johannes Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Stadt Seeland, OT Gatersleben, Germany
| | - Darin Peshev
- Lab of Molecular Plant Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee (2434), Belgium
| | - Winfriede Weschke
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Stadt Seeland, OT Gatersleben, Germany
| | - Wim Van den Ende
- Lab of Molecular Plant Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee (2434), Belgium
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Stadt Seeland, OT Gatersleben, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Stadt Seeland, OT Gatersleben, Germany
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Valluru R, Reynolds MP, Salse J. Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1463-89. [PMID: 24913362 DOI: 10.1007/s00122-014-2332-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 05/15/2014] [Indexed: 05/21/2023]
Abstract
Transferring the knowledge bases between related species may assist in enlarging the yield potential of crop plants. Being cereals, rice and wheat share a high level of gene conservation; however, they differ at metabolic levels as a part of the environmental adaptation resulting in different yield capacities. This review focuses on the current understanding of genetic and molecular regulation of yield-associated traits in both crop species, highlights the similarities and differences and presents the putative knowledge gaps. We focus on the traits associated with phenology, photosynthesis, and assimilate partitioning and lodging resistance; the most important drivers of yield potential. Currently, there are large knowledge gaps in the genetic and molecular control of such major biological processes that can be filled in a translational biology approach in transferring genomics and genetics informations between rice and wheat.
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Affiliation(s)
- Ravi Valluru
- Wheat Physiology, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56130, Mexico DF, Mexico,
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Lorenz C, Rolletschek H, Sunderhaus S, Braun HP. Brassica napus seed endosperm - metabolism and signaling in a dead end tissue. J Proteomics 2014; 108:382-426. [PMID: 24906024 DOI: 10.1016/j.jprot.2014.05.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 02/04/2023]
Abstract
UNLABELLED Oilseeds are an important element of human nutrition and of increasing significance for the production of industrial materials. The development of the seeds is based on a coordinated interplay of the embryo and its surrounding tissue, the endosperm. This study aims to give insights into the physiological role of endosperm for seed development in the oilseed crop Brassica napus. Using protein separation by two-dimensional (2D) isoelectric focusing (IEF)/SDS polyacrylamide gel electrophoresis (PAGE) and protein identification by mass spectrometry three proteome projects were carried out: (i) establishment of an endosperm proteome reference map, (ii) proteomic characterization of endosperm development and (iii) comparison of endosperm and embryo proteomes. The endosperm proteome reference map comprises 930 distinct proteins, including enzymes involved in genetic information processing, carbohydrate metabolism, environmental information processing, energy metabolism, cellular processes and amino acid metabolism. To investigate dynamic changes in protein abundance during seed development, total soluble proteins were extracted from embryo and endosperm fractions at defined time points. Proteins involved in sugar converting and recycling processes, ascorbate metabolism, amino acid biosynthesis and redox balancing were found to be of special importance for seed development in B. napus. Implications for the seed filling process and the function of the endosperm for seed development are discussed. BIOLOGICAL SIGNIFICANCE The endosperm is of key importance for embryo development during seed formation in plants. We present a broad study for characterizing endosperm proteins in the oilseed plant B. napus. Furthermore, a project on the biochemical interplay between the embryo and the endosperm during seed development is presented. We provide evidence that the endosperm includes a complete set of enzymes necessary for plant primary metabolism. Combination of our results with metabolome data will further improve systems-level understanding of the seed filling process and provide rational strategies for plant bioengineering.
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Affiliation(s)
- Christin Lorenz
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Stephanie Sunderhaus
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, 30419 Hannover, Germany.
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Allen DK, Evans BS, Libourel IGL. Analysis of isotopic labeling in peptide fragments by tandem mass spectrometry. PLoS One 2014; 9:e91537. [PMID: 24626471 PMCID: PMC3953442 DOI: 10.1371/journal.pone.0091537] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/13/2014] [Indexed: 01/18/2023] Open
Abstract
Phenotype in multicellular organisms is the consequence of dynamic metabolic events that occur in a spatially dependent fashion. This spatial and temporal complexity presents challenges for investigating metabolism; creating a need for improved methods that effectively probe biochemical events such as amino acid biosynthesis. Isotopic labeling can provide a temporal-spatial recording of metabolic events through, for example, the description of enriched amino acids in the protein pool. Proteins are therefore an important readout of metabolism and can be assessed with modern mass spectrometers. We compared the measurement of isotopic labeling in MS2 spectra obtained from tandem mass spectrometry under either higher energy collision dissociation (HCD) or collision induced dissociation (CID) at varied energy levels. Developing soybean embryos cultured with or without 13C-labeled substrates, and Escherichia coli MG1655 enriched by feeding 7% uniformly labeled glucose served as a source of biological material for protein evaluation. CID with low energies resulted in a disproportionate amount of heavier isotopologues remaining in the precursor isotopic distribution. HCD resulted in fewer quantifiable products; however deviation from predicted distributions were small relative to the CID-based comparisons. Fragment ions have the potential to provide information on the labeling of amino acids in peptides, but our results indicate that without further development the use of this readout in quantitative methods such as metabolic flux analysis is limited.
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Affiliation(s)
- Doug K. Allen
- United States Department of Agriculture, Agricultural Research Service, Plant Genetic Research Unit, St. Louis, Missouri, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Bradley S. Evans
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Igor G. L. Libourel
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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Hay JO, Shi H, Heinzel N, Hebbelmann I, Rolletschek H, Schwender J. Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. FRONTIERS IN PLANT SCIENCE 2014; 5:724. [PMID: 25566296 PMCID: PMC4271587 DOI: 10.3389/fpls.2014.00724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/01/2014] [Indexed: 05/19/2023]
Abstract
The use of large-scale or genome-scale metabolic reconstructions for modeling and simulation of plant metabolism and integration of those models with large-scale omics and experimental flux data is becoming increasingly important in plant metabolic research. Here we report an updated version of bna572, a bottom-up reconstruction of oilseed rape (Brassica napus L.; Brassicaceae) developing seeds with emphasis on representation of biomass-component biosynthesis. New features include additional seed-relevant pathways for isoprenoid, sterol, phenylpropanoid, flavonoid, and choline biosynthesis. Being now based on standardized data formats and procedures for model reconstruction, bna572+ is available as a COBRA-compliant Systems Biology Markup Language (SBML) model and conforms to the Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM) standards for annotation of external data resources. Bna572+ contains 966 genes, 671 reactions, and 666 metabolites distributed among 11 subcellular compartments. It is referenced to the Arabidopsis thaliana genome, with gene-protein-reaction (GPR) associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using B. napus seed specific transcriptome data, expression was verified for 78% of bna572+ genes and 97% of reactions. Alongside bna572+ we also present a revised carbon centric model for (13)C-Metabolic Flux Analysis ((13)C-MFA) with all its reactions being referenced to bna572+ based on linear projections. By integration of flux ratio constraints obtained from (13)C-MFA and by elimination of infinite flux bounds around thermodynamically infeasible loops based on COBRA loopless methods, we demonstrate improvements in predictive power of Flux Variability Analysis (FVA). Using this combined approach we characterize the difference in metabolic flux of developing seeds of two B. napus genotypes contrasting in starch and oil content.
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Affiliation(s)
- Jordan O. Hay
- Biological, Environment and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
| | - Hai Shi
- Biological, Environment and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
| | - Nicolas Heinzel
- Department of Molecular Genetics, Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
| | - Inga Hebbelmann
- Biological, Environment and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
| | - Jorg Schwender
- Biological, Environment and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
- *Correspondence: Jorg Schwender, Brookhaven National Laboratory, Biological, Environment and Climate Sciences Department, Building 463, Upton, NY 11973, USA e-mail:
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Grafahrend-Belau E, Junker A, Schreiber F, Junker BH. Flux balance analysis as an alternative method to estimate fluxes without labeling. Methods Mol Biol 2013; 1090:281-99. [PMID: 24222422 DOI: 10.1007/978-1-62703-688-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The analysis of plant metabolic networks essentially contributes to the understanding of the efficiency of plant systems in terms of their biotechnological usage. Metabolic fluxes are determined by biochemical parameters such as metabolite concentrations as well as enzyme properties and activities, which in turn are the result of various regulatory events at various levels between control of transcription and posttranslational regulation of enzyme protein activity. Thus, knowledge about metabolic fluxes on a large scale provides an integrated view on the functional state of a metabolically active cell, organ, or system. In this chapter, we introduce flux balance analysis as a constraint-based method for the prediction of optimal metabolic fluxes in a given metabolic network. Furthermore, we provide a step-by-step protocol for metabolic network reconstruction and constraint-based analysis using the COBRA Toolbox.
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Affiliation(s)
- Eva Grafahrend-Belau
- Leibniz-Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany
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Borisjuk L, Rolletschek H, Neuberger T. Nuclear magnetic resonance imaging of lipid in living plants. Prog Lipid Res 2013; 52:465-87. [DOI: 10.1016/j.plipres.2013.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/15/2013] [Accepted: 05/28/2013] [Indexed: 01/13/2023]
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Grafahrend-Belau E, Junker A, Eschenröder A, Müller J, Schreiber F, Junker BH. Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. PLANT PHYSIOLOGY 2013; 163:637-47. [PMID: 23926077 PMCID: PMC3793045 DOI: 10.1104/pp.113.224006] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/05/2013] [Indexed: 05/16/2023]
Abstract
Plant metabolism is characterized by a unique complexity on the cellular, tissue, and organ levels. On a whole-plant scale, changing source and sink relations accompanying plant development add another level of complexity to metabolism. With the aim of achieving a spatiotemporal resolution of source-sink interactions in crop plant metabolism, a multiscale metabolic modeling (MMM) approach was applied that integrates static organ-specific models with a whole-plant dynamic model. Allowing for a dynamic flux balance analysis on a whole-plant scale, the MMM approach was used to decipher the metabolic behavior of source and sink organs during the generative phase of the barley (Hordeum vulgare) plant. It reveals a sink-to-source shift of the barley stem caused by the senescence-related decrease in leaf source capacity, which is not sufficient to meet the nutrient requirements of sink organs such as the growing seed. The MMM platform represents a novel approach for the in silico analysis of metabolism on a whole-plant level, allowing for a systemic, spatiotemporally resolved understanding of metabolic processes involved in carbon partitioning, thus providing a novel tool for studying yield stability and crop improvement.
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Affiliation(s)
| | | | - André Eschenröder
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, D–06466 Gatersleben, Germany (E.G.-B., A.J., F.S., B.H.J.)
- Institute of Computer Science (F.S.), Institute of Agricultural and Nutritional Sciences (A.E., J.M.), and Institute of Pharmacy (B.H.J.), Martin Luther University Halle-Wittenberg, D–06120 Halle, Germany; and
- Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Johannes Müller
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, D–06466 Gatersleben, Germany (E.G.-B., A.J., F.S., B.H.J.)
- Institute of Computer Science (F.S.), Institute of Agricultural and Nutritional Sciences (A.E., J.M.), and Institute of Pharmacy (B.H.J.), Martin Luther University Halle-Wittenberg, D–06120 Halle, Germany; and
- Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Falk Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, D–06466 Gatersleben, Germany (E.G.-B., A.J., F.S., B.H.J.)
- Institute of Computer Science (F.S.), Institute of Agricultural and Nutritional Sciences (A.E., J.M.), and Institute of Pharmacy (B.H.J.), Martin Luther University Halle-Wittenberg, D–06120 Halle, Germany; and
- Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
| | - Björn H. Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, D–06466 Gatersleben, Germany (E.G.-B., A.J., F.S., B.H.J.)
- Institute of Computer Science (F.S.), Institute of Agricultural and Nutritional Sciences (A.E., J.M.), and Institute of Pharmacy (B.H.J.), Martin Luther University Halle-Wittenberg, D–06120 Halle, Germany; and
- Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (F.S.)
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47
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Verboven P, Herremans E, Borisjuk L, Helfen L, Ho QT, Tschiersch H, Fuchs J, Nicolaï BM, Rolletschek H. Void space inside the developing seed of Brassica napus and the modelling of its function. THE NEW PHYTOLOGIST 2013; 199:936-947. [PMID: 23692271 PMCID: PMC3784975 DOI: 10.1111/nph.12342] [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: 02/15/2013] [Accepted: 04/23/2013] [Indexed: 05/04/2023]
Abstract
The developing seed essentially relies on external oxygen to fuel aerobic respiration, but it is currently unknown how oxygen diffuses into and within the seed, which structural pathways are used and what finally limits gas exchange. By applying synchrotron X-ray computed tomography to developing oilseed rape seeds we uncovered void spaces, and analysed their three-dimensional assembly. Both the testa and the hypocotyl are well endowed with void space, but in the cotyledons, spaces were small and poorly inter-connected. In silico modelling revealed a three orders of magnitude range in oxygen diffusivity from tissue to tissue, and identified major barriers to gas exchange. The oxygen pool stored in the voids is consumed about once per minute. The function of the void space was related to the tissue-specific distribution of storage oils, storage protein and starch, as well as oxygen, water, sugars, amino acids and the level of respiratory activity, analysed using a combination of magnetic resonance imaging, specific oxygen sensors, laser micro-dissection, biochemical and histological methods. We conclude that the size and inter-connectivity of void spaces are major determinants of gas exchange potential, and locally affect the respiratory activity of a developing seed.
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Affiliation(s)
- Pieter Verboven
- BIOSYST- MeBioS, Faculty of Bioscience Engineering, University of LeuvenW. de Croylaan 42, 3001, Leuven, Belgium
| | - Els Herremans
- BIOSYST- MeBioS, Faculty of Bioscience Engineering, University of LeuvenW. de Croylaan 42, 3001, Leuven, Belgium
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Lukas Helfen
- IPS/ANKA, Karlsruhe Institute of TechnologyPO Box 3640, 76021, Karlsruhe, Germany
- ESRF6 rue Jules Horowitz, BP220, 38043, Grenoble Cedex, France
| | - Quang Tri Ho
- BIOSYST- MeBioS, Faculty of Bioscience Engineering, University of LeuvenW. de Croylaan 42, 3001, Leuven, Belgium
| | - Henning Tschiersch
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Johannes Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Bart M Nicolaï
- BIOSYST- MeBioS, Faculty of Bioscience Engineering, University of LeuvenW. de Croylaan 42, 3001, Leuven, Belgium
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3, 06466, Gatersleben, Germany
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48
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Bihmidine S, Hunter CT, Johns CE, Koch KE, Braun DM. Regulation of assimilate import into sink organs: update on molecular drivers of sink strength. FRONTIERS IN PLANT SCIENCE 2013; 4:177. [PMID: 23761804 PMCID: PMC3671192 DOI: 10.3389/fpls.2013.00177] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/17/2013] [Indexed: 05/18/2023]
Abstract
Recent developments have altered our view of molecular mechanisms that determine sink strength, defined here as the capacity of non-photosynthetic structures to compete for import of photoassimilates. We review new findings from diverse systems, including stems, seeds, flowers, and fruits. An important advance has been the identification of new transporters and facilitators with major roles in the accumulation and equilibration of sugars at a cellular level. Exactly where each exerts its effect varies among systems. Sugarcane and sweet sorghum stems, for example, both accumulate high levels of sucrose, but may do so via different paths. The distinction is central to strategies for targeted manipulation of sink strength using transporter genes, and shows the importance of system-specific analyses. Another major advance has been the identification of deep hypoxia as a feature of normal grain development. This means that molecular drivers of sink strength in endosperm operate in very low oxygen levels, and under metabolic conditions quite different than previously assumed. Successful enhancement of sink strength has nonetheless been achieved in grains by up-regulating genes for starch biosynthesis. Additionally, our understanding of sink strength is enhanced by awareness of the dual roles played by invertases (INVs), not only in sucrose metabolism, but also in production of the hexose sugar signals that regulate cell cycle and cell division programs. These contributions of INV to cell expansion and division prove to be vital for establishment of young sinks ranging from flowers to fruit. Since INV genes are themselves sugar-responsive "feast genes," they can mediate a feed-forward enhancement of sink strength when assimilates are abundant. Greater overall productivity and yield have thus been attained in key instances, indicating that even broader enhancements may be achievable as we discover the detailed molecular mechanisms that drive sink strength in diverse systems.
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Affiliation(s)
- Saadia Bihmidine
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Missouri Maize Center, University of MissouriColumbia, MO, USA
| | - Charles T. Hunter
- Horticultural Sciences Department, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | - Christine E. Johns
- Horticultural Sciences Department, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | - Karen E. Koch
- Horticultural Sciences Department, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | - David M. Braun
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Missouri Maize Center, University of MissouriColumbia, MO, USA
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49
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Collakova E, Aghamirzaie D, Fang Y, Klumas C, Tabataba F, Kakumanu A, Myers E, Heath LS, Grene R. Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos. Metabolites 2013; 3:347-72. [PMID: 24957996 PMCID: PMC3901275 DOI: 10.3390/metabo3020347] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/16/2013] [Accepted: 05/07/2013] [Indexed: 01/08/2023] Open
Abstract
Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.
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Affiliation(s)
- Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
| | - Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA.
| | - Yihui Fang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
| | - Curtis Klumas
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA.
| | | | - Akshay Kakumanu
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA, USA.
| | - Elijah Myers
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA.
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
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50
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Borisjuk L, Neuberger T, Schwender J, Heinzel N, Sunderhaus S, Fuchs J, Hay JO, Tschiersch H, Braun HP, Denolf P, Lambert B, Jakob PM, Rolletschek H. Seed architecture shapes embryo metabolism in oilseed rape. THE PLANT CELL 2013; 25:1625-40. [PMID: 23709628 PMCID: PMC3694696 DOI: 10.1105/tpc.113.111740] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/27/2013] [Accepted: 05/03/2013] [Indexed: 05/03/2023]
Abstract
Constrained to develop within the seed, the plant embryo must adapt its shape and size to fit the space available. Here, we demonstrate how this adjustment shapes metabolism of photosynthetic embryo. Noninvasive NMR-based imaging of the developing oilseed rape (Brassica napus) seed illustrates that, following embryo bending, gradients in lipid concentration became established. These were correlated with the local photosynthetic electron transport rate and the accumulation of storage products. Experimentally induced changes in embryo morphology and/or light supply altered these gradients and were accompanied by alterations in both proteome and metabolome. Tissue-specific metabolic models predicted that the outer cotyledon and hypocotyl/radicle generate the bulk of plastidic reductant/ATP via photosynthesis, while the inner cotyledon, being enclosed by the outer cotyledon, is forced to grow essentially heterotrophically. Under field-relevant high-light conditions, major contribution of the ribulose-1,5-bisphosphate carboxylase/oxygenase-bypass to seed storage metabolism is predicted for the outer cotyledon and the hypocotyl/radicle only. Differences between in vitro- versus in planta-grown embryos suggest that metabolic heterogeneity of embryo is not observable by in vitro approaches. We conclude that in vivo metabolic fluxes are locally regulated and connected to seed architecture, driving the embryo toward an efficient use of available light and space.
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Affiliation(s)
- Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Thomas Neuberger
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Bioengineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jörg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Nicolas Heinzel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | | | - Johannes Fuchs
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- University of Würzburg, Institute of Experimental Physics 5, 97074 Wuerzburg, Germany
| | - Jordan O. Hay
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Henning Tschiersch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany
| | | | | | - Peter M. Jakob
- University of Würzburg, Institute of Experimental Physics 5, 97074 Wuerzburg, Germany
- Research Center Magnetic Resonance Bavaria, 97074 Wuerzburg, Germany
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
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