1
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Bakala HS, Devi J, Singh G, Singh I. Drought and heat stress: insights into tolerance mechanisms and breeding strategies for pigeonpea improvement. PLANTA 2024; 259:123. [PMID: 38622376 DOI: 10.1007/s00425-024-04401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024]
Abstract
MAIN CONCLUSION Pigeonpea has potential to foster sustainable agriculture and resilience in evolving climate change; understanding bio-physiological and molecular mechanisms of heat and drought stress tolerance is imperative to developing resilience cultivars. Pigeonpea is an important legume crop that has potential resilience in the face of evolving climate scenarios. However, compared to other legumes, there has been limited research on abiotic stress tolerance in pigeonpea, particularly towards drought stress (DS) and heat stress (HS). To address this gap, this review delves into the genetic, physiological, and molecular mechanisms that govern pigeonpea's response to DS and HS. It emphasizes the need to understand how this crop combats these stresses and exhibits different types of tolerance and adaptation mechanisms through component traits. The current article provides a comprehensive overview of the complex interplay of factors contributing to the resilience of pigeonpea under adverse environmental conditions. Furthermore, the review synthesizes information on major breeding techniques, encompassing both conventional methods and modern molecular omics-assisted tools and techniques. It highlights the potential of genomics and phenomics tools and their pivotal role in enhancing adaptability and resilience in pigeonpea. Despite the progress made in genomics, phenomics and big data analytics, the complexity of drought and heat tolerance in pigeonpea necessitate continuous exploration at multi-omic levels. High-throughput phenotyping (HTP) is crucial for gaining insights into perplexed interactions among genotype, environment, and management practices (GxExM). Thus, integration of advanced technologies in breeding programs is critical for developing pigeonpea varieties that can withstand the challenges posed by climate change. This review is expected to serve as a valuable resource for researchers, providing a deeper understanding of the mechanisms underlying abiotic stress tolerance in pigeonpea and offering insights into modern breeding strategies that can contribute to the development of resilient varieties suited for changing environmental conditions.
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Affiliation(s)
- Harmeet Singh Bakala
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jomika Devi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
- Texas A&M University, AgriLife Research Center, Beaumont, TX, 77713, USA.
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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2
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Ghatak A, Chaturvedi P, Waldherr S, Subbarao GV, Weckwerth W. PANOMICS at the interface of root-soil microbiome and BNI. TRENDS IN PLANT SCIENCE 2023; 28:106-122. [PMID: 36229336 DOI: 10.1016/j.tplants.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Steffen Waldherr
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guntur Venkata Subbarao
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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3
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Abadie C, Lalande J, Tcherkez G. Exact mass GC-MS analysis: Protocol, database, advantages and application to plant metabolic profiling. PLANT, CELL & ENVIRONMENT 2022; 45:3171-3183. [PMID: 35899865 PMCID: PMC9543805 DOI: 10.1111/pce.14407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 05/14/2023]
Abstract
Plant metabolomics has been used widely in plant physiology, in particular to analyse metabolic responses to environmental parameters. Derivatization (via trimethylsilylation and methoximation) followed by GC-MS metabolic profiling is a major technique to quantify low molecular weight, common metabolites of primary carbon, sulphur and nitrogen metabolism. There are now excellent opportunities for new generation analyses, using high resolution, exact mass GC-MS spectrometers that are progressively becoming relatively cheap. However, exact mass GC-MS analyses for routine metabolic profiling are not common, since there is no dedicated available database. Also, exact mass GC-MS is usually dedicated to structural resolution of targeted secondary metabolites. Here, we present a curated database for exact mass metabolic profiling (made of 336 analytes, 1064 characteristic exact mass fragments) focused on molecules of primary metabolism. We show advantages of exact mass analyses, in particular to resolve isotopic patterns, localise S-containing metabolites, and avoid identification errors when analytes have common nominal mass peaks in their spectrum. We provide a practical example using leaves of different Arabidopsis ecotypes and show how exact mass GC-MS analysis can be applied to plant samples and identify metabolic profiles.
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Affiliation(s)
- Cyril Abadie
- Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAeBeaucouzéFrance
| | - Julie Lalande
- Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAeBeaucouzéFrance
| | - Guillaume Tcherkez
- Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAeBeaucouzéFrance
- Research School of Biology, College of Science, Australian National UniversityCanberra ACTAustralia
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4
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Amara A, Frainay C, Jourdan F, Naake T, Neumann S, Novoa-del-Toro EM, Salek RM, Salzer L, Scharfenberg S, Witting M. Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. Front Mol Biosci 2022; 9:841373. [PMID: 35350714 PMCID: PMC8957799 DOI: 10.3389/fmolb.2022.841373] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/18/2022] [Indexed: 01/19/2023] Open
Abstract
Both targeted and untargeted mass spectrometry-based metabolomics approaches are used to understand the metabolic processes taking place in various organisms, from prokaryotes, plants, fungi to animals and humans. Untargeted approaches allow to detect as many metabolites as possible at once, identify unexpected metabolic changes, and characterize novel metabolites in biological samples. However, the identification of metabolites and the biological interpretation of such large and complex datasets remain challenging. One approach to address these challenges is considering that metabolites are connected through informative relationships. Such relationships can be formalized as networks, where the nodes correspond to the metabolites or features (when there is no or only partial identification), and edges connect nodes if the corresponding metabolites are related. Several networks can be built from a single dataset (or a list of metabolites), where each network represents different relationships, such as statistical (correlated metabolites), biochemical (known or putative substrates and products of reactions), or chemical (structural similarities, ontological relations). Once these networks are built, they can subsequently be mined using algorithms from network (or graph) theory to gain insights into metabolism. For instance, we can connect metabolites based on prior knowledge on enzymatic reactions, then provide suggestions for potential metabolite identifications, or detect clusters of co-regulated metabolites. In this review, we first aim at settling a nomenclature and formalism to avoid confusion when referring to different networks used in the field of metabolomics. Then, we present the state of the art of network-based methods for mass spectrometry-based metabolomics data analysis, as well as future developments expected in this area. We cover the use of networks applications using biochemical reactions, mass spectrometry features, chemical structural similarities, and correlations between metabolites. We also describe the application of knowledge networks such as metabolic reaction networks. Finally, we discuss the possibility of combining different networks to analyze and interpret them simultaneously.
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Affiliation(s)
- Adam Amara
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Clément Frainay
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabien Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Thomas Naake
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Steffen Neumann
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Elva María Novoa-del-Toro
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | - Liesa Salzer
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Sarah Scharfenberg
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Freising, Germany
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5
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Menéndez AB, Ruiz OA. Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes. PeerJ 2021; 9:e12110. [PMID: 34909267 PMCID: PMC8641479 DOI: 10.7717/peerj.12110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/14/2021] [Indexed: 11/20/2022] Open
Abstract
Although legumes are of primary economic importance for human and livestock consumption, the information regarding signalling networks during plant stress response in this group is very scarce. Lotus japonicus is a major experimental model within the Leguminosae family, whereas L. corniculatus and L. tenuis are frequent components of natural and agricultural ecosystems worldwide. These species display differences in their perception and response to diverse stresses, even at the genotype level, whereby they have been used in many studies aimed at achieving a better understanding of the plant stress-response mechanisms. However, we are far from the identification of key components of their stress-response signalling network, a previous step for implementing transgenic and editing tools to develop legume stress-resilient genotypes, with higher crop yield and quality. In this review we scope a body of literature, highlighting what is currently known on the stress-regulated signalling elements so far reported in Lotus spp. Our work includes a comprehensive review of transcription factors chaperones, redox signals and proteins of unknown function. In addition, we revised strigolactones and genes regulating phytochelatins and hormone metabolism, due to their involvement as intermediates in several physiological signalling networks. This work was intended for a broad readership in the fields of physiology, metabolism, plant nutrition, genetics and signal transduction. Our results suggest that Lotus species provide a valuable information platform for the study of specific protein-protein (PPI) interactions, as a starting point to unravel signalling networks underlying plant acclimatation to bacterial and abiotic stressors in legumes. Furthermore, some Lotus species may be a source of genes whose regulation improves stress tolerance and growth when introduced ectopically in other plant species.
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Affiliation(s)
- Ana B Menéndez
- Departamento de Biodiversidad y Biología Experimental. Facultad de Ciencias Exactas y Naturales., Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Overseas, Argentina.,Instituto de Micología y Botánica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Overseas, Argentina
| | - Oscar Adolfo Ruiz
- Instituto Tecnológico de Chascomús, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús, Buenos Aires, Argentina
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6
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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7
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Almeida T, Pinto G, Correia B, Gonçalves S, Meijón M, Escandón M. In-depth analysis of the Quercus suber metabolome under drought stress and recovery reveals potential key metabolic players. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110606. [PMID: 32900444 DOI: 10.1016/j.plantsci.2020.110606] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/12/2020] [Accepted: 07/16/2020] [Indexed: 05/08/2023]
Abstract
Cork oak (Quercus suber L.) is a species of ecological, social and economic importance in the Mediterranean region. Given its xerophytic adaptability, the study of cork oak's response to drought stress conditions may provide important data in the global scenario of climate change. The mechanisms behind cork oak's adaptation to drought conditions can inform the design and development of tools to better manage this species under the changing climate patterns. Metabolomics is one of the most promising omics layers to capture a snapshot of a particular physiological state and to identify putative biomarkers of stress tolerance. Drastic changes were observed in the leaf metabolome of Q. suber between the different experimental conditions, namely at the beginning of the drought stress treatment, after one month under drought and post rehydration. All experimental treatments were analyzed through sPLS to inspect for global changes and stress and rehydration responses were analyzed independently for specific alterations. This allowed a more in-depth study and a search for biomarkers specific to a given hydric treatment. The metabolome analyses showed changes in both primary and secondary metabolism, but highlighted the role of secondary metabolism. In addition, a compound-specific response was observed in stress and rehydration. Key compounds such as L-phenylalanine and epigallocatechin 3-gallate were identified in relation to early drought response, terpenoid leonuridine and the flavonoid glycoside (-)-epicatechin-3'-O-glucuronide in long-term drought response, and flavone isoscoparine was identified in relation to the recovery process. The results here obtained provide novel insights into the biology of cork oak, highlighting pathways and metabolites potentially involved in the response of this species during drought and recovery that may be essential for its adaptation to long periods of drought. It is expected that this knowledge can encourage further functional studies in order to validate potential biomarkers of drought and recovery that maybe used to support decision-making in cork oak breeding programs.
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Affiliation(s)
- Tânia Almeida
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, Beja, Portugal; Centre for Research in Ceramics & Composite Materials (CICECO), University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal; Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Gloria Pinto
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal..
| | - Barbara Correia
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, Beja, Portugal
| | - Mónica Meijón
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Escandón
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal..
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8
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Mass spectrometry-based metabolomics for an in-depth questioning of human health. Adv Clin Chem 2020; 99:147-191. [PMID: 32951636 DOI: 10.1016/bs.acc.2020.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Today, metabolomics is becoming an indispensable tool to get a more comprehensive analysis of complex living systems, providing insights on multiple aspects of physiology. Although its application in large scale population-based studies is very challenging due to the processing of large sample sets as well as the complexity of data information, its potential to characterize human health is well recognized. Technological advances in metabolomics pave the way for the efficient biomarker discovery of disease etiology, diagnosis and prognosis. Here, different steps of the metabolomics workflow, particularly mass spectrometry-based approaches, are discussed to demonstrate the potential of metabolomics to address biological questioning in human health. First an overview of metabolomics is provided with its interest in human health studies. Analytical development and advances in mass spectrometry instrumentation and computational tools are discussed regarding their application limits. Advancing metabolomics for applicability in human health and large-scale studies is presented and discussed in conclusion.
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9
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Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
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Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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10
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Ghatak A, Chaturvedi P, Weckwerth W. Metabolomics in Plant Stress Physiology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 164:187-236. [PMID: 29470599 DOI: 10.1007/10_2017_55] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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11
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Walker TWN, Weckwerth W, Bragazza L, Fragner L, Forde BG, Ostle NJ, Signarbieux C, Sun X, Ward SE, Bardgett RD. Plastic and genetic responses of a common sedge to warming have contrasting effects on carbon cycle processes. Ecol Lett 2018; 22:159-169. [PMID: 30556313 PMCID: PMC6334510 DOI: 10.1111/ele.13178] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 02/02/2023]
Abstract
Climate warming affects plant physiology through genetic adaptation and phenotypic plasticity, but little is known about how these mechanisms influence ecosystem processes. We used three elevation gradients and a reciprocal transplant experiment to show that temperature causes genetic change in the sedge Eriophorum vaginatum. We demonstrate that plants originating from warmer climate produce fewer secondary compounds, grow faster and accelerate carbon dioxide (CO2) release to the atmosphere. However, warmer climate also caused plasticity in E. vaginatum, inhibiting nitrogen metabolism, photosynthesis and growth and slowing CO2 release into the atmosphere. Genetic differentiation and plasticity in E. vaginatum thus had opposing effects on CO2 fluxes, suggesting that warming over many generations may buffer, or reverse, the short‐term influence of this species over carbon cycle processes. Our findings demonstrate the capacity for plant evolution to impact ecosystem processes, and reveal a further mechanism through which plants will shape ecosystem responses to climate change.
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Affiliation(s)
- Tom W N Walker
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK.,Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Wolfram Weckwerth
- Department of Ecogenomics & Systems Biology, University of Vienna, 1090, Vienna, Austria.,Vienna Metabolomics Centre (VIME), University of Vienna, 1090, Vienna, Austria
| | - Luca Bragazza
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 1015, Lausanne, Switzerland.,Ecological Systems Laboratory (ECOS), École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Life Science and Biotechnologies, University of Ferrara, 44100, Ferrara, Italy
| | - Lena Fragner
- Department of Ecogenomics & Systems Biology, University of Vienna, 1090, Vienna, Austria.,Vienna Metabolomics Centre (VIME), University of Vienna, 1090, Vienna, Austria
| | - Brian G Forde
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Nicholas J Ostle
- Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK.,Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Constant Signarbieux
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 1015, Lausanne, Switzerland.,Ecological Systems Laboratory (ECOS), École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Xiaoliang Sun
- Department of Ecogenomics & Systems Biology, University of Vienna, 1090, Vienna, Austria.,Vienna Metabolomics Centre (VIME), University of Vienna, 1090, Vienna, Austria
| | - Susan E Ward
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, Lancaster, UK
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
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12
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Interaction between PGPR and PGR for water conservation and plant growth attributes under drought condition. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0127-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Brockman SA, Roden EV, Hegeman AD. Van Krevelen diagram visualization of high resolution-mass spectrometry metabolomics data with OpenVanKrevelen. Metabolomics 2018; 14:48. [PMID: 30830359 DOI: 10.1007/s11306-018-1343-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/27/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Van Krevelen (VK) diagrams provide a promising but uncommon solution to a number of challenges associated with the visualization of metabolomics data. VK diagrams are created by plotting H:C ratios against O:C ratios of the compounds in a chemical mixture. OBJECTIVES The aim of this manuscript is to present an open-source software tool and reference map that we have developed to make VK diagrams for visualization of metabolomics data. METHODS Software was created with a prompt-driven command line user interface and was written using Python 2.7. We empirically derived an accompanying map by plotting where compounds from seven biomolecule types fall within the VK plot space. RESULTS We've created an easy to use, open source software tool named OpenVanKrevelen for making a range of VK diagrams that is available on GitHub: https://github.com/HegemanLab/VanKrevelenLocal . The empirical mapping approach has produced several improvements from previously published maps. CONCLUSIONS OpenVanKrevelen provides the metabolomics community with access to a new tool for visualization of complex metabolomics datasets.
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Affiliation(s)
- Stephen A Brockman
- Microbial and Plant Genomics Institute and the Departments of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, 1970 Folwell Avenue, St. Paul, MN, USA
| | - Eric V Roden
- Microbial and Plant Genomics Institute and the Departments of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, 1970 Folwell Avenue, St. Paul, MN, USA
| | - Adrian D Hegeman
- Microbial and Plant Genomics Institute and the Departments of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, 1970 Folwell Avenue, St. Paul, MN, USA.
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Nagler M, Nägele T, Gilli C, Fragner L, Korte A, Platzer A, Farlow A, Nordborg M, Weckwerth W. Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field. FRONTIERS IN PLANT SCIENCE 2018; 9:1556. [PMID: 30459786 PMCID: PMC6232504 DOI: 10.3389/fpls.2018.01556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 10/04/2018] [Indexed: 05/05/2023]
Abstract
Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation of plant metabolism to the environment. However, recent studies have demonstrated that it is hardly possible to predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This is particularly due to the high molecular variance of in situ samples induced by environmental fluctuations. An approach of functional metabolome interpretation of field samples would be desirable in order to be able to identify and trace back the impact of environmental changes on plant metabolism. To test the applicability of metabolomics studies for a characterization of plant populations in the field, we have identified and analyzed in situ samples of nearby grown natural populations of Arabidopsis thaliana in Austria. A. thaliana is the primary molecular biological model system in plant biology with one of the best functionally annotated genomes representing a reference system for all other plant genome projects. The genomes of these novel natural populations were sequenced and phylogenetically compared to a comprehensive genome database of A. thaliana ecotypes. Experimental results on primary and secondary metabolite profiling and genotypic variation were functionally integrated by a data mining strategy, which combines statistical output of metabolomics data with genome-derived biochemical pathway reconstruction and metabolic modeling. Correlations of biochemical model predictions and population-specific genetic variation indicated varying strategies of metabolic regulation on a population level which enabled the direct comparison, differentiation, and prediction of metabolic adaptation of the same species to different habitats. These differences were most pronounced at organic and amino acid metabolism as well as at the interface of primary and secondary metabolism and allowed for the direct classification of population-specific metabolic phenotypes within geographically contiguous sampling sites.
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Affiliation(s)
- Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- LMU Munich, Plant Evolutionary Cell Biology, Munich, Germany
| | - Christian Gilli
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Alexander Platzer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Ashley Farlow
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- *Correspondence: Wolfram Weckwerth,
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Escandón M, Meijón M, Valledor L, Pascual J, Pinto G, Cañal MJ. Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata. FRONTIERS IN PLANT SCIENCE 2018; 9:485. [PMID: 29719546 PMCID: PMC5914196 DOI: 10.3389/fpls.2018.00485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/29/2018] [Indexed: 05/19/2023]
Abstract
The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata, identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata, with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata, as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature.
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Affiliation(s)
- Mónica Escandón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- *Correspondence: Mónica Escandón, ; María Jesús Cañal,
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
| | - Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Gloria Pinto
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
- *Correspondence: Mónica Escandón, ; María Jesús Cañal,
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16
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Jaeger C, Hoffmann F, Schmitt CA, Lisec J. Automated Annotation and Evaluation of In-Source Mass Spectra in GC/Atmospheric Pressure Chemical Ionization-MS-Based Metabolomics. Anal Chem 2016; 88:9386-9390. [PMID: 27584561 DOI: 10.1021/acs.analchem.6b02743] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Gas chromatography using atmospheric pressure chemical ionization coupled to mass spectrometry (GC/APCI-MS) is an emerging metabolomics platform, providing much-enhanced capabilities for structural mass spectrometry as compared to traditional electron ionization (EI)-based techniques. To exploit the potential of GC/APCI-MS for more comprehensive metabolite annotation, a major bottleneck in metabolomics, we here present the novel R-based tool InterpretMSSpectrum assisting in the common task of annotating and evaluating in-source mass spectra as obtained from typical full-scan experiments. After passing a list of mass-intensity pairs, InterpretMSSpectrum locates the molecular ion (M0), fragment, and adduct peaks, calculates their most likely sum formula combination, and graphically summarizes results as an annotated mass spectrum. Using (modifiable) filter rules for the commonly used methoximated-trimethylsilylated (MeOx-TMS) derivatives, covering elemental composition, typical substructures, neutral losses, and adducts, InterpretMSSpectrum significantly reduces the number of sum formula candidates, minimizing manual effort for postprocessing candidate lists. We demonstrate the utility of InterpretMSSpectrum for 86 in-source spectra of derivatized standard compounds, in which rank-1 sum formula assignments were achieved in 84% of the cases, compared to only 63% when using mass and isotope information on the M0 alone. We further use, for the first time, automated annotation to evaluate the purity of pseudospectra generated by different metabolomics preprocessing tools, showing that automated annotation can serve as an integrative quality measure for peak picking/deconvolution methods. As an R package, InterpretMSSpectrum integrates flexibly into existing metabolomics pipelines and is freely available from CRAN ( https://cran.r-project.org/ ).
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Affiliation(s)
- Carsten Jaeger
- Charité - Universitätsmedizin Berlin , Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Augustenburger Platz 1, 13353 Berlin, Germany.,Berlin Institute of Health (BIH) , Kapelle-Ufer 2, 10117 Berlin, Germany
| | - Friederike Hoffmann
- Charité - Universitätsmedizin Berlin , Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Clemens A Schmitt
- Charité - Universitätsmedizin Berlin , Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Augustenburger Platz 1, 13353 Berlin, Germany.,Berlin Institute of Health (BIH) , Kapelle-Ufer 2, 10117 Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Jan Lisec
- Charité - Universitätsmedizin Berlin , Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Augustenburger Platz 1, 13353 Berlin, Germany.,German Cancer Consortium, Deutsches Krebsforschungzentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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17
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Wang L, Nägele T, Doerfler H, Fragner L, Chaturvedi P, Nukarinen E, Bellaire A, Huber W, Weiszmann J, Engelmeier D, Ramsak Z, Gruden K, Weckwerth W. System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:318-32. [PMID: 27136060 DOI: 10.1111/tpj.13201] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 03/04/2016] [Accepted: 04/22/2016] [Indexed: 05/19/2023]
Abstract
Theobroma cacao and its popular product, chocolate, are attracting attention due to potential health benefits including antioxidative effects by polyphenols, anti-depressant effects by high serotonin levels, inhibition of platelet aggregation and prevention of obesity-dependent insulin resistance. The development of cacao seeds during fruit ripening is the most crucial process for the accumulation of these compounds. In this study, we analyzed the primary and the secondary metabolome as well as the proteome during Theobroma cacao cv. Forastero seed development by applying an integrative extraction protocol. The combination of multivariate statistics and mathematical modelling revealed a complex consecutive coordination of primary and secondary metabolism and corresponding pathways. Tricarboxylic acid (TCA) cycle and aromatic amino acid metabolism dominated during the early developmental stages (stages 1 and 2; cell division and expansion phase). This was accompanied with a significant shift of proteins from phenylpropanoid metabolism to flavonoid biosynthesis. At stage 3 (reserve accumulation phase), metabolism of sucrose switched from hydrolysis into raffinose synthesis. Lipids as well as proteins involved in lipid metabolism increased whereas amino acids and N-phenylpropenoyl amino acids decreased. Purine alkaloids, polyphenols, and raffinose as well as proteins involved in abiotic and biotic stress accumulated at stage 4 (maturation phase) endowing cacao seeds the characteristic astringent taste and resistance to stress. In summary, metabolic key points of cacao seed development comprise the sequential coordination of primary metabolites, phenylpropanoid, N-phenylpropenoyl amino acid, serotonin, lipid and polyphenol metabolism thereby covering the major compound classes involved in cacao aroma and health benefits.
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Affiliation(s)
- Lei Wang
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME); University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Hannes Doerfler
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Anke Bellaire
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Werner Huber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Doris Engelmeier
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Ziva Ramsak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME); University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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18
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Doppler M, Kluger B, Bueschl C, Schneider C, Krska R, Delcambre S, Hiller K, Lemmens M, Schuhmacher R. Stable Isotope-Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants. Int J Mol Sci 2016; 17:ijms17071017. [PMID: 27367667 PMCID: PMC4964393 DOI: 10.3390/ijms17071017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 12/21/2022] Open
Abstract
The evaluation of extraction protocols for untargeted metabolomics approaches is still difficult. We have applied a novel stable isotope-assisted workflow for untargeted LC-HRMS-based plant metabolomics , which allows for the first time every detected feature to be considered for method evaluation. The efficiency and complementarity of commonly used extraction solvents, namely 1 + 3 (v/v) mixtures of water and selected organic solvents (methanol, acetonitrile or methanol/acetonitrile 1 + 1 (v/v)), with and without the addition of 0.1% (v/v) formic acid were compared. Four different wheat organs were sampled, extracted and analysed by LC-HRMS. Data evaluation was performed with the in-house-developed MetExtract II software and R. With all tested solvents a total of 871 metabolites were extracted in ear, 785 in stem, 733 in leaf and 517 in root samples, respectively. Between 48% (stem) and 57% (ear) of the metabolites detected in a particular organ were found with all extraction mixtures, and 127 of 996 metabolites were consistently shared between all extraction agent/organ combinations. In aqueous methanol, acidification with formic acid led to pronounced pH dependency regarding the precision of metabolite abundance and the number of detectable metabolites, whereas extracts of acetonitrile-containing mixtures were less affected. Moreover, methanol and acetonitrile have been found to be complementary with respect to extraction efficiency. Interestingly, the beneficial properties of both solvents can be combined by the use of a water-methanol-acetonitrile mixture for global metabolite extraction instead of aqueous methanol or aqueous acetonitrile alone.
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Affiliation(s)
- Maria Doppler
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Bernhard Kluger
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Christoph Bueschl
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Christina Schneider
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Rudolf Krska
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Campus Belval, Avenue du Swing 6, 4367 Esch-Belval, Luxembourg.
| | - Karsten Hiller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Campus Belval, Avenue du Swing 6, 4367 Esch-Belval, Luxembourg.
| | - Marc Lemmens
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
- Institute for Biotechnology in Plant Production, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria.
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Yi L, Dong N, Yun Y, Deng B, Ren D, Liu S, Liang Y. Chemometric methods in data processing of mass spectrometry-based metabolomics: A review. Anal Chim Acta 2016; 914:17-34. [PMID: 26965324 DOI: 10.1016/j.aca.2016.02.001] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 01/03/2023]
Abstract
This review focuses on recent and potential advances in chemometric methods in relation to data processing in metabolomics, especially for data generated from mass spectrometric techniques. Metabolomics is gradually being regarded a valuable and promising biotechnology rather than an ambitious advancement. Herein, we outline significant developments in metabolomics, especially in the combination with modern chemical analysis techniques, and dedicated statistical, and chemometric data analytical strategies. Advanced skills in the preprocessing of raw data, identification of metabolites, variable selection, and modeling are illustrated. We believe that insights from these developments will help narrow the gap between the original dataset and current biological knowledge. We also discuss the limitations and perspectives of extracting information from high-throughput datasets.
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Affiliation(s)
- Lunzhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Naiping Dong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, 999077, China
| | - Yonghuan Yun
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Baichuan Deng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dabing Ren
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming, 650500, China
| | - Shao Liu
- Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yizeng Liang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
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20
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Meijón M, Feito I, Oravec M, Delatorre C, Weckwerth W, Majada J, Valledor L. Exploring natural variation ofPinus pinasterAiton using metabolomics: Is it possible to identify the region of origin of a pine from its metabolites? Mol Ecol 2016; 25:959-76. [DOI: 10.1111/mec.13525] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/12/2015] [Accepted: 12/10/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Mónica Meijón
- Regional Institute for Research and Agro-Food Development in Asturias; Experimental Station “La Mata”; 33820 Grado Spain
| | - Isabel Feito
- Regional Institute for Research and Agro-Food Development in Asturias; Experimental Station “La Mata”; 33820 Grado Spain
| | - Michal Oravec
- Czechglobe; Academy of Sciences of the Czech Republic; Bělidla 986/4a, 603 00 Brno Czech Republic
| | - Carolina Delatorre
- Regional Institute for Research and Agro-Food Development in Asturias; Experimental Station “La Mata”; 33820 Grado Spain
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology; Faculty of Life Sciences; University of Vienna; Althanstrasse 14 1090 Vienna
- Vienna Metabolomics Center; University of Vienna; Universitätsring 1 1010 Vienna
| | - Juan Majada
- Forest and Wood Technology Research Centre; Experimental Station “La Mata” 33820 Grado
| | - Luis Valledor
- Czechglobe; Academy of Sciences of the Czech Republic; Bělidla 986/4a, 603 00 Brno Czech Republic
- Plant Physiology; University of Oviedo; Catedrático Rodrigo Uría 33006 Oviedo
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Karpe AV, Beale DJ, Godhani NB, Morrison PD, Harding IH, Palombo EA. Untargeted Metabolic Profiling of Winery-Derived Biomass Waste Degradation by Penicillium chrysogenum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10696-704. [PMID: 26611372 DOI: 10.1021/acs.jafc.5b04834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Winery-derived biomass waste was degraded by Penicillium chrysogenum under solid state fermentation over 8 days in a (2)H2O-supplemented medium. Multivariate statistical analysis of the gas chromatography-mass spectrometry (GC-MS) data resulted in the identification of 94 significant metabolites, within 28 different metabolic pathways. The majority of biomass sugars were utilized by day 4 to yield products such as sugars, fatty acids, isoprenoids, and amino acids. The fungus was observed to metabolize xylose to xylitol, an intermediate of ethanol production. However, enzyme inhibition and autolysis were observed from day 6, indicating 5 days as the optimal time for fermentation. P. chrysogenum displayed metabolism of pentoses (to alcohols) and degraded tannins and lignins, properties that are lacking in other biomass-degrading ascomycetes. Rapid fermentation (3-5 days) may not only increase the pentose metabolizing efficiency but also increase the yield of medicinally important metabolites, such as syringate.
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Affiliation(s)
- Avinash V Karpe
- Department of Chemistry and Biotechnology, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), P.O. Box 2583, Dutton Park, Queensland 4001, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), P.O. Box 2583, Dutton Park, Queensland 4001, Australia
| | - Nainesh B Godhani
- Department of Mechanical and Product Design Engineering, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Paul D Morrison
- Australian Centre for Research on Separation Science, School of Applied Sciences, RMIT University , P.O. Box 2547, Melbourne, Victoria 3000, Australia
| | - Ian H Harding
- Department of Chemistry and Biotechnology, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology , P.O. Box 218, Hawthorn, Victoria 3122, Australia
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23
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Misra BB, van der Hooft JJJ. Updates in metabolomics tools and resources: 2014-2015. Electrophoresis 2015; 37:86-110. [DOI: 10.1002/elps.201500417] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/04/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Biswapriya B. Misra
- Department of Biology, Genetics Institute; University of Florida; Gainesville FL USA
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Zivy M, Wienkoop S, Renaut J, Pinheiro C, Goulas E, Carpentier S. The quest for tolerant varieties: the importance of integrating "omics" techniques to phenotyping. FRONTIERS IN PLANT SCIENCE 2015; 6:448. [PMID: 26217344 PMCID: PMC4496562 DOI: 10.3389/fpls.2015.00448] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
The primary objective of crop breeding is to improve yield and/or harvest quality while minimizing inputs. Global climate change and the increase in world population are significant challenges for agriculture and call for further improvements to crops and the development of new tools for research. Significant progress has been made in the molecular and genetic analysis of model plants. However, is science generating false expectations? Are 'omic techniques generating valuable information that can be translated into the field? The exploration of crop biodiversity and the correlation of cellular responses to stress tolerance at the plant level is currently a challenge. This viewpoint reviews concisely the problems one encounters when working on a crop and provides an outline of possible workflows when initiating cellular phenotyping via "-omic" techniques (transcriptomics, proteomics, metabolomics).
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Affiliation(s)
- Michel Zivy
- Department Génétique Quantitative et Évolution, Le Moulon INRA, CNRS, AgroParisTech, Plateforme PAPPSO, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Jenny Renaut
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, Oeiras, Portugal
- Faculdade de Ciências e Tecnologia, New University of Lisbon, Caparica, Portugal
| | - Estelle Goulas
- Department of Sciences et Technologies, CNRS/Université Lille, Villeneuve d’Ascq, France
| | - Sebastien Carpentier
- Department of Biosystems, University of Leuven, Leuven, Belgium
- SYBIOMA, University of Leuven, Leuven, Belgium
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25
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Wolfender JL, Marti G, Thomas A, Bertrand S. Current approaches and challenges for the metabolite profiling of complex natural extracts. J Chromatogr A 2015; 1382:136-64. [DOI: 10.1016/j.chroma.2014.10.091] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/11/2022]
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26
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Yi L, Dong N, Yun Y, Deng B, Liu S, Zhang Y, Liang Y. WITHDRAWN: Recent advances in chemometric methods for plant metabolomics: A review. Biotechnol Adv 2014:S0734-9750(14)00183-9. [PMID: 25461504 DOI: 10.1016/j.biotechadv.2014.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 12/17/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Lunzhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming 650500, China.
| | - Naiping Dong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, Hong Kong, China
| | - Yonghuan Yun
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Baichuan Deng
- Department of Chemistry, University of Bergen, Bergen N-5007, Norway
| | - Shao Liu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Yizeng Liang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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27
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Ma Y, Kind T, Yang D, Leon C, Fiehn O. MS2Analyzer: A software for small molecule substructure annotations from accurate tandem mass spectra. Anal Chem 2014; 86:10724-31. [PMID: 25263576 PMCID: PMC4222628 DOI: 10.1021/ac502818e] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/27/2014] [Indexed: 01/08/2023]
Abstract
Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/ . As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae.
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Affiliation(s)
- Yan Ma
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
| | - Tobias Kind
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
| | - Dawei Yang
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
- SPKLOMHNM
and Central Laboratory, Zhong Yuan Academy of Biological Medicine, Liaocheng University, Liaocheng People’s Hospital, Liaocheng, Shandong 252000, P. R. China
| | - Carlos Leon
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
- Biomedical
Engineering School, Carlos III University, Avda Universidad 30, 28911, Leganes, Madrid, Spain
| | - Oliver Fiehn
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
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28
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Sévin DC, Kuehne A, Zamboni N, Sauer U. Biological insights through nontargeted metabolomics. Curr Opin Biotechnol 2014; 34:1-8. [PMID: 25461505 DOI: 10.1016/j.copbio.2014.10.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/03/2014] [Accepted: 10/03/2014] [Indexed: 01/10/2023]
Abstract
Metabolomics is increasingly employed to investigate metabolism and its reciprocal crosstalk with cellular signaling and regulation. In recent years, several nontargeted metabolomics methods providing substantial metabolome coverage have been developed. Here, we review and compare the contributions of traditional targeted and nontargeted metabolomics in advancing different research areas ranging from biotechnology to human health. Although some studies demonstrated the power of nontargeted profiling in generating unexpected and yet highly important insights, we found that most mechanistic links were still revealed by hypothesis-driven targeted methods. Novel computational approaches for formal interpretation of complex metabolic patterns and integration of complementary molecular layers are required to tap the full potential of nontargeted metabolomics for data-driven, discovery-oriented research and rapidly nucleating novel biological insights.
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Affiliation(s)
- Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland; PhD Program on Systems Biology, Life Science Zurich, Switzerland
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland; PhD Program on Systems Biology, Life Science Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
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