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Metabolites
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Metabolomics in Plant Metabolic Engineering
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Metabolomics in Plant Metabolic Engineering

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: closed (28 February 2013) | Viewed by 34243

Special Issue Editor

Prof. Dr. Ute Roessner

E-Mail Website
Guest Editor
Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Interests: metabolomics; analytical biochemistry; metabolism; crop improvement; biomarker discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolomics as a technology in the post-genomics era has rapidly advanced in the past decade for the detection and quantification of steady-state levels of hundreds of metabolites. Developments in instrumentation used for metabolomics and subsequent data analysis pipelines have resulted in numerous applications of metabolomics in the plant sciences. However, in order to determine the carbon and/or nitrogen flow across metabolic pathways and reconstruct metabolic models, sophisticated flux analysis has to be utilized by admission of stable isotope labeled precursors and subsequent quantification of label in each metabolite detectable. This allows a quantification of fluxes through individual pathways; an important necessity for any metabolic engineering approach. Here we aim to collect expert opinions and experiences of how metabolomics has advanced the science of fluxomics to increase our understanding of plasticity of metabolism and improve metabolic engineering attempts in plants as bioreactor organisms. 
This special issue “Metabolomics of Plant Metabolic Engineering” of Metabolites will be dedicated to methods used to determine metabolic fluxes, to interpret resulting data and to integrate data with genome-wide models of metabolism. Additionally we aim to present selected examples of metabolic engineering approaches of biotechnologically and pharmaceutically important products in planta.

Dr. Ute Roessner
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolomics
  • flux
  • modeling
  • metabolic engineering
  • plants
  • bioreactor

Published Papers (4 papers)

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Research

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536 KiB  
Article
Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos
by Eva Collakova, Delasa Aghamirzaie, Yihui Fang, Curtis Klumas, Farzaneh Tabataba, Akshay Kakumanu, Elijah Myers, Lenwood S. Heath and Ruth Grene
Metabolites 2013, 3(2), 347-372; https://doi.org/10.3390/metabo3020347 - 14 May 2013
Cited by 49 | Viewed by 9924
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Metabolomics in Plant Metabolic Engineering)
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415 KiB  
Article
Development of a Direct Headspace Collection Method from Arabidopsis Seedlings Using HS-SPME-GC-TOF-MS Analysis
by Miyako Kusano, Yumiko Iizuka, Makoto Kobayashi, Atsushi Fukushima and Kazuki Saito
Metabolites 2013, 3(2), 223-242; https://doi.org/10.3390/metabo3020223 - 09 Apr 2013
Cited by 16 | Viewed by 9833
Abstract
Plants produce various volatile organic compounds (VOCs), which are thought to be a crucial factor in their interactions with harmful insects, plants and animals. Composition of VOCs may differ when plants are grown under different nutrient conditions, i.e., macronutrient-deficient conditions. However, in [...] Read more.
Plants produce various volatile organic compounds (VOCs), which are thought to be a crucial factor in their interactions with harmful insects, plants and animals. Composition of VOCs may differ when plants are grown under different nutrient conditions, i.e., macronutrient-deficient conditions. However, in plants, relationships between macronutrient assimilation and VOC composition remain unclear. In order to identify the kinds of VOCs that can be emitted when plants are grown under various environmental conditions, we established a conventional method for VOC profiling in Arabidopsis thaliana (Arabidopsis) involving headspace-solid-phase microextraction-gas chromatography-time-of-flight-mass spectrometry (HS-SPME-GC-TOF-MS). We grew Arabidopsis seedlings in an HS vial to directly perform HS analysis. To maximize the analytical performance of VOCs, we optimized the extraction method and the analytical conditions of HP-SPME-GC-TOF-MS. Using the optimized method, we conducted VOC profiling of Arabidopsis seedlings, which were grown under two different nutrition conditions, nutrition-rich and nutrition-deficient conditions. The VOC profiles clearly showed a distinct pattern with respect to each condition. This study suggests that HS-SPME-GC-TOF-MS analysis has immense potential to detect changes in the levels of VOCs in not only Arabidopsis, but other plants grown under various environmental conditions. Full article
(This article belongs to the Special Issue Metabolomics in Plant Metabolic Engineering)
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2281 KiB  
Article
Characterization of Flavan-3-ols and Expression of MYB and Late Pathway Genes Involved in Proanthocyanidin Biosynthesis in Foliage of Vitis bellula
by Yue Zhu, Qing-Zhong Peng, Ci Du, Ke-Gang Li and De-Yu Xie
Metabolites 2013, 3(1), 185-203; https://doi.org/10.3390/metabo3010185 - 19 Mar 2013
Cited by 7 | Viewed by 6499
Abstract
Proanthocyanidins (PAs) are fundamental nutritional metabolites in different types of grape products consumed by human beings. Although the biosynthesis of PAs in berry of Vitis vinifera has gained intensive investigations, the understanding of PAs in other Vitis species is limited. In this study, [...] Read more.
Proanthocyanidins (PAs) are fundamental nutritional metabolites in different types of grape products consumed by human beings. Although the biosynthesis of PAs in berry of Vitis vinifera has gained intensive investigations, the understanding of PAs in other Vitis species is limited. In this study, we report PA formation and characterization of gene expression involved in PA biosynthesis in leaves of V. bellula, a wild edible grape species native to south and south-west China. Leaves are collected at five developmental stages defined by sizes ranging from 0.5 to 5 cm in length. Analyses of thin layer chromatography (TLC) and high performance liquid chromatography-photodiode array detector (HPLC-PAD) show the formation of (+)-catechin, (−)-epicatechin, (+)-gallocatechin and (−)-epigallocatechin during the entire development of leaves. Analyses of butanol-HCl boiling cleavage coupled with spectrometry measurement at 550 nm show a temporal trend of extractable PA levels, which is characterized by an increase from 0.5 cm to 1.5 cm long leaves followed by a decrease in late stages. TLC and HPLC-PAD analyses identify cyanidin, delphinidin and pelargonidin produced from the cleavage of PAs in the butanol-HCl boiling, showing that the foliage PAs of V. bellula include three different types of extension units. Four cDNAs, which encode VbANR, VbDFR, VbLAR1 and VbLAR2, respectively, are cloned from young leaves. The expression patterns of VbANR and VbLAR2 but not VbLAR1 and VbDFR follow a similar trend as the accumulation patterns of PAs. Two cDNAs encoding VbMYBPA1 and VbMYB5a, the homologs of which have been demonstrated to regulate the expression of both ANR and LAR in V. vinifera, are also cloned and their expression profiles are similar to those of VbANR and VbLAR2. In contrast, the expression profiles of MYBA1 and 2 homologs involved in anthocyanin biosynthesis are different from those of VbANR and VbLAR2. Our data show that both ANR and LAR branches are involved in PA biosynthesis in leaves of V. bellula. Full article
(This article belongs to the Special Issue Metabolomics in Plant Metabolic Engineering)
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Review

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731 KiB  
Review
Coordinating Metabolite Changes with Our Perception of Plant Abiotic Stress Responses: Emerging Views Revealed by Integrative—Omic Analyses
by Jordan D. Radomiljac, James Whelan and Margaretha Van der Merwe
Metabolites 2013, 3(3), 761-786; https://doi.org/10.3390/metabo3030761 - 06 Sep 2013
Cited by 8 | Viewed by 7323
Abstract
Metabolic configuration and adaptation under a range of abiotic stresses, including drought, heat, salinity, cold, and nutrient deprivation, are subjected to an intricate span of molecular pathways that work in parallel in order to enhance plant fitness and increase stress tolerance. In recent [...] Read more.
Metabolic configuration and adaptation under a range of abiotic stresses, including drought, heat, salinity, cold, and nutrient deprivation, are subjected to an intricate span of molecular pathways that work in parallel in order to enhance plant fitness and increase stress tolerance. In recent years, unprecedented advances have been made in identifying and linking different abiotic stresses, and the current challenge in plant molecular biology is deciphering how the signaling responses are integrated and transduced throughout metabolism. Metabolomics have often played a fundamental role in elucidating the distinct and overlapping biochemical changes that occur in plants. However, a far greater understanding and appreciation of the complexity in plant metabolism under specific stress conditions have become apparent when combining metabolomics with other—omic platforms. This review focuses on recent advances made in understanding the global changes occurring in plant metabolism under abiotic stress conditions using metabolite profiling as an integrated discovery platform. Full article
(This article belongs to the Special Issue Metabolomics in Plant Metabolic Engineering)
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