1
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Chen J, Lou Y, Liu Y, Deng B, Zhu Z, Yang S, Chen D. Advances in Chromatographic and Mass Spectrometric Techniques for Analyzing Reducing Monosaccharides and Their Phosphates in Biological Samples. Crit Rev Anal Chem 2024:1-23. [PMID: 38855933 DOI: 10.1080/10408347.2024.2364232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Reducing monosaccharides and their phosphates are critical metabolites in the central carbon metabolism pathway of living organisms. Variations in their content can indicate abnormalities in metabolic pathways and the onset of certain diseases, necessitating their analysis and detection. Reducing monosaccharides and their phosphates exhibit significant variations in content within biological samples and are present in many isomers, which makes the accurate quantification of reducing monosaccharides and their phosphates in biological samples a challenging task. Various analytical methods such as spectroscopy, fluorescence detection, colorimetry, nuclear magnetic resonance spectroscopy, sensor-based techniques, chromatography, and mass spectrometry are employed to detect monosaccharides and phosphates. In comparison, chromatography and mass spectrometry are highly favored for their ability to simultaneously analyze multiple components and their high sensitivity and selectivity. This review thoroughly evaluates the current chromatographic and mass spectrometric methods used for detecting reducing monosaccharides and their phosphates from 2013 to 2023, highlighting their efficacy and the advancements in these analytical technologies.
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Affiliation(s)
- Jiaqi Chen
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yifeng Lou
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuwei Liu
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Bowen Deng
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zheng Zhu
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Sen Yang
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Nanomedicine for Targeting Diagnosis and Treatment, Zhengzhou University, Zhengzhou, China
| | - Di Chen
- Zhengzhou Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Nanomedicine for Targeting Diagnosis and Treatment, Zhengzhou University, Zhengzhou, China
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2
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Sirén H. Research of saccharides and related biocomplexes: A review with recent techniques and applications. J Sep Sci 2024; 47:e2300668. [PMID: 38699940 DOI: 10.1002/jssc.202300668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 05/05/2024]
Abstract
Saccharides and biocompounds as saccharide (sugar) complexes have various roles and biological functions in living organisms due to modifications via nucleophilic substitution, polymerization, and complex formation reactions. Mostly, mono-, di-, oligo-, and polysaccharides are stabilized to inactive glycosides, which are formed in metabolic pathways. Natural saccharides are important in food and environmental monitoring. Glycosides with various functionalities are significant in clinical and medical research. Saccharides are often studied with the chromatographic methods of hydrophilic interaction liquid chromatography and anion exchange chromatograpy, but also with capillary electrophoresis and mass spectrometry with their on-line coupling systems. Sample preparation is important in the identification of saccharide compounds. The cases discussed here focus on bioscience, clinical, and food applications.
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Affiliation(s)
- Heli Sirén
- Chemicum Building, University of Helsinki, Helsinki, Finland
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3
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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4
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Kambhampati S, Hubbard AH, Koley S, Gomez JD, Marsolais F, Evans BS, Young JD, Allen DK. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Commun Biol 2024; 7:172. [PMID: 38347116 PMCID: PMC10861564 DOI: 10.1038/s42003-024-05844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
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Affiliation(s)
- Shrikaar Kambhampati
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Allen H Hubbard
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Javier D Gomez
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frédéric Marsolais
- London Research and Development Center, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bradley S Evans
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jamey D Young
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Agricultural Research Service, US Department of Agriculture, St. Louis, MO, 63132, USA.
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5
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Mohanasundaram B, Koley S, Allen DK, Pandey S. Physcomitrium patens response to elevated CO 2 is flexible and determined by an interaction between sugar and nitrogen availability. THE NEW PHYTOLOGIST 2024; 241:1222-1235. [PMID: 37929754 DOI: 10.1111/nph.19348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Mosses hold a unique position in plant evolution and are crucial for protecting natural, long-term carbon storage systems such as permafrost and bogs. Due to small stature, mosses grow close to the soil surface and are exposed to high levels of CO2 , produced by soil respiration. However, the impact of elevated CO2 (eCO2 ) levels on mosses remains underexplored. We determined the growth responses of the moss Physcomitrium patens to eCO2 in combination with different nitrogen levels and characterized the underlying physiological and metabolic changes. Three distinct growth characteristics, an early transition to caulonema, the development of longer, highly pigmented rhizoids, and increased biomass, define the phenotypic responses of P. patens to eCO2 . Elevated CO2 impacts growth by enhancing the level of a sugar signaling metabolite, T6P. The quantity and form of nitrogen source influences these metabolic and phenotypic changes. Under eCO2 , P. patens exhibits a diffused growth pattern in the presence of nitrate, but ammonium supplementation results in dense growth with tall gametophores, demonstrating high phenotypic plasticity under different environments. These results provide a framework for comparing the eCO2 responses of P. patens with other plant groups and provide crucial insights into moss growth that may benefit climate change models.
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Affiliation(s)
| | - Somnath Koley
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
- USDA-ARS, Saint Louis, MO, 63132, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
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6
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Zhu M, Jiang S, Huang J, Li Z, Xu S, Liu S, He Y, Zhang Z. Biochemical and Transcriptome Analyses Reveal a Stronger Capacity for Photosynthate Accumulation in Low-Tillering Rice Varieties. Int J Mol Sci 2024; 25:1648. [PMID: 38338929 PMCID: PMC10855222 DOI: 10.3390/ijms25031648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Moderate control of rice tillering and the development of rice varieties with large panicles are important topics for future high-yield rice breeding. Herein, we found that low-tillering rice varieties stopped tillering earlier and had a larger leaf area of the sixth leaf. Notably, at 28 days after sowing, the rice seedlings of the low-tillering group had an average single-culm above-ground biomass of 0.84 g, significantly higher than that of the multi-tillering group by 56.26%, and their NSC (non-structural carbohydrate) and starch contents in sheaths were increased by 43.34% and 97.75%, respectively. These results indicated that the low-tillering group of rice varieties had a stronger ability to store photosynthetic products in the form of starch in their sheaths, which was thus more beneficial for their large panicle development. The results of carbon and nitrogen metabolism analyses showed that the low-tillering group had a relatively strong carbon metabolism activity, which was more favorable for the accumulation of photosynthesis products and the following development of large panicles, while the multi-tillering group showed relatively strong nitrogen metabolism activity, which was more beneficial for the development and formation of new organs, such as tillers. Accordingly, in the low-tillering rice varieties, the up-regulated genes were enriched in the pathways mainly related to the synthesis of carbohydrates, while the down-regulated genes were mainly enriched in the nitrogen metabolism pathways. This study provides new insights into the mechanism of rice tillering regulation and promotes the development of new varieties with ideal plant types.
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Affiliation(s)
- Mingqiang Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Shan Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Jinqiu Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Zhihui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Shuang Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Shaojia Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
| | - Yonggang He
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
| | - Zhihong Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.Z.); (S.J.); (J.H.); (Z.L.); (S.X.); (S.L.)
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7
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Dellero Y, Berardocco S, Bouchereau A. U- 13C-glucose incorporation into source leaves of Brassica napus highlights light-dependent regulations of metabolic fluxes within central carbon metabolism. JOURNAL OF PLANT PHYSIOLOGY 2024; 292:154162. [PMID: 38103478 DOI: 10.1016/j.jplph.2023.154162] [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: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Plant central carbon metabolism comprises several important metabolic pathways acting together to support plant growth and yield establishment. Despite the emergence of 13C-based dynamic approaches, the regulation of metabolic fluxes between light and dark conditions has not yet received sufficient attention for agronomically relevant plants. Here, we investigated the impact of light/dark conditions on carbon allocation processes within central carbon metabolism of Brassica napus after U-13C-glucose incorporation into leaf discs. Leaf gas-exchanges and metabolite contents were weakly impacted by the leaf disc method and the incorporation of glucose. 13C-analysis by GC-MS showed that U-13C-glucose was converted to fructose for de novo biosynthesis of sucrose at similar rates in both light and dark conditions. However, light conditions led to a reduced commitment of glycolytic carbons towards respiratory substrates (pyruvate, alanine, malate) and TCA cycle intermediates compared to dark conditions. Analysis of 13C-enrichment at the isotopologue level and metabolic pathway isotopic tracing reconstructions identified the contribution of multiple pathways to serine biosynthesis in light and dark conditions. However, the direct contribution of the glucose-6-phosphate shunt to serine biosynthesis was not observed. Our results also provided isotopic evidences for an active metabolic connection between the TCA cycle, glycolysis and photorespiration in light conditions through a rapid reallocation of TCA cycle decarboxylations back to the TCA cycle through photorespiration and glycolysis. Altogether, these results suggest the active coordination of core metabolic pathways across multiple compartments to reorganize C-flux modes.
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Affiliation(s)
- Younès Dellero
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France.
| | - Solenne Berardocco
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France
| | - Alain Bouchereau
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France
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8
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Lim JS, Lee SH, Yun H, Lee DY, Cho N, Yoo G, Choi JU, Lee KY, Bach TT, Park SJ, Cho YC. Inhibitory Effects of Ehretia tinifolia Extract on the Excessive Oxidative and Inflammatory Responses in Lipopolysaccharide-Stimulated Mouse Kupffer Cells. Antioxidants (Basel) 2023; 12:1792. [PMID: 37891872 PMCID: PMC10604099 DOI: 10.3390/antiox12101792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Ehretia tinifolia (E. tinifolia) L., an evergreen tree with substantial biological activity, including antioxidant and anti-inflammatory effects, has been used in many herbal and traditional medicines. To elucidate its antioxidant and anti-inflammatory activity and the underlying mechanisms, we applied a methanol extract of E. tinifolia (ETME) to lipopolysaccharide (LPS)-stimulated mouse immortalized Kupffer cells. ETME suppressed the LPS-induced increase in nitric oxide, a mediator for oxidative stress and inflammation, and restored LPS-mediated depletion of total glutathione level by stabilizing antioxidative nuclear factor erythroid 2-related factor 2 (Nrf2) and the subsequent increase in heme oxygenase-1 levels. Furthermore, ETME inhibited the LPS-induced production of pro-inflammatory cytokines, including tumor necrosis factor-α, interleukin (IL)-1β, and IL-6. The inhibitory effects of ETME on pro-inflammatory responses were regulated by ETME-mediated dephosphorylation of mitogen-activated protein kinases (MAPKs: p38, p44/p42, and stress-associated protein kinase/c-Jun N-terminal kinase) and inhibition of nuclear localization of nuclear factor kappa B (NF-κB). These results suggest that ETME is a possible candidate for protecting Kupffer cells from LPS-mediated oxidative stress and excessive inflammatory responses by activating antioxidant Nrf2/HO-1 and inhibiting pro-inflammatory NF-κB and MAPKs, respectively.
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Affiliation(s)
- Jae Sung Lim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
| | - Sung Ho Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Da Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
| | - Namki Cho
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
| | - Guijae Yoo
- Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun 55365, Republic of Korea;
| | - Jeong Uk Choi
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
| | - Kwang Youl Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
| | - Tran The Bach
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122000, Vietnam;
| | - Su-Jin Park
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si 56212, Republic of Korea
| | - Young-Chang Cho
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju 61186, Republic of Korea; (J.S.L.); (S.H.L.); (D.Y.L.); (N.C.); (J.U.C.); (K.Y.L.)
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9
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Morley SA, Ma F, Alazem M, Frankfater C, Yi H, Burch-Smith T, Clemente TE, Veena V, Nguyen H, Allen DK. Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans. THE NEW PHYTOLOGIST 2023. [PMID: 36829298 DOI: 10.1111/nph.18835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Central metabolism produces amino and fatty acids for protein and lipids that establish seed value. Biosynthesis of storage reserves occurs in multiple organelles that exchange central intermediates including two essential metabolites, malate, and pyruvate that are linked by malic enzyme. Malic enzyme can be active in multiple subcellular compartments, partitioning carbon and reducing equivalents for anabolic and catabolic requirements. Prior studies based on isotopic labeling and steady-state metabolic flux analyses indicated malic enzyme provides carbon for fatty acid biosynthesis in plants, though genetic evidence confirming this role is lacking. We hypothesized that increasing malic enzyme flux would alter carbon partitioning and result in increased lipid levels in soybeans. Homozygous transgenic soybean plants expressing Arabidopsis malic enzyme alleles, targeting the translational products to plastid or outside the plastid during seed development, were verified by transcript and enzyme activity analyses, organelle proteomics, and transient expression assays. Protein, oil, central metabolites, cofactors, and acyl-acyl carrier protein (ACPs) levels were quantified overdevelopment. Amino and fatty acid levels were altered resulting in an increase in lipids by 0.5-2% of seed biomass (i.e. 2-9% change in oil). Subcellular targeting of a single gene product in central metabolism impacts carbon and reducing equivalent partitioning for seed storage reserves in soybeans.
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Affiliation(s)
- Stewart A Morley
- United States Department of Agriculture, Agricultural Research Service, 975 N Warson Rd, St Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Fangfang Ma
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Mazen Alazem
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Cheryl Frankfater
- United States Department of Agriculture, Agricultural Research Service, 975 N Warson Rd, St Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Hochul Yi
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Tessa Burch-Smith
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Tom Elmo Clemente
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, 202 Keim Hall, Lincoln, NE, 68583, USA
| | - Veena Veena
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Hanh Nguyen
- Center for Plant Science Innovation, University of Nebraska, N300 Beadle Center, 1901 Vine St., Lincoln, NE, 68588, USA
| | - Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 N Warson Rd, St Louis, MO, 63132, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
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10
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Koley S, Chu KL, Mukherjee T, Morley SA, Klebanovych A, Czymmek KJ, Allen DK. Metabolic synergy in Camelina reproductive tissues for seed development. SCIENCE ADVANCES 2022; 8:eabo7683. [PMID: 36306367 PMCID: PMC9616503 DOI: 10.1126/sciadv.abo7683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis in fruits is well documented, but its contribution to seed development and yield remains largely unquantified. In oilseeds, the pods are green and elevated with direct access to sunlight. With 13C labeling in planta and through an intact pod labeling system, a unique multi-tissue comprehensive flux model mechanistically described how pods assimilate up to one-half (33 to 45%) of seed carbon by proximal photosynthesis in Camelina sativa. By capturing integrated tissue metabolism, the studies reveal the contribution of plant architecture beyond leaves, to enable seed filling and maximize the number of viable seeds. The latent capacity of the pod wall in the absence of leaves contributes approximately 79% of seed biomass, supporting greater seed sink capacity and higher theoretical yields that suggest an opportunity for crop productivity gains.
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Affiliation(s)
- Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kevin L. Chu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Stewart A. Morley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
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11
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Metabolomics and modelling approaches for systems metabolic engineering. Metab Eng Commun 2022; 15:e00209. [PMID: 36281261 PMCID: PMC9587336 DOI: 10.1016/j.mec.2022.e00209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering. Constraint-based models, such as genome scale models, have been used successfully to enhance the yield of desired compounds from engineered microbes, however, unlike kinetic or dynamic models, constraint-based models do not incorporate regulatory effects. Nevertheless, the lack of time-series metabolomic data generation has hindered the usefulness of dynamic models till today. In this review, we show that improvements in automation, dynamic real-time analysis and high throughput workflows can drive the generation of more quality data for dynamic models through time-series metabolomics data generation. Spatial metabolomics also has the potential to be used as a complementary approach to conventional metabolomics, as it provides information on the localization of metabolites. However, more effort must be undertaken to identify metabolites from spatial metabolomics data derived through imaging mass spectrometry, where machine learning approaches could prove useful. On the other hand, single-cell metabolomics has also seen rapid growth, where understanding cell-cell heterogeneity can provide more insights into efficient metabolic engineering of microbes. Moving forward, with potential improvements in automation, dynamic real-time analysis, high throughput workflows, and spatial metabolomics, more data can be produced and studied using machine learning algorithms, in conjunction with dynamic models, to generate qualitative and quantitative predictions to advance metabolic engineering efforts.
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Suh MC, Uk Kim H, Nakamura Y. Plant lipids: trends and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2715-2720. [PMID: 35560206 DOI: 10.1093/jxb/erac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Mi Chung Suh
- Department of Life Science, Sogang University, Seoul 04107, South Korea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, South Korea
| | - Yuki Nakamura
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Japan
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