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Bacher A, Chen F, Eisenreich W. Decoding Biosynthetic Pathways in Plants by Pulse-Chase Strategies Using (13)CO₂ as a Universal Tracer †. Metabolites 2016; 6:E21. [PMID: 27429012 PMCID: PMC5041120 DOI: 10.3390/metabo6030021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/03/2016] [Accepted: 07/04/2016] [Indexed: 01/14/2023] Open
Abstract
(13)CO₂ pulse-chase experiments monitored by high-resolution NMR spectroscopy and mass spectrometry can provide (13)C-isotopologue compositions in biosynthetic products. Experiments with a variety of plant species have documented that the isotopologue profiles generated with (13)CO₂ pulse-chase labeling are directly comparable to those that can be generated by the application of [U-(13)C₆]glucose to aseptically growing plants. However, the application of the (13)CO₂ labeling technology is not subject to the experimental limitations that one has to take into account for experiments with [U-(13)C₆]glucose and can be applied to plants growing under physiological conditions, even in the field. In practical terms, the results of biosynthetic studies with (13)CO₂ consist of the detection of pairs, triples and occasionally quadruples of (13)C atoms that have been jointly contributed to the target metabolite, at an abundance that is well above the stochastic occurrence of such multiples. Notably, the connectivities of jointly transferred (13)C multiples can have undergone modification by skeletal rearrangements that can be diagnosed from the isotopologue data. As shown by the examples presented in this review article, the approach turns out to be powerful in decoding the carbon topology of even complex biosynthetic pathways.
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Affiliation(s)
- Adelbert Bacher
- Lehrstuhl für Biochemie, Technische Universität München, 85748 Garching, Germany.
| | - Fan Chen
- Lehrstuhl für Biochemie, Technische Universität München, 85748 Garching, Germany.
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Technische Universität München, 85748 Garching, Germany.
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Rice DM, Romaniuk JAH, Cegelski L. Frequency-selective REDOR and spin-diffusion relays in uniformly labeled whole cells. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 72:132-9. [PMID: 26493462 PMCID: PMC4674448 DOI: 10.1016/j.ssnmr.2015.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 06/05/2023]
Abstract
Solid-state NMR is a powerful and non-perturbative method to measure and define chemical composition and architecture in bacterial cell walls, even in the context of whole cells. Most NMR studies on whole cells have used selectively labeled samples. Here, we introduce an NMR sequence relay using frequency-selective REDOR (fsREDOR) and spin diffusion elements to probe a unique amine contribution in uniformly (13)C- and (15)N-labeled Staphylococcus aureus whole cells that we attribute to the d-alanine of teichoic acid. In addition to the primary peptidoglycan structural scaffold, cell walls can contain significant amounts of teichoic acid that contribute to cell-wall function. When incorporated into teichoic acid, d-alanine is present as an ester, connected via its carbonyl to a ribitol carbon, and thus has a free amine. Teichoic acid d-Ala is removed during cell-wall isolations and can only be detected in the context of whole cells. The sequence presented here begins with fsREDOR and a chemical shift evolution period for 2D data acquisition, followed by DARR spin diffusion and then an additional fsREDOR period. fsREDOR elements were used for (13)C observation to avoid complications from (13)C-(13)C couplings due to uniform labeling and for (15)N dephasing to achieve selectivity in the nitrogens serving as dephasers. The results show that the selected amine nitrogen of interest is near to teichoic acid ribitol carbons and also the methyl group carbon associated with alanine. In addition, its carbonyl is not significantly dephased by amide nitrogens, consistent with the expected microenvironment around teichoic acid.
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Affiliation(s)
- David M Rice
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford, CA 94305, USA
| | - Joseph A H Romaniuk
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford, CA 94305, USA
| | - Lynette Cegelski
- Stanford University, Department of Chemistry, 380 Roth Way, Stanford, CA 94305, USA.
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Dirks RC, Singh M, Potter GS, Sobotka LG, Schaefer J. Glycine metabolism in leaves of Glycine max in 200 and 600-ppm CO2 environments. THE NEW PHYTOLOGIST 2013; 198:339-342. [PMID: 23437894 DOI: 10.1111/nph.12206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Rebecca C Dirks
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Gregory S Potter
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Lee G Sobotka
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
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Dirks RC, Singh M, Potter GS, Sobotka LG, Schaefer J. Carbon partitioning in soybean (Glycine max) leaves by combined (11) C and (13) C labeling. THE NEW PHYTOLOGIST 2012; 196:1109-1121. [PMID: 22998467 DOI: 10.1111/j.1469-8137.2012.04333.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/09/2012] [Indexed: 05/26/2023]
Abstract
We labeled soybean (Glycine max) leaves with 200 and 600 ppm (13) CO(2) spiked with (11) CO(2) and examined the effects of light intensity and water stress on metabolism by using a combination of direct positron imaging and solid-state (13) C nuclear magnetic resonance (NMR) of the same leaf. We first made 60-min movies of the transport of photosynthetically assimilated (11) C labels. The positron imaging identified zones or patches within which variations in metabolism could be probed later by NMR. At the end of each movie, the labeled leaf was frozen in liquid nitrogen to stop metabolism, the leaf was lyophilized, and solid-state NMR was used either on the whole leaf or on various leaf fragments. The NMR analysis determined total (13) C incorporation into sugars, starch, proteins, and protein precursors. The combination of (11) C and (13) C analytical techniques has led to three major conclusions regarding photosynthetically heterogeneous soybean leaves: transient starch deposition is not the temporary storage of sucrose excluded from a saturated sugar-transport system; peptide synthesis is reduced under high-light, high CO(2) conditions; and all glycine from the photorespiratory pathway is routed to proteins within photosynthetically active zones when the leaf is water stressed and under high-light and low CO(2) conditions.
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Affiliation(s)
- Rebecca C Dirks
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Gregory S Potter
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Lee G Sobotka
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St Louis, MO, 63130, USA
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Matsuoka S. [Structural study on small molecules in biological solid samples by using solid state NMR]. YAKUGAKU ZASSHI 2012; 132:969-78. [PMID: 23023412 DOI: 10.1248/yakushi.132.969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many small molecule drugs have molecular targets that are non-crystalline and insoluble biological matrices, such as proteins embedded in lipid membrane, cell membranes, and cell walls. To understand the action mechanisms, it is essential to determine the binding structure with atomic-level resolution. Although solution nuclear magnetic resonance (NMR) and X-ray crystallography have been used to determine molecular structures of cell membrane and membrane proteins, these methods are unable to reproduce the complexity of biological systems because either solubilization or crystallization of target molecules is requisite. For structural studies of insoluble non-crystalline biological samples, so-called "biological solids", high resolution distance measurements using solid-state NMR are indispensable techniques, of which rotational-echo double-resonance (REDOR) is one of the most widely used methods. In this paper, a brief introduction to REDOR NMR and its applications to structural studies on the antifungal amphotericin B-membrane phospholipid complex and a structural elucidation of photorespiration metabolites in plant cells without extraction or isolation is provided.
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Affiliation(s)
- Shigeru Matsuoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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Quantitative NMR for bioanalysis and metabolomics. Anal Bioanal Chem 2012; 404:1165-79. [PMID: 22766756 DOI: 10.1007/s00216-012-6188-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/04/2012] [Accepted: 06/08/2012] [Indexed: 01/16/2023]
Abstract
Over the last several decades, significant technical and experimental advances have made quantitative nuclear magnetic resonance (qNMR) a valuable analytical tool for quantitative measurements on a wide variety of samples. In particular, qNMR has emerged as an important method for metabolomics studies where it is used for interrogation of large sets of biological samples and the resulting spectra are treated with multivariate statistical analysis methods. In this review, recent developments in instrumentation and pulse sequences will be discussed as well as the practical considerations necessary for acquisition of quantitative NMR experiments with an emphasis on their use for bioanalysis. Recent examples of the application of qNMR for metabolomics/metabonomics studies, the characterization of biologicals such as heparin, antibodies, and vaccines, and the analysis of botanical natural products will be presented and the future directions of qNMR discussed.
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Gullion T, Yu TY, Singh M, Patti GJ, Potter GS, Schaefer J. Oxygen-17 appears only in protein in water-stressed soybean leaves labeled by (17)O2. J Am Chem Soc 2010; 132:10802-7. [PMID: 20681713 DOI: 10.1021/ja102264w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used a rotational-echo adiabatic-passage double-resonance (13)C{(17)O} solid-state NMR experiment to prove that the glycine produced in the oxygenase reaction of ribulose bisphosphate carboxylase-oxygenase is incorporated exclusively into protein (or protein precursors) of intact, water-stressed soybean leaves exposed to (13)CO(2) and (17)O(2). The water stress increased stomatal resistance and decreased gas exchange so that the Calvin cycle in the leaf chloroplasts was no more than 35% (13)C isotopically enriched. Labeled O(2) levels were sufficient, however, to increase the (17)O isotopic concentration of oxygenase products 20-fold over the natural-abundance level of 0.04%. The observed direct incorporation of glycine into protein shows that water stress suppresses photorespiration in soybean leaves.
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Affiliation(s)
- Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, USA
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