Utilization of 13C-13C Coupling in Structural and Biosynthetic Studies Double Labeling Method

A new method which utilizes ¹³C-¹³C coupling for structural and biosynthetic studies on acetate-derived metabolites is described. The ¹³C-NMR spectra of dihydrolatumcidins separately labeled with ¹³CH₃¹³C0₂Na and with a 1: 1 mixture of ¹³CH₃CO₂-Na and CH313C02-Na gave enough information to establish its structure.     

13C-labeled oligodeoxyribonucleotides: A solution study of a CCAAT-containing sequence at the nuclear factor I recognition site of human adenovirus

The solution behavior of the single-stranded CCAAT-containing octamer 1 , d(AGCCAATA), that comprises part of the nuclear factor I (NF-I) recognition site at the origin of replication of human adenovirus has been studied by nmr spectroscopy at 500 and 600 MHz. Proton resonance assignments for 1 were aided by selective ¹³C enrichment at C1′ of A₁ or A₅. High-resolution ¹³C-¹H heteronuclear multiple-bond coherence spectra of the ¹³C-labeled oligomers permitted the selective detection of furanosyl ring protons within each labeled residue due to short- and long-range ¹³C-¹H couplings to the enriched C1′. The resulting assignments provided firm starting points in the interpretation of double quantum filtered correlated spectra, yielding information supplemented by total correlated spectroscopy (TOCSY) and rotating frame nuclear Overhauser effect spectroscopic data to completely assign the ¹H-nmr spectrum of 1 and extract ³J_HH values for furanose con-formational analysis. Several ¹³C-¹H spin-coupling constants within the ¹³C-enriched A₁ or A₅ residues were measured from cross-peak shifts in TOCSY spectra, and their signs determined by inspection of the relative orientations of these shifts. ¹H-²-H and ¹³C-¹H spin-couplings both indicate a preference (> 75%) for south (C2′-endo) conformations by the furanosyl rings of 1 . © 1994 John Wiley & Sons, Inc.     

REGIOSELECTIVE SYNTHESIS OF 1,3,5-13C3 AND 2,4-13C2-LABELED 2-DEOXYRIBONOLACTONES

The synthesis of 1,3,5-¹³C₃- and 2,4-¹³C₂-labeled 5-O-bromobenzyl-2-deoxyribonolactones 2, precursors to ¹³C-enriched nucleoside phosphoramidites for solid-phase synthesis of DNA oligonucletides, is described. An equimolar combination of these two multiply labeled lactones affords a “population-labeled” mixture of isotopomers which exhibits an approximately 50-fold increase in the sensitivity of ¹³C-NMR compared to natural abundance measurements. The ¹³C-¹³C 2-bond and 4-bond coupling constants are reported for the lactones; all are < 2 Hz, confirming that this labeling scheme should be especially useful for NMR-relaxation measurements.     

Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins

Analysis of 2D [¹³C,¹H]-HSQC spectra of biosynthetic fractionally ¹³C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of Phe and Tyr aromatic signals. This is the case, in part, because the fractional ¹³C labeling yields aromatic rings in which some of the ¹³C-¹³C J-couplings, present in uniformly labeled samples, are absent. Also, the number of homonuclear J-coupling partners differs for the -, - and -carbons. This enabled us to vary their signal intensities in distinctly different ways by appropriately setting the ¹³C constant-time period in 2D [¹³C,¹H]-HSQC spectra. We illustrate the application of this approach to an 18 kDa protein, c-VIAF, a modulator of apoptosis. In addition, we show that cancellation of the aromatic ¹³C CSA and ¹³C-¹H dipolar interactions can be fruitfully utilized in the case of the fractionally labeled sample to obtain high resolution ¹³C constant-time spectra with good sensitivity.     

Sucrose unloading in the hypocotyl of the Ricinus communis L. seedling measured by 13C-nuclear magnetic resonance spectroscopy in vivo

The unloading of sucrose in the apical part of the hypocotyl of Ricinus communis L. seedlings was measured by ¹³C-nuclear magnetic resonance (NMR) spectroscopy. The cotyledons of the seedling were immersed in 5 mM Mes buffer containing 100 mM ¹³C-labeled sucrose. At intervals of 70–90 min, ¹³C-NMR spectra with broadband decoupling and nuclear Overhauser enhancement were acquired in vivo. The spectra showed growing ¹³C-resonances of the labeled positions in the sucrose molecule reaching steady-state labeling within 7–8 h. The specific ¹³C labeling of sucrose in the G₁-position changed from 0.38 in the supplied sucrose solution to 0.16 in the sucrose extracted from the hypocotyl piece at the end of the experiment (13 h). Labeling of starch (and other insolubles) in the hypocotyl piece was ca. 0.10. It is proposed that the decreased specific labeling of unloaded sucrose is mostly due to the separate local pools of sucrose in the cortex and pith parenchyma, respectively, and less to continuous starch degradation and conversion to sucrose. The report gives an example of the application of ¹³C-NMR spectroscopy in assimilate allocation studies. Received: 10 October 1998 / Accepted: 31 December 1998     

Solid-State NMR Evidence for β-Hairpin Structure within MAX8 Designer Peptide Nanofibers

MAX8, a designer peptide known to undergo self-assembly following changes in temperature, pH, and ionic strength, has demonstrated usefulness for tissue engineering and drug delivery. It is hypothesized that the self-assembled MAX8 nanofiber structure consists of closed β-hairpins aligned into antiparallel β-sheets. Here, we report evidence from solid-state NMR spectroscopy that supports the presence of the hypothesized β-hairpin conformation within the nanofiber structure. Specifically, our ¹³C-¹³C two-dimensional exchange data indicate spatial proximity between V3 and K17, and ¹³C-¹³C dipolar coupling measurements reveal proximity between the V3 and V18 backbone carbonyls. Moreover, isotopic dilution of labeled MAX8 nanofibers did not result in a loss of the ¹³C-¹³C dipolar couplings, showing that these couplings are primarily intramolecular. NMR spectra also indicate the existence of a minor conformation, which is discussed in terms of previously hypothesized nanofiber physical cross-linking and possible nanofiber polymorphism.     

Soil carbon and nitrogen across a chronosequence of woody plant expansion in North Dakota

In annual crops, the partitioning of photosynthates to support root growth, respiration and rhizodeposition should be greater during early development than in later reproductive stages due to source/sink relationships in the plant. Therefore, seasonal fluctuations in carbon dioxide (CO₂) and nitrous oxide (N₂O) production from roots and root-associated soil may be related to resource partitioning by the crop. Greenhouse studies used ¹³C and ¹⁵N stable isotopes to evaluate the carbon (C) partitioning and nitrogen (N) uptake by corn and soybean. We also measured the CO₂ and N₂O production from planted pots as affected by crop phenology and N fertilization. Specific root-derived respiration was related to the ¹³C allocated to roots and was greatest during early vegetative growth. Root-derived respiration and rhizodeposition were greater for corn than soybean. The ¹⁵N uptake by corn increased between vegetative growth, tasseling and milk stages, but the ¹⁵N content in soybean was not affected by phenology. A peak in N₂O production was observed with corn at the milk stage, suggesting that the corn rhizosphere supported microbial communities that produced N₂O. Most of the ¹⁵N-NO₃ applied to soybean was not taken up by the plant and negative N₂O production during vegetative growth and floral initiation stages suggests that soybean roots supported the reduction of N₂O to dinitrogen (N₂). We conclude that crop phenology and soil N availability exert important controls on rhizosphere processes, leading to temporal variation in CO₂ and N₂O production.     

Responses to dietary starch or sucrose on protein and glucose kinetics in goats fed a high-concentrate diet

Abstract

Responses of whole body protein synthesis (WBPS) and glucose irreversible loss rate (ILR) were compared between dietary starch and sucrose in four male goats. Diets were fed at 1.2 times maintenance requirements of ME and CP with 30% of the ME as starch, starch plus sucrose or sucrose, twice daily. The diets consisted of 33, 32, 11 and 24% of alfalfa hay, corn, soybean meal and the carbohydrates, respectively. The WBPS and glucose ILR during 5 – 7 h after feeding were determined by an isotope dilution method of [²H₅]phenylalanine, [²H₂]tyrosine, [²H₄]tyrosine and [¹³C₆]glucose. Sucrose elevated ammonia nitrogen and lowered acetate concentrations in the rumen, but did not differ from starch in nitrogen retention. Glucose ILR and WBPS were similar between the carbohydrates. It was concluded that dietary sucrose would have effects similar to starch on WBPS and glucose kinetics in the absorptive state in goats fed a high-concentrate diet.     

Multiplet component separation for measurement of methyl 13C-1H dipolar couplings in weakly aligned proteins

A simple spectral editing procedure is described that generates separate subspectra for the methyl ¹³C-¹H₃ multiplet components of ¹H-¹³C HSQC spectra. The editing procedure relies on co-addition of in-phase and antiphase spectra and yields ¹H-coupled constant-time HSQC subspectra for the methyl region that have the simplicity of the regular decoupled CT-HSQC spectrum. Resulting spectra permit rapid and reliable measurement of ¹H-¹³C J and dipolar couplings. The editing procedure is illustrated for a Ca²⁺-calmodulin sample in isotropic and liquid crystalline phases.     

Carbon-13 Nuclear Magnetic Resonance Analysis of Metabolism in Soybean Labeled by CO(2)

Fourier transform ¹³C nuclear magnetic resonance spectra have been obtained of intact, fresh soybean ovules (Glycine max L. cv. Dare) harvested from pods subtended by a trifoliolate exposed to ¹³CO₂ 1 to 3 days earlier. The high resolution spectra are interpreted in terms of the labeled sugars and lipids in the ovule. Comparison of the spectra taken over the 3-day period permits qualitative estimates of sugar metabolism and rates of lipid synthesis. The spectra also contain information about the distribution of labels within the lipid chains. This information leads to a method of estimating the extent to which glucose degradation in the synthesizing soybean ovule is involved in the reactions of the phosphogluconate pathway.     

Source pool kinetics for C-photosynthate translocation in morning glory and soybean

The kinetic behavior of translocation profiles indicates that their shape is determined largely by the rate at which tracer enters the sieve tubes in the source leaf. Confirmation of this relationship was sought by investigating the kinetics of ¹⁴C in the immediate source pool for translocated sucrose in soybean (Glycine max L., cv. Bragg) and morning glory (Ipomea nil Roth, cv. Scarlet O'Hara) leaves. Quantitative microautoradiography was used to follow the water-soluble ¹⁴C contents of the companion cells in minor veins after pulse-labeling with ¹⁴CO₂. In both morning glory and soybean, the observed kinetics in the companion cells matched reasonably well those expected from the shape of the translocation profiles.

Marked compartmentation of sucrose was evident in soybean leaves in that the specific radioactivity of total leaf sucrose was greatest immediately after labeling and quickly declined, whereas labeling in the companion cells was low at first and did not reach a maximum for about 35 minutes. In morning glory leaves, the kinetics of sucrose specific radioactivity and of companion cell-labeling more closely paralleled one another.

     

<Superscript>13</Superscript>C-<Superscript>13</Superscript>C NOESY: A constructive use of <Superscript>13</Superscript>C-<Superscript>13</Superscript>C spin-diffusion

¹³C-¹³C NOESY experiments were performed under long mixing time conditions on reduced human superoxide dismutase (32 kDa, ¹⁵N, ^13C and 70% ²H labeled). ¹³C-¹³C couplings were successfully eliminated through post-processing of in-phase-anti-phase (IPAP) data. It appears that at mixing time _m of 3.0 s the spin diffusion mechanism allows the detection of 96% of the two-bond correlations involving C and C. The interpretation was confirmed by simulations. This approach broadens the range of applicability of ¹³C-¹³C NOESY spectroscopy.     

Effects and Absorption of Sethoxydim in Cell Cycle Progression of Corn (Zea mays) and Pea (Pisum sativum)

The mechanisms of selective herbicidal action of sethoxydim were investigated by using cultured root tips of corn (Zea mays L. cv Goldencrossbantam) and pea (Pisum sativum L. cv Alaska). Meristematic cells in the cultured roots were arrested in G₁ and G₂ of the cell division cycle by sucrose starvation and resumed growth and cell division (proliferation) when sucrose was provided. Corn root growth after sucrose addition was inhibited by sethoxydim at concentrations of 0.01 micromolar and greater when roots were treated in the presence of sucrose but was not inhibited at 10 micromolar sethoxydim when they were treated during sucrose starvation. Greater absorption of [¹⁴C]sethoxydim into the meristematic region of corn roots was observed when cells were in proliferative condition but not when they were arrested by sucrose starvation, whereas no greater absorption of the herbicide into pea meristems was observed in either growth condition. In the cell cycle study, greater absorption of [¹⁴C]sethoxydim into the corn root meristem was observed at a certain limited time before S (DNA synthesis) stage. The physiological effects and the greater absorption of sethoxydim clearly depended on cell cycle progression of corn root meristem, whereas fatty acid synthesis, as well as its inhibition by sethoxydim, was not associated with either cell cycle progression or greater absorption of the herbicide.     

Intracellular concentrations and metabolism of carbon compounds in tobacco callus cultures: effects of light and auxin

Callus cultures derived from pith tissue of Nicotiana tabacum were grown on two media either under continuous illumination or in complete darkness. The first medium limited greening ability of callus grown in the light (3 milligrams per liter naphthalene acetic acid, 0.3 milligram per liter 2-isopentenylaminopurine, Murashige and Skoog salts, and 2% sucrose). The second medium encouraged chlorophyll synthesis (greening) though not shoot formation (0.3 milligram per liter naphthalene acetic acid; 0.3 milligrans per liter 2-isopentylaminopurine). To measure intracellular concentrations, calli were grown for 15 days on these standard media containing [U-¹⁴C]sucrose. The dry weight proportions of the calli (as a fraction of fresh weight) and many metabolite concentrations nearly doubled in light-grown cells compared to dark-grown cells and increased 30 to 40% on low-auxin media relative to high-auxin media. Glutamine concentrations (from 4 to 26 millimolar) were very high, probably due to the NH₃ content of the media. Proline concentrations were 20-fold higher in calli grown on low-auxin media in the light (green cells), possibly a stress response to high osmotic potentials in these cells. To analyze sucrose metabolism, callus cells were allowed to take up 0.2% (weight per volume) [U-¹⁴C]sucrose for up to 90 minutes. In callus tissues and in pith sections from stems of tobacco plants, sucrose was primarily metabolized through invertase activity, producing equal amounts of labeled glucose and fructose. Respiration of ¹⁴CO₂ followed the labeling patterns of tricarboxylic acid cycle intermediates. Photorespiration activity was low.     

The Assignment of the 13C-NMR Spectrum of Lysocellin and Its Biosynthesis

The complete ¹⁸C-NMR assignment of lysocellin sodium salt has been obtained based on the ¹³C-¹³C double labeling method and comparison with its retroaldol degradation product as well as a structurally related polyether antibiotic, lasalocid A.

In parallel, the biosynthesis of lysocellin was investigated by feeding ¹³C-labeled precursors followed by analyzing the resulting labeling patterns of the ¹³C-NMR spectra; a pathway to the antibiotic molecule is suggested which proceeds through condensation of two butyrate, eight propionate and one acetate units.

In addition, a conversion of butyrate to propionate during the metabolic process has been disclosed.     

The role of light in soybean seed filling metabolism

Soybean (Glycine max) yields high levels of both protein and oil, making it one of the most versatile and important crops in the world. Light has been implicated in the physiology of developing green seeds including soybeans but its roles are not quantitatively understood. We have determined the light levels reaching growing soybean embryos under field conditions and report detailed redox and energy balance analyses for them. Direct flux measurements and labeling patterns for multiple labeling experiments including [U‐¹³C₆]‐glucose, [U‐¹³C₅]‐glutamine, the combination of [U‐¹⁴C₁₂]‐sucrose + [U‐¹⁴C₆]‐glucose + [U‐¹⁴C₅]‐glutamine + [U‐¹⁴C₄]‐asparagine, or ¹⁴CO₂ labeling were performed at different light levels to give further insight into green embryo metabolism during seed filling and to develop and validate a flux map. Labeling patterns (protein amino acids, triacylglycerol fatty acids, starch, cell wall, protein glycan monomers, organic acids), uptake fluxes (glutamine, asparagine, sucrose, glucose), fluxes to biomass (protein amino acids, oil), and respiratory fluxes (CO₂, O₂) were established by a combination of gas chromatography‐mass spectrometry, ¹³C‐ and ¹H‐NMR, scintillation counting, HPLC, gas chromatography‐flame ionization detection, C:N and amino acid analyses, and infrared gas analysis, yielding over 750 measurements of metabolism. Our results show: (i) that developing soybeans receive low but significant light levels that influence growth and metabolism; (ii) a role for light in generating ATP but not net reductant during seed filling; (iii) that flux through Rubisco contributes to carbon conversion efficiency through generation of 3‐phosphoglycerate; and (iv) a larger contribution of amino acid carbon to fatty acid synthesis than in other oilseeds analyzed to date.     

Characterization of Acetate and Pyruvate Metabolism in Suspension Cultures of Zea mays by C NMR Spectroscopy

Carbon-13 nuclear magnetic resonance (NMR) spectroscopy has been applied to the direct observation of acetate and pyruvate metabolism in suspension cultures of Zea mays (var Black Mexican Sweet). Growth of the corn cells in the presence of 2 millimolar [2-¹³C]acetate resulted in a rapid uptake of the substrate from the medium and initial labeling (0-4 hours) of primarily the intracellular glutamate and malate pools. Further metabolism of these intermediates resulted in labeling of glutamine, aspartate, and alanine. With [1-¹³C]acetate as the substrate very little incorporation into intermediary metabolites was observed in the ¹³C NMR spectra due to loss of the label as ¹³CO₂. Uptake of [3-¹³C]pyruvate by the cells was considerably slower than with [2-¹³C]acetate; however, the labelling patterns were similar with the exception of increased [3-¹³C] alanine generation with pyruvate as the substrate. Growth of the cells for up to 96 hours with 2 millimolar [3-¹³C]pyruvate ultimately resulted in labeling of valine, leucine, isoleucine, threonine, and the polyamine putrescine.     

Production of Specifically Labeled Compounds by Methanobacterium espanolae Grown on H2-CO2 plus [13C]Acetate

Methanobacterium espanolae, an acidiphilic methanogen, required acetate for maximal growth on H₂-CO₂. In the presence of 5 to 15 mM acetate, at a growth pH of 5.5, the μ_max was 0.05 h^-1. M. espanolae consumed 12.3 mM acetate during 96 h of incubation at 35°C with shaking at 100 rpm. At initial acetate levels of 2.5 to 10.0 mM, the amount of biomass produced was dependent on the amount of acetate in the medium. ¹³C nuclear magnetic resonance spectra of protein hydrolysates obtained from cultures grown on [1-¹³C]- or [2-¹³C]acetate indicated that an incomplete tricarboxylic acid pathway, operating in the reductive direction, was functional in this methanogen. The amino acids were labeled with a very high degree of specificity and at greater than 90% enrichment levels. Less than 2% label randomization occurred between positions primarily labeled from either the carboxyl or methyl group of acetate, and very little label was transferred to positions primarily labeled from CO₂. The labeling pattern of carbohydrates was typical for glucogenesis from pyruvate. This methanogen, by virtue of the properties described above and its ability to incorporate all of the available acetate (10 mM or lower) from the growth medium, has advantages over other microorganisms for use in the production of specifically labeled compounds.     

Spectral editing of alanine,serine, and threonine in uniformly labeled proteins based on frequency-selective homonuclear recoupling in solid-state NMR

Spectral editing is crucial to simplify the crowded solid-state NMR spectra of proteins. New techniques are introduced to edit ¹³C-¹³C correlations of uniformly labeled proteins under moderate magic-angle spinning (MAS), based on our recent frequency-selective homonuclear recoupling sequences [Zhang et al., J. Phys. Chem. Lett. 2020, 11, 8077–8083]. The signals of alanine, serine, or threonine residues are selected out by selective ¹³Cα-¹³Cβ double-quantum filtering (DQF). The ¹³Cα-¹³Cβ correlations of alanine residues are selectively established with efficiency up to?~?1.8 times that by dipolar-assisted rotational resonance (DARR). The techniques are shown in 2D/3D NCCX experiments and applied to the uniformly ¹³C, ¹⁵N labeled Aquaporin Z (AqpZ) membrane protein, demonstrating their potential to simplify spectral analyses in biological solid-state NMR.

     

Resonance assignment of 13C/15N labeled solid proteins by two- and three-dimensional magic-angle-spinning NMR

The comprehensive structure determination of isotopically labeled proteins by solid-state NMR requires sequence-specific assignment of ¹³C and ¹⁵ N spectra. We describe several 2D and 3D MAS correlation techniques for resonance assignment and apply them, at 7.0 Tesla, to ¹³C and ¹⁵N labeled ubiquitin to examine the extent of resonance assignments in the solid state. Both interresidue and intraresidue assignments of the ¹³C and ¹⁵N resonances are addressed. The interresidue assignment was carried out by an N(CO)CA technique, which yields N_i-C_i–1 connectivities in protein backbones via two steps of dipolar-mediated coherence transfer. The intraresidue connectivities were obtained from a new 3D NCACB technique, which utilizes the well resolved C chemical shift to distinguish the different amino acids. Additional amino acid type assignment was provided by a ¹³C spin diffusion experiment, which exhibits ¹³C spin pairs as off-diagonal intensities in the 2D spectrum. To better resolve carbons with similar chemical shifts, we also performed a dipolar-mediated INADEQUATE experiment. By cross-referencing these spectra and exploiting the selective and extensive ¹³ C labeling approach, we assigned 25% of the amino acids in ubiquitin sequence-specifically and 47% of the residues to the amino acid types. The sensitivity and resolution of these experiments are evaluated, especially in the context of the selective and extensive ¹³C labeling approach.