Measurements of abundances of 15N and 13C as tools in retrospective studies of N balances and water stress in forests: A discussion of preliminary results

Preliminary attempts to make retrospective studies of N balances and water stress in forest fertilization experiments by analyzing changes in the abundances of ¹⁵N and ¹³C, respectively, are discussed. Most evidence is from the Swedish Forest Optimum Nutrition Experiments, which have been running for two decades. Annual additions of N have been given either alone or in combination with other elements, notably P and K, every third year. Processes leading to loss of N, e.g. volatilization of ammonia, nitrification followed by leaching or denitrification, and denitrification alone, discriminate against the heavy isotope ¹⁵N. A correlation was found between fractional losses of added N and the change in ¹⁵N () during 19 years in current needles in a Scots pine forest, irrespective of source of N. Isotope effects were larger on urea than on ammonium nitrate plots (2 as compared to 9 ¹⁵N ()) because of ammonia volatilization and higher rates of nitrification. They developed gradually over time, which opens possibilities to analyse the development of N saturation. However, the analysis may be confounded by shifts in ¹⁵N abundance of fertilizer N. In another trial, N isotope effects could be seen in both plants and soils 10 years after the last fertilization; they were smaller in soils because of a large pretreatment memory effect, but we expect them to persist there for decades.The enzyme RuBisCo discriminates strongly against the heavy isotope ¹³C during photosynthesis, but this effect becomes less expressed as stomata close because of water stress. The supply of N may also affect the ¹³C () via effects on rates of photosynthesis, and the source of N may have an influence directly via non-RubisCo carboxylations, and indirectly via effects on water use efficiency. In a trial with Norway spruce, the effect of N fertilization on the ¹³C () of current needles was strongly correlated with production and weakly so with foliar biomass a dry year, but not a wet year. This suggested that these variations are primarily related to induced differences in the balance between supply and demand for water. Hence, studies of {au13}C abundance can disentangle the role of water as such from its effects on mineralization of N and flow of N.     

Variation in the export of 13C and 15N from soybean leaf: the effects of nitrogen application and sink removal

Translocation of carbon and nitrogen within a single source-sink unit, comprising a trifoliated leaf, the axillary pod and the subtending internode, and from this unit to the rest of the plant was examined in soybean (Glycine max L. cv. Akishirome) plant by feeding ¹³CO₂ and ¹⁵NO₃. The plants were grown at two levels of nitrogen in the basal medium, i.e. low-N (2 g N m^–2) and high-N (35 g N m^–2) and a treatment of depodding was imposed by removing all the pods from the plant, except the pod of the source sink unit, 13 days after flowering. The plants at high-N accumulated more biomass in its organs compared to low-N and pod removal increased the weight of the vegetative organs. When the terminal leaflet of the source-sink unit was fed with ¹³CO₂, almost all of the radioactive materials were retained inside the source-sink unit and translocation to rest of the plants was insignificant under any of the treatments imposed. Out of the¹³C exported by the terminal leaflet, less than half went into the axillary pod, as the lateral leaflets claimed equal share and very little material was deposited in the petiole. Pod removal decreased ¹³C export at high-N , but not at low-N. Similar to ¹³C, the source-sink unit retained all the ¹⁵N fed to the terminal leaflet at high-N. At low-N, the major part of ¹⁵N partitioning occurred in favour of the rest of the plant outside the source-sink unit, but removal of the competitve sinks from the rest of the plants nullified any partitioning outside the unit. Unlike the situation in ¹³C, no partitioning of ¹⁵N occurred in favour of the lateral leaflets from the terminal leaflet inside the unit. It is concluded that sink demand influences partitioning of both C and N and the translocation of carbon is different from that of nitrogen within a source-sink unit. The translocation of the N is more adjustive to a demand from other sink units compared to the C.     

Specific 15N, NH correlations for residues in15 N, 13C and fractionally deuterated proteins that immediately follow methyl-containing amino acids

A triple-resonance pulse scheme is described which records¹⁵N, NH correlations of residues that immediately follow amethyl-containing amino acid. The experiment makes use of a¹⁵N, ¹³C and fractionally deuterated proteinsample and selects for CH₂D methyl types. The experiment isthus useful in the early stages of the sequential assignment process as wellas for the confirmation of backbone ¹⁵N, NH chemical shiftassignments at later stages of data analysis. A simple modification of thesequence also allows the measurement of methyl side-chain dynamics. This isparticularly useful for studying side-chain dynamic properties in partiallyunfolded and unfolded proteins where the resolution of aliphatic carbon andproton chemical shifts is limited compared to that of amide nitrogens.     

Simultaneous CT-13C and VT-15N chemical shift labelling: Application to 3D NOESY-CH3NH and 3D 13C,15N HSQC-NOESY-CH3NH

Based on the HSQC scheme, we have designed a 2D heterocorrelated experiment which combines constant time (CT) ¹³C and variable time (VT) ¹⁵N chemical shift labelling. Although applicable to all carbons, this mode is particularly suitable for simultaneous recording of methyl-carbon and nitrogen chemical shifts at high digital resolution. The methyl carbon magnetisation is in the transverse plane during the whole CT period (1/J_CC=28.6 ms). The magnetisation originating from NH protons is initially stored in the 2H_zN_z state, then prior to the VT chemical shift labelling period is converted into 2H_zN_y coherence. The VT -¹⁵N mode eliminates the effect of ¹ J _N,CO and ^1,2 J _N,CA coupling constants without the need for band-selective carbon pulses. An optional editing procedure is incorporated which eliminates signals from CH₂ groups, thus removing any potential overlap with the CH₃ signals. The CT-¹³CH₃,VT-¹⁵N HSQC building block is used to construct two 3D experiments: 3D NOESY-CH₃NH and 3D ¹³C,¹⁵N HSQC-NOESY-CH₃NH. Combined use of these experiments yields proton and heteronuclear chemical shifts for moieties experiencing NOEs with CH₃ and NH protons. These NOE interactions are resolved as a consequence of the high digital resolution in the carbon and nitrogen chemical shifts of CH₃ and NH groups, respectively. The techniques are illustrated using a double labelled sample of the CH domain from calponin.     

Conformationally Restricted 2-Substituted Wyosine Derivatives. 1H, 13C,and 15N NMR Study

Abstract

It was found by ¹H, ¹³C and ¹⁵N NMR study that substitution of 4,9-dihydro-4, 6-dimethyl-9-oxo-3-(2′,3′,5′-tri-O-acetyl-β-D-ribofuranosyl) imidazo [1,2-a]purine (wyosine triacetate, 1) at C2 position with electronegative groups CH₃O and C₆H₅CH₂O results in a noticeable electron distribution disturbance in the “left-hand” imidazole ring and a significant increase in the North conformer population of the sugar moiety.     

A combined HNCA/HNCO experiment for 15N labeled proteins with 13C at natural abundance

A triple resonance NMR experiment is presented for the simultaneous recording of HNCA and HNCO data sets on ¹⁵N, natural abundance ¹³C samples. The experiment exploits the fact that transfers of magnetization from ¹⁵N to ¹³CO and from ¹⁵N to ¹³C (and back) proceed independently for samples that are not enriched in ¹³C. A factor of 2 in measuring time is gained by recording the two data sets simultaneously with no compromise in spectral quality. An application to a 0.5 mM ¹⁵N labeled sample of protein-L is presented with all expected correlations observed in spectra recorded with a cryogenic probe at 500 MHz.     

Time-saving methods for heteronuclear multidimensional NMR of (13C, 15N) doubly labeled proteins

Summary Heteronuclear 2D (¹³C, ¹H) and (¹⁵N, ¹H) correlation spectra of (¹³C, ¹⁵N) fully enriched proteins can be acquired simultaneously with virtually no sensitivity loss or increase in artefact levels. Three pulse sequences are described, for 2D time-shared or TS-HSQC, 2D TS-HMQC and 2D TS-HSMQC spectra, respectively. Independent spectral widths can be sampled for both heteronuclei. The sequences can be greatly improved by combining them with field-gradient methods. By applying the sequences to 3D and 4D NMR spectroscopy, considerable time savings can be obtained. The method is demonstrated for the 18 kDa HU protein.Abbreviations HMQC heteronuclear multiple-quantum coherence spectroscopy - HSQC heteronuclear single-quantum coherence spectroscopy - HSMQC heteronuclear single- and multiple-quantum coherence spectroscopy - NOESY nuclear Overhauser enhancement spectroscopy     

1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects

Summary In this study we report on the ¹H, ¹³C and ¹⁵N NMR chemical shifts for the random coil state and nearest-neighbor sequence effects measured from the protected linear hexapeptide Gly-Gly-X-Y-Gly-Gly (where X and Y are any of the 20 common amino acids). We present data for a set of 40 peptides (of the possible 400) including Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly, measured under identical aqueous conditions. Because all spectra were collected under identical experimental conditions, the data from the Gly-Gly-X-Ala-Gly-Gly series provide a complete and internally consistent set of ¹H, ¹³C and ¹⁵N random coil chemical shifts for all 20 common amino acids. In addition, studies were also conducted into nearest-neighbor effects on the random coil shift arising from a variety of X and Y positional substitutions. Comparisons between the chemical shift measurements obtained from Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly reveal significant systematic shift differences arising from the presence of proline in the peptide sequence. Similarly, measurements of the chemical shift changes occurring for both alanine and proline (i.e., the residues in the Y position) are found to depend strougly on the type of amino acid substituted into the X position. These data lend support to the hypothesis that sequence effects play a significant role in determining peptide and protein chemical shifts.     

1H, 15N, 13C and 13CO assignments and secondary structure determination of basic fibroblast growth factor using 3D heteronuclear NMR spectroscopy

Summary The assignments of the ¹H, ¹⁵N, ¹³CO and ¹³C resonances of recombinant human basic fibroblast growth factor (FGF-2), a protein comprising 154 residues and with a molecular mass of 17.2 kDa, is presented based on a series of three-dimensional triple-resonance heteronuclear NMR experiments. These studies employ uniformly labeled ¹⁵N- and ¹⁵N-/¹³C-labeled FGF-2 with an isotope incorporation >95% for the protein expressed in E. coli. The sequence-specific backbone assignments were based primarily on the interresidue correlation of C, C and H to the backbone amide ¹H and ¹⁵N of the next residue in the CBCA(CO)NH and HBHA(CO)NH experiments and the intraresidue correlation of C, C and H to the backbone amide ¹H and ¹⁵N in the CBCANH and HNHA experiments. In addition, C and C chemical shift assignments were used to determine amino acid types. Sequential assignments were verified from carbonyl correlations observed in the HNCO and HCACO experiments and C correlations from the carbonyl correlations observed in the HNCO and HCACO experiments and C correlations from the HNCA experiment. Aliphatic side-chain spin systems were assigned primarily from H(CCO)NH and C(CO)NH experiments that correlate all the aliphatic ¹H and ¹³C resonances of a given residue with the amide resonance of the next residue. Additional side-chain assignments were made from HCCH-COSY and HCCH-TOCSY experiments. The secondary structure of FGF-2 is based on NOE data involving the NH, H and H protons as well as ³J_H n _H coupling constants, amide exchange and ¹³C and ¹³C secondary chemical shifts. It is shown that FGF-2 consists of 11 well-defined antiparallel -sheets (residues 30–34, 39–44, 48–53, 62–67, 71–76, 81–85, 91–94, 103–108, 113–118, 123–125 and 148–152) and a helix-like structure (residues 131–136), which are connected primarily by tight turns. This structure differs from the refined X-ray crystal structures of FGF-2, where residues 131–136 were defined as -strand XI. The discovery of the helix-like region in the primary heparin-binding site (residues 128–138) instead of the -strand conformation described in the X-ray structures may have important implications in understanding the nature of heparin-FGF-2 interactions. In addition, two distinct conformations exist in solution for the N-terminal residues 9–28. This is consistent with the X-ray structures of FGF-2, where the first 17–19 residues were ill defined.     

Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins

Two triple resonance experiments, HNN and HN(C)N, are presented which correlate H^N and ¹⁵N resonances sequentially along the polypeptide chain of a doubly (¹³C, ¹⁵N) labeled protein. These incorporate several improvements over the previously published sequences for a similar purpose and have several novel features. The spectral characteristics enable direct identification of certain triplets of residues, which provide many starting points for the sequential assignment procedure. The experiments are sensitive and their utility has been demonstrated with a 22 kDa protein under unfolding conditions where most of the standard triple resonance experiments such as HNCA, CBCANH etc. have limited success because of poor amide, C and C chemical shift dispersions.     

A bioassay of the availability of residual 15N fertilizer eight years after application to a forest soil in interior British Columbia

Although a high proportion of fertilizer N may be immobilized in organic forms in the soil, no studies have examined the long-term availability of residual fertilizer ¹⁵N in forestry situations. We investigated this by growing lodgepole pine (Pinus contorta) seedlings in surface (0–10 cm) soil sample eight years after application of ¹⁵N-urea, ¹⁵NH₄NO₃ and NH₄ ¹⁵NO₃ to lodgepole pine in interior British Columbia. After nine months of growth in the greenhouse, seedlings took up an average of 8.5% of the ¹⁵N and 4.6% of the native N per pot. Most of the mineral N in the pots without seedlings was in the form of nitrate, while pots with seedlings had very low levels of mineral N. In contrast to the greenhouse study, there was no significantuptake of ¹⁵N by trees in the field study after the first growing season, although half of the soil organic ¹⁵N was lost between one and eight years after fertilization. This indicates the need to understand the mechanisms which limit the uptake of mineral N by trees in the field, and the possible mismatch of tree demand and mineral N availability.     

Complete 1H, 13C and 15N NMR assignments and secondary structure of the 269-residue serine protease PB92 from Bacillus alcalophilus

Summary The ¹H, ¹³C and ¹⁵N NMR resonances of serine protease PB92 have been assigned using 3D tripleresonance NMR techniques. With a molecular weight of 27 kDa (269 residues) this protein is one of the largest monomeric proteins assigned so far. The side-chain assignments were based mainly on 3D H(C)CH and 3D (H)CCH COSY and TOCSY experiments. The set of assignments encompasses all backbone carbonyl and CH_n carbons, all amide (NH and NH₂) nitrogens and 99.2% of the amide and CH_n protons. The secondary structure and general topology appear to be identical to those found in the crystal structure of serine protease PB92 [Van der Laan et al. (1992) Protein Eng., 5, 405–411], as judged by chemical shift deviations from random coil values, NH exchange data and analysis of NOEs between backbone NH groups.Abbreviations 2D/3D/4D two-/three-/four-dimensional - HSQC heteronuclear single-quantum coherence - HMQC heteronuclear multiple-quantum coherence - COSY correlation spectroscopy - TOCSY total correlation spectroscopy - NOE nuclear Overhauser enhancement (connectivity) - NOESY 2D NOE spectroscopy Experiment nomenclature (H(C)CH, etc.) follows the conventions used elsewhere [e.g. Ikura et al. (1990) Biochemistry, 29, 4659–4667].     

Characterizing the feeding habits of the testate amoebae Hyalosphenia papilio and Nebela tincta along a narrow "fen-bog" gradient using digestive vacuole content and 13C and 15N isotopic analyses

Population dynamics and feeding habits of the testate amoebae Nebela tincta and Hyalosphenia papilio were studied along a short "fen" to "bog" gradient in a Sphagnum-dominated mire (Jura, France). Samples were collected in living "top segments" (0-3 cm) and early declining "bottom segments" (3-6 cm) of Sphagnum fallax peat. Observations of digestive vacuole content and stable isotope analyses ((13)C and (15)N) were used to establish the feeding behavior of both testate amoeba species. Owing to their vertical distribution, the feeding habit of H. papilio was described from top segments, and that of N. tincta from bottom segments. Among identified food sources, those most frequently ingested by N. tincta were spores and mycelia of fungi (55%), microalgae (25%) and cyanobacteria (8.5%). For H. papilio, the most frequently ingested prey were ciliates (55%) and microalgae (35%). Nonmetric Multidimensional Scaling analysis clearly demonstrated that the two species did not have the same feeding habit along the "fen-bog" gradient, and furthermore that a significant spatial split exists in the feeding behavior of H. papilio. Additionally, isotope analyses suggested that H. papilio and N. tincta did not have the same trophic position in the microbial food web, probably resulting from their different feeding strategies.     

Production,standing biomass and natural abundance of <Superscript>15</Superscript>N and <Superscript>13</Superscript>C in ectomycorrhizal mycelia collected at different soil depths in two forest types

Nutrient uptake by forest trees is dependent on ectomycorrhizal (EM) mycelia that grow out into the soil from the mycorrhizal root tips. We estimated the production of EM mycelia in root free samples of pure spruce and mixed spruce-oak stands in southern Sweden as mycelia grown into sand-filled mesh bags placed at three different soil depths (0–10, 10–20 and 20–30 cm). The mesh bags were collected after 12 months and we found that 590±70 kg ha^–1 year^–1 of pure mycelia was produced in spruce stands and 420±160 kg ha^–1 year^–1 in mixed stands. The production of EM mycelia in the mesh bags decreased with soil depth in both stand types but tended to be more concentrated in the top soil in the mixed stands compared to the spruce stands. The fungal biomass was also determined in soil samples taken from different depths by using phospholipid fatty acids as markers for fungal biomass. Subsamples were incubated at 20°C for 5 months and the amount of fungal biomass that degraded during the incubation period was used as an estimate of EM fungal biomass. The EM biomass in the soil profile decreased with soil depth and did not differ significantly between the two stand types. The total EM biomass in the pure spruce stands was estimated to be 4.8±0.9×10³ kg ha^–1 and in the mixed stands 5.8±1.1×10³ kg ha^–1 down to 70 cm depth. The biomass and production estimates of EM mycelia suggest a very long turnover time or that necromass has been included in the biomass estimates. The amount of N present in EM mycelia was estimated to be 121 kg N ha^–1 in spruce stands and 187 kg N ha^–1 in mixed stands. The ¹³C value for mycelia in mesh bags was not influenced by soil depth, indicating that the fungi obtained all their carbon from the tree roots. The ¹³C values in mycelia collected from mixed stands were intermediate to values from pure spruce and pure oak stands suggesting that the EM mycelia received carbon from both spruce and oak trees in the mixed stands. The ¹⁵N value for the EM mycelia and the surrounding soil increased with soil depth suggesting that they obtained their entire N from the surrounding soil.     

The fate of labelled15N urea and ammonium nitrate applied to a winter wheat crop

Labelled urea or ammonium nitrate was applied to winter wheat growing on a loamy soil in Northern France. Two applications of fertilizer were given: 50 kg N ha^–1 at tillering (early March) and 110 kg N ha^–1 at the beginning of stem elongation (mid-April). The kinetics of urea hydrolysis, nitrification of ammonium and the disappearance of inorganic nitrogen were followed at frequent intervals. Inorganic nitrogen soon disappeared, mainly immobilized by soil microflora and absorbed by the crop. Net immobilization of fertilizer N occured at a very similar rate for urea and ammonium nitrate. Maximum immobilization (16 kg N ha¹) was found at harvest for the first dressing and at anthesis for the second dressing (23 kg N ha¹). During the nitrification period, the labelled ammonium pool was immobilized two to three times faster than the labelled nitrate pool. No significant net¹⁵N remineralization was found during the growth cycle.The actual denitrification and volatilization losses were probably more important than indicated from calculations made by extrapolation of fluxes measured over short intervals. However microbial immobilization was the most important of the processes which compete with plant uptake for nitrogen.     

Efficient 13C/15N double labeling of the avirulence protein AVR4 in a methanol-utilizing strain (Mut+) of Pichia pastoris

Cost effective ¹³C/¹⁵N-isotope labeling of the avirulence protein AVR4 (10 kDa) of the fungal tomato pathogen Cladosporium fulvum was achieved with the methylotrophic yeast Pichia pastoris in a fermentor. The ¹³C/¹⁵N-labeled AVR4 protein accumulated to 30 mg/L within 48 h in an initial fermentation volume of only 300 mL, while prolonged optimized overexpressions yielded 126 mg/L. These protein yields were 24-fold higher in a fermentor than in flask cultures. In order to achieve these protein expression levels, we used the methanol-utilizing strain (Mut⁺) of Pichia pastoris which has a high growth rate while growing on methanol as the only carbon source. In contrast, the methanol-sensitive strain (Mut^S) could intrinsically yield comparable protein expression levels, but at the expense of additional carbon sources. Although both strains are generally used for heterologous protein expression, we show that the costs for ¹³C-isotope labeling can be substantially reduced using the Mut⁺ strain compared to the Mut^S strain, as no ¹³C₃-glycerol is required during the methanol-induction phase. Finally, nitrogen limitations were precluded for ¹⁵N-labeling by an optimal supply of 10 g/L (¹⁵NH₄)₂SO₄ every 24 h.