Measurement of 13Cα-13CO cross-relaxation rates in 15N-/13C-labelled proteins

Summary Internal motions play an important role in the biological function of proteins and NMR relaxation studies may characterize them over a wide range of frequencies. An experimental pulse scheme is proposed for the measurement of the ¹³CO-¹³C cross-relaxation rate. For sensitivity reasons, this measurement is performed in an indirect manner through several coherence transfer steps, which should thus be calibrated independently. Contributions of other relaxation pathways can be eliminated by the determination of the initial slope of the buildup curve. The cross-relaxation rates have been determined on a ¹⁵N-/¹³C-labelled 116-residue protein and the significant variations along the sequence have been interpreted as evidence of an increased amount of fast local motion.     

δ13C-variations of leaves in forests as an indication of reassimilated CO2 from the soil

Summary An attempt has been made to evaluate the contribution of soil respired CO₂ to the total assimilation of a forest tree, by heeding the ¹³C-concentrations of CO₂ from the free atmosphere and from mineralization processes within the soil respectively. An expression has been derived, according to which the assimilated fraction of CO₂ from the soil at a particular height of a tree is given by the ¹³C-value of the corresponding leaves, ¹³C of atmospheric CO₂, ¹³C of soil respired CO₂ and the physiological state of the leaves expressed as the ratio of total respiration over gross photosynthesis and internal over external CO₂-concentration. In the particular case investigated, a ¹³C-difference of 5 has been determined from bottom to top of a beech tree which results in a CO₂ contribution from the soil of about 22% for the lower forest strata, while the total contribution of soil respired CO₂ accounts for about 5% of the overall assimilation.     

Does the 13C of foliage‐respired CO2 and biochemical pools reflect the 13C of recently assimilated carbon?

Isotopic labelling experiments were conducted to assess relationships among ¹³C of recently assimilated carbon ( δC _A), foliage respiration ( δC _F), soluble carbohydrate ( δC _SC), leaf waxes ( δC _LW) and bulk organic matter ( δC _OM). Slash pine, sweetgum and maize were grown under ¹³C depleted CO₂ to label biomass and then placed under ambient conditions to monitor the loss of label. In pine and sweetgum, δC _F of labelled plants (∼−44 and −35‰, respectively) rapidly approached control values but remained depleted by ∼4–6‰ after 3–4 months. For these tree species, no or minimal label was lost from δC _SC, δC _LW and δC _OM during the observation periods. δC _F and δC _SC of labelled maize plants rapidly changed and were indistinguishable from controls after 1 month, while δC _LW and δC _OM more slowly approached control values and remained depleted by 2–6‰. Changes in δC _F in slash pine and sweetgum fit a two-pool exponential model, with the fast turnover metabolic pool (∼3–4 d half-life) constituting only 1–2% of the total. In maize, change in δC _F fits a single pool model with a half-life of 6.4 d. The ¹³C of foliage respiration and biochemical pools reflect temporally integrated values of δC _A, with change in isotopic composition dampened by the size of metabolic carbon reserves and turnover rates.     

TROSY-based HNCO pulse sequences for the measurement of 1HN-15N, 15N-13CO, 1HN-13CO, 13CO-13Cα and 1HN-13Cα dipolar couplings in 15N, 13C, 2H-labeled proteins

HNCO-based 3D pulse schemes are presented for measuring ¹HN-¹⁵N,¹⁵N-¹³CO, ¹HN-¹³CO,¹³CO-¹³C and ¹HN-¹³C dipolar couplings in ¹⁵N,¹³C,²-labeled proteins. The experiments are based on recently developed TROSY methodology for improving spectral resolution and sensitivity. Data sets recorded on a complex of Val, Leu, Ile (1 only) methyl protonated ¹⁵N,¹³C,²H-labeled maltose binding protein and -cyclodextrin as well as ¹⁵N,¹³C,²H-labeled human carbonic anhydrase II demonstrate that precise dipolar couplings can be obtained on proteins in the 30–40 kDa molecular weight range. These couplings will serve as powerful restraints for obtaining global folds of highly deuterated proteins.     

The 13C/12C isotopic signal of day-respired CO2 in variegated leaves of Pelargonium × hortorum

In leaves, although it is accepted that CO(2) evolved by dark respiration after illumination is naturally (13) C-enriched compared to organic matter or substrate sucrose, much uncertainty remains on whether day respiration produces (13) C-depleted or (13) C-enriched CO(2). Here, we applied equations described previously for mesocosm CO(2) exchange to investigate the carbon isotope composition of CO(2) respired by autotrophic and heterotrophic tissues of Pelargonium × hortorum leaves, taking advantage of leaf variegation. Day-respired CO(2) was slightly (13) C-depleted compared to organic matter both under 21% O(2) and 2% O(2). Furthermore, most, if not all CO(2) molecules evolved in the light came from carbon atoms that had been fixed previously before the experiments, in both variegated and green leaves. We conclude that the usual definition of day respiratory fractionation, that assumes carbon fixed by current net photosynthesis is the respiratory substrate, is not valid in Pelargonium leaves under our conditions. In variegated leaves, total organic matter was slightly (13) C-depleted in white areas and so were most primary metabolites. This small isotopic difference between white and green areas probably came from the small contribution of photosynthetic CO(2) refixation and the specific nitrogen metabolism in white leaf areas.     

Accurate measurements of the effects of deuteration at backbone amide positions on the chemical shifts of 15N, 13Cα, 13Cβ, 13CO and 1Hα nuclei in proteins

An approach towards accurate NMR measurements of deuterium isotope effects on the chemical shifts of all backbone nuclei in proteins (¹⁵N, ¹³C_α, ¹³CO, ¹H_α) and ¹³C_β nuclei arising from ¹H-to-D substitutions at amide nitrogen positions is described. Isolation of molecular species with a defined protonation/deuteration pattern at successive backbone nitrogen positions in the polypeptide chain allows quantifying all deuterium isotope shifts of these nuclei from the first to the fourth order. Some of the deuterium isotope shifts measured in the proteins ubiquitin and GB1 can be interpreted in terms of backbone geometry via empirical relationships describing their dependence on (φ; ψ) backbone dihedral angles. Because of their relatively large variability and notable dependence on the protein secondary structure, the two- and three-bond ¹³C_α isotope shifts, ²ΔC_α(N_iD) and ³ΔC_α(N_i+1D), and three-bond ¹³C_β isotope shifts, ³ΔC_β(N_iD), are useful reporters of the local geometry of the protein backbone.     

δ(13) C of leaf-respired CO(2) reflects intrinsic water-use efficiency in barley

Leaf intrinsic water-use efficiency (WUE), the ratio of photosynthetic rate to stomatal conductance (A/g(s) ), is a key plant trait linking terrestrial carbon and water cycles. A rapid, integrative proxy for A/g(s) is of benefit to crop breeding programmes aiming to improve WUE, but also for ecologists interested in plant carbon-water balance in natural systems. We hypothesize that the carbon isotope composition of leaf-respired CO(2) (δ(13) C(Rl) ), two hours after leaves are transferred to the dark, records photosynthetic carbon isotope discrimination and so provides a proxy for A/g(s) . To test this hypothesis, δ(13) C(Rl) was measured in four barley cultivars grown in the field at two levels of water availability and compared to leaf-level gas exchange (the ratio of leaf intercellular to ambient CO(2) partial pressure, C(i) /C(a) , and A/g(s) ). Leaf-respired CO(2) was more (13) C-depleted in plants grown at higher water availability, varied between days as environmental conditions changed, and was significantly different between cultivars. A strong relationship between δ(13) C(Rl) and δ(13) C of sucrose was observed. δ(13) C(Rl) was converted into apparent photosynthetic discrimination (Δ(13) C(Rl) ) revealing strong relationships between Δ(13) C(Rl) and C(i) /C(a) and A/g(s) during the vegetative stage of growth. We therefore conclude that δ(13) C(Rl) may provide a rapid, integrative proxy for A/g(s) in barley.     

Analysis of δ13C of CO2 distinguishes between microbial respiration of added C4-sucrose and other soil respiration in a C3-ecosystem

The main aim of this study was to test various hypotheses regarding the changes in ¹³C of emitted CO₂ that follow the addition of C₄-sucrose to the soil of a C₃-ecosystem. It forms part of an experimental series designed to assess whether or not the contributions from C₃-respiration (root and microbial) and C₄-respiration (microbial) to total soil respiration can be calculated from such changes. A series of five experiments, three on sieved (root-free) mor-layer material, and two in the field with intact mor-layer (and consequently with active roots), were performed. Both in the experiments on sieved mor-layer and the field experiments, we found a C₄-sucrose-induced increase in C₃-respiration that accounted for between 30% and 40% of the respiration increase 1 h after sucrose addition. When the course of C₃-, C₄- and total respiration was followed in sieved material over four days following addition of C₄-sucrose, the initially increased respiration of C₃-C was transient, passing within less than 24 h. In a separate pot experiment, neither ectomycorrhizal Pinus sylvestrisL. roots nor non-mycorrhizal roots of this species showed respiratory changes in response to exogenous sucrose. No shift in the ¹³C of the evolved CO₂ after adding C₃-sucrose to sieved mor-layer material was found, confirming that the sucrose-induced increase in respiration of endogenous C was not an artefact of discrimination against ¹³C during respiration. Furthermore, we conclude that the C₄-sucrose induced transient increase in C₃-respiration is most likely the result of accelerated turnover of C in the microbial biomass. Thus, neither respiration of mycorrhizal roots, nor processes discriminating against ¹³C were likely sources of error in the field. The estimated ¹³C of evolved soil CO₂ in three field experiments lay between –25.2 and –23.6. The study shows that we can distinguish between CO₂ evolved from microbial mineralisation of added C₄-sucrose, and CO₂ evolved from endogenous carbon sources (roots and microbial respiration).     

Transgenic maize phosphoenolpyruvate carboxylase alters leaf–atmosphere CO2 and 13CO2 exchanges in Oryza sativa

Photosynthesis Research - The engineering process of C4 photosynthesis into C3 plants requires an increased activity of phosphoenolpyruvate carboxylase (PEPC) in the cytosol of leaf mesophyll...     

Upward increase of kerogen δ13C in the Peru Margin Upper Oligocene: possible implications for the Cenozoic evolution of atmospheric CO2

Carbon isotopic composition of predominantly marine kerogen in latest Oligocene mudstones of the Peru Margin ODP 682A Hole shows an about 3.5‰ increase with decreasing age. Py-GC and elemental (C/N ratio) analysis of the kerogen plus sulphur isotopic study together with earlier knowledge on geological setting and organic geochemistry results in a better understanding of depositionary environment and allows to separation of the influence of concentration of water dissolved carbon dioxide (c_e) on kerogen δ¹³C from that of other factors (bacterial degradation, sea surface temperature, DIC δ¹³C, productivity, and admixture of land plant OM). Based on this analysis, the major part of the kerogen shift is considered as a result of the latest Oligocene decrease of marine photosynthetic carbon isotopic fractionation in the Peru Margin photic zone, which in turn possibly reflects a simultaneous drop in atmospheric CO₂ level. Uncertainties in the evaluation of the factors affecting the marine photosynthetic carbon isotopic fractionation and the extent of ocean–atmosphere disequilibrium do not permit calculation of the decrease of the atmospheric CO₂.     

Synthesis and bioevaluation of ω-N-amino analogs of B13

Novel ω-N-amino analogs of B13 (Class E) were designed, synthesized and tested as inhibitors of acid ceramidase (ACDase) and potential anticancer agents deprived of unwanted lysosomal destabilization and ACDase proteolytic degradation properties of LCL204 [Szulc, Z. M.; Mayroo, N.; Bai, A.; Bielawski, J.; Liu, X.; Norris, J. S.; Hannun, Y. A.; Bielawska, A. Bioorg. Med. Chem. 2008, 16, 1015].Representative analog LCL464, (1R,2R)-2-N-(12′-N,N-dimethylaminododecanoyl amino)-1-(4″-nitrophenyl)-1,3-propandiol, inhibited ACDase activity in vitro, with a similar potency as B13 but higher than LCL204. LCL464 caused an early inhibition of this enzyme at a cellular level corresponding to decrease of sphingosine and specific increase of C₁₄- and C₁₆-ceramide. LCL464 did not induce lysosomal destabilization nor degradation of ACDase, showed increased cell death demonstrating inherent anticancer activity in a wide range of different cancer cell lines, and induction of apoptosis via executioner caspases activation. LCL464 represents a novel structural lead as chemotherapeutic agent acting via the inhibition of ACDase.     

Quantifying Lipari–Szabo modelfree parameters from 13CO NMR relaxation experiments

It is proposed to obtain effective Lipari–Szabo order parameters and local correlation times for relaxation vectors of protein ¹³CO nuclei by carrying out a ¹³CO-R₁ auto relaxation experiment, a transverse CSA/dipolar cross correlation and a transverse ¹³CO CSA/¹³CO–¹⁵N CSA/dipolar cross correlation experiment. Given the global rotational correlation time from ¹⁵N relaxation experiments, a new program COMFORD (CO-Modelfree Fitting Of Relaxation Data) is presented to fit the ¹³CO data to an effective order parameter , an effective local correlation time and the orientation of the CSA tensor with respect to the molecular frame. It is shown that the effective is least sensitive to rotational fluctuations about an imaginary axis and most sensitive to rotational fluctuations about an imaginary axis parallel to the NH bond direction. As such, the information is fully complementary to the ¹⁵N relaxation order parameter, which is least sensitive to fluctuations about the NH axis and most sensitive to fluctuations about the axis. The new paradigm is applied on data of Ca²⁺ saturated Calmodulin, and on available literature data for Ubiquitin. Our data indicate that the order parameters rapport on slower, and sometimes different, motions than the ¹⁵N relaxation order parameters. The CO local correlation times correlate well with the calmodulin’s secondary structure. Electronic Supplementary Material Supplementary material is available to authorized users in the online version of this article at .     

松鸡科13种鸟类COⅠ序列变异及系统发育分析

线粒体DNA中的细胞色素C氧化酶亚基Ⅰ基因,即COⅠ是DNA条形编码的主要基因,是一个很好的物种鉴定工具,目前广泛应用于鸟类系统发育研究。通过测定花尾榛鸡和黑琴鸡COⅠ基因的序列,并结合GenBank中松鸡科13种鸟类的同源序列,对松鸡科鸟类进行了序列变异和系统发育分析。结果显示,松鸡科物种的种间变异大于种内变异。序列分歧和系统分析结果支持花尾榛鸡Tetrastes bonasia归于松鸡科Tetraonidae榛鸡属Tetrastes。黑琴鸡Lyrurus tetrix与Tetrao属中其它物种的分歧小于松鸡科其它属间分歧,且黑琴鸡聚在Tetrao内,研究结果倾向支持黑琴鸡归于松鸡属Tetrao。     

13C–13C NOESY spectra of a 480 kDa protein: solution NMR of ferritin

Molecular size has limited solution NMR analyses of proteins. We report ¹³C–¹³C NOESY experiments on a 480 kDa protein, the multi-subunit ferritin nanocage with gated pores. By exploiting ¹³C-resonance-specific chemical shifts and spin diffusion effects, we identified 75% of the amino acids, with intraresidue C–C connectivities between nuclei separated by 1–4 bonds. These results show the potential of ¹³C–¹³C NOESY for solution studies of molecular assemblies >100 kDa.     

Metabolism of 13-cis-retinoic acid: Identification of 13-cis-retinoyl-and 13-cis-4-oxoretinoyl-β-glucuronides in the bile of vitamin A-normal rats

The metabolism of 13-cis-[11-³H]retinoic acid has been examined in vitamin A-normal rats. Within 24 h after intravenous administration of the parent retinoid (15 μg/kg) to animals with biliary fistulas, 69 ± 9% of the dose was detected in the bile with 9 ± 6% being found in the urine. Analysis of the bile by reverse-phase high-pressure liquid chromatography demonstrated that the retinoic acid was being metabolized to several more polar compounds. A number of these compounds were sensitive to incubation with β-glucuronidase as evidenced by a change in their chromatographic behavior after treatment with the enzyme. Two of the metabolites have been identified as 13-cis-4-oxoretinoyl-β-glucuronide (8.1 ± 1.0% of the dose during the first 4 h after administration of the parent compound) and 13-cis-retinoyl-β-glucuronide (7.0 ± 4.4% of the dose). A comparison of the chromatographic profiles of bile from 13-cis- versus all-trans-retinoic acid-treated rats indicated a difference in their metabolism, with a greater proportion of the all-trans-retinoic acid being converted to compounds that eluted in the more polar regions of the column effluent.     

Transplacental Passage of Interleukins 4 and 13?

The mechanisms by which prenatal events affect development of adult disease are incompletely characterized. Based on findings in a murine model of maternal transmission of asthma risk, we sought to test the role of the pro-asthmatic cytokines interleukin IL-4 and -13. To assess transplacental passage of functional cytokines, we assayed phosphorylation of STAT-6, a marker of IL-4 and -13 signaling via heterodimeric receptor complexes which require an IL-4 receptor alpha subunit. IL-4 receptor alpha−/− females were mated to wild-type males, and pregnant females were injected with supraphysiologic doses of IL-4 or 13. One hour after injection, the receptor heterozygotic embryos were harvested and tissue nuclear proteins extracts assayed for phosphorylation of STAT-6 by Western blot. While direct injection of embryos produced a robust positive control, no phosphorylation was seen after maternal injection with either IL-4 or -13, indicating that neither crossed the placenta in detectable amounts. The data demonstrate a useful approach to assay for transplacental passage of functional maternal molecules, and indicate that molecules other than IL-4 and IL-13 may mediate transplacental effects in maternal transmission of asthma risk.     

Production of 13C-labelled β-carotenefrom Dunaliella salina

A 4.5 litre photobioreactor was developed and used to produce ¹³ C-labelled b-carotene by feeding ¹³ CO₂ to growing ells of the marine alga Dunaliella salina. Three runs were carried out using different feeding regimes producing b-carotene containing 40, 56 and 76 Atom% ¹³ C. Approximately 145 mg b-carotene was recovered from each run. Incorporation of ¹³ C into b-carotene ranged from 1.4 to 2.8%. The labelled b-carotene produced would allow multiple tracer experiments for the study of human carotenoid metabolism. This revised version was published online in November 2006 with corrections to the Cover Date.