NMR assignments of 1H, 13C and 15N resonances of the C-terminal subunit from Azotobacter vinelandii mannuronan C5-epimerase 6 (AlgE6R3)

The 19.9 kDa C-terminal module (R3) from Azotobacter vinelandii mannronan C5-epimerase AlgE6 has been ¹³C, ¹⁵N isotopically labelled and recombinantly expressed. We report here the ¹H, ¹³C, ¹⁵N resonance assignment of AlgE6R3.     

1H, 15N, 13C resonance assignment of the AlgE6R1 subunit from the Azotobacter vinelandii mannuronan C5-epimerase

Isotopically labelled, ¹³C/¹⁵N from of recombinant subunit of the first R-module from alginate C5-epimerase 6 (AlgE6R1) from Azotobacter vinelandii mannuronan C5-epimerase was produced. We report here the ¹H, ¹⁵N, ¹³C resonance assignment of this subunit from AlgE6 epimerase.     

Use of protein trans-splicing to produce active and segmentally 2H, 15N labeled mannuronan C5-epimerase AlgE4

Alginate epimerases are large multidomain proteins capable of epimerising C5 on β‐D ‐mannuronic acid (M) turning it into α‐L ‐guluronic acid (G) in a polymeric alginate. Azotobacter vinelandii secretes a family of seven epimerases, each of which is capable of producing alginates with characteristic G distribution patterns. All seven epimerases consist of two types of modules, denoted A and R, in varying numbers. Attempts to study these enzymes with solution‐state NMR are hampered by their size—the smallest epimerase, AlgE4, consisting of one A‐ and one R‐module, is 58 kDa, resulting in heavy signal overlap impairing the interpretation of NMR spectra. Thus we obtained segmentally ²H, ¹⁵N labeled AlgE4 isotopomeres (A‐[²H, ¹⁵N]‐R and [²H, ¹⁵N]‐A‐R) by protein trans‐splicing using the naturally split intein of Nostoc punctiforme. The NMR spectra of native AlgE4 and the ligated versions coincide well proving the conservation of protein structure. The activity of the ligated AlgE4 was verified by two different enzyme activity assays, demonstrating that ligated AlgE4 displays the same catalytic activity as wild‐type AlgE4.     

1H, 15N and 13C NMR assignments of mouse methionine sulfoxide reductase B2

A recombinant mouse methionine-r-sulfoxide reductase 2 (MsrB2ΔS) isotopically labeled with ¹⁵N and ¹⁵N/¹³C was generated. We report here the ¹H, ¹⁵N, and ¹³C NMR assignments of the reduced form of this protein. An erratum to this article can be found at     

Regional movement patterns of a small‐bodied shark revealed by stable‐isotope analysis

This study used stable‐isotope analysis to define the nearshore regional residency and movements of the small‐bodied Australian sharpnose shark Rhizoprionodon taylori. Plasma and muscle δ¹³C and δ¹⁵N of R. taylori were collected from across five embayments and compared with values of seagrass and plankton from each bay. Linear distances between adjacent bays ranged from 30 to 150 km. There was a positive geographic correlation between R. taylori tissue and environmental δ¹³C values. Populations with the highest tissue δ¹⁵N were collected from bays that had the highest environmental δ¹⁵N values. These results suggest that R. taylori did not forage more than 100 km away from their capture location within 6 months to 1 year. The successful application of isotope analysis to define R. taylori movement demonstrates that this technique may be used in addition to traditional methods to study the movement of sharks, even within similar habitats across regionally small spatial scales (<100 km).     

Isotopic enrichment in Rhizoprionodon porosus (Poey, 1861) and Carcharhinus porosus (Ranzani, 1840) embryos

Isotopic values of two Caribbean sharpnose shark Rhizoprionodon porosus litters (Poey, 1861) with two and three embryos and one litter of 11 smalltail shark Carcharhinus porosus embryos showed enriched ¹⁵N and ¹³C compared to their mothers. In R. porosus, embryonic isotope values were 3.06 ± 0.07‰ and 0.69 ± 0.15‰ greater than their mothers' for δ¹⁵N and δ¹³C, respectively, whereas in C. porosus, δ¹⁵N and δ¹³C were 1.79 ± 0.09‰ and 1.31 ± 0.17‰ greater in embryos than their mothers.     

High-level 2H/13C/15N labeling of proteins for NMR studies

Summary The protein human carbonic anhydrase II (HCA II) has been isotopically labeled with ²H, ¹³C and ¹⁵N for high-resolution NMR assignment studies and pulse sequence development. To increase the sensitivity of several key ¹H/¹³C/¹⁵N triple-resonance correlation experiments, ²H has been incorporated into HCA II in order to decrease the rates of ¹³C and ¹H_N T₂ relaxation. NMR quantities of protein with essentially complete aliphatic ²H incorporation have been obtained by growth of E. coli in defined media containing D₂O, [1,2-¹³C₂, 99%] sodium acetate, and [¹⁵N, 99%] ammonium chloride. Complete aliphatic deuterium enrichment is optimal for ¹³C and ¹⁵N backbone NMR assignment studies, since the ¹³C and ¹H_N T₂ relaxation times and, therefore, sensitivity are maximized. In addition, complete aliphatic deuteration increases both resolution and sensitivity by eliminating the differential ²H isotopic shift observed for partially deuterated CH_nD_m moieties.     

NMR assignments of 1H, 13C and 15N spectra of methionine sulfoxide reductase B1 from Mus musculus

Isotopically labeled, ¹⁵N and ¹⁵N/¹³C forms of recombinant methionine-r-sulfoxide reductase 1 (MsrB1, SelR) from Mus musculus were produced, in which catalytic selenocysteine was replaced with cysteine. We report here the ¹H, ¹⁵N and ¹³C NMR assignment of the reduced form of this mammalian protein.     

Differences in δ13C and δ15N stable isotopes in the pearly razorfish Xyrichtys novacula related to the sex,location and spawning period

In the present study, Xyrichtys novacula (Labridae) were sampled at five locations around the islands of Ibiza and Formentera (western Mediterranean Sea). Isotopic signatures of δ¹³C, δ¹⁵N and the C:N ratio were analysed in relation to locality, sex and size differences. δ¹³C and δ¹⁵N partitioning was also studied in the reproductive spawning period. There were significant differences in the δ¹³C signature between localities for both sexes, but not for δ¹⁵N. Sex differences were also found with a mean ±s.e . value of ?17·38 ± 0·06‰δ¹³C and 8·36 ± 0·05‰δ¹⁵N for females and ?17·17 ± 0·07‰δ¹³C and 8·80 ± 0·06‰δ¹⁵N for males. Increasing total length in both sexes was positively correlated with δ¹⁵N enrichment and a significant positive linear regression was established for both variables. During the reproductive spawning period, there were changes in δ¹³C fractioning with enrichment in postspawning females and males (with respect to prespawning and spawning periods) and δ¹⁵N impoverishment in postspawning females (with respect to prespawning and spawning periods). Xyrichtys novacula uses local food sources, as confirmed by δ¹³C and δ¹⁵N, and females and males use different food sources, thus avoiding intraspecific competition. This was confirmed by δ¹⁵N enrichment as size increased. Spawning leads to special requirements for gonad maturation, which is reflected in the isotopic signatures for both sexes.     

A high field NMR study of the products ensuing from konjak glucomannan C(6)-oxidation followed by enzymatic C(5)-epimerization

Konjak glucomannan (KGM) is a water-soluble linear copolymer of (1-->4) linked beta-D-mannopyranosyl and beta-D-glucopyranosyl units. It has been selectively C6-oxidized by a 2,2,6,6-tetramethylpiperidin-1-oxy mediated reaction to obtain the corresponding uronan. Oxidized KGM has been treated with three different C-5 epimerases, AlgE4, AlgE6, and AlgE1, to obtain uronans with a various content of alpha-L-gulopyranuronate residues, namely, KGME4, KGME6, and KGME1. By use of 1D selective and 2D NMR techniques, a full assignment of the high field (600 MHz) NMR spectra of the purified native KGM and of the oxidized and epimerized derivatives has been obtained. Since in the anomeric region of the (1)H NMR spectrum of native KGM, diads sensitivity is present, the glucose-glucose, glucose-mannose, mannose-mannose, and mannose-glucose distribution has been obtained. In the (13)C spectrum of oxidized KGM, due to the presence of triad sensitivity on the C-4 resonance of glucuronic and mannuronic units, a better sequential investigation has been possible. As a result the average length of mannuronic blocks, N(M) is obtained. When AlgE4, AlgE6, and AlgE1 enzymes are used for the epimerization of oxidized KGM, the reaction products differ significantly both in the proportion and in the distribution of the mannuronic and guluronic residues. In epimerized KGM derivatives, a careful deconvolution of (1)H spectra allows the measurement of the degree of epimerization. In the case of KGME1 and KGME6, the average blocks length, N(G), of the guluronic blocks introduced in the polysaccharidic chain with the epimerization has also been calculated. Due to the shortness of mannuronic blocks in the oxidized KGM before the epimerization, N(G) in the epimerized compounds is also very low.     

1H, 13C, and 15N NMR assignments of the actinoporin Sticholysin I

Sticholysin I is an actinoporin, a pore forming toxin, of 176 aminoacids produced by the sea anemone Stichodactyla heliantus. Isotopically labelled ¹³C/¹⁵N recombinant protein was produced in E. coli. Here we report the complete NMR ¹⁵N, ¹³C and ¹H chemical shifts assignments of Stn I at pH 4.0 and 25°C (BMRB No. 15927).     

Stable‐isotope comparisons between embryos and mothers of a placentatrophic shark species

Stable nitrogen (δ¹⁵N) and carbon (δ¹³C) isotopes of Atlantic sharpnose shark Rhizoprionodon terraenovae embryos and mothers were analysed. Embryos were generally enriched in ¹⁵N in all studied tissue relative to their mothers' tissue, with mean differences between mother and embryo δ¹⁵N (i.e. Δδ¹⁵N) being 1·4‰ for muscle, 1·7‰ for liver and 1·1‰ for cartilage. Embryo muscle and liver were enriched in ¹³C (both Δδ¹³C means = 1·5‰) and embryo cartilage was depleted (Δδ¹³C mean = ?1·01‰) relative to corresponding maternal tissues. While differences in δ¹⁵N and δ¹³C between mothers and their embryos were significant, muscle δ¹⁵N values indicated embryos to be within the range of values expected if they occupied a similar trophic position as their respective mothers. Positive linear relationships existed between embryo total length (L_T) and Δδ¹⁵N for muscle and liver and embryo L_T and Δδ¹³C for muscle, with those associations possibly resulting from physiological differences between smaller and larger embryos or differences associated with the known embryonic nutrition shift (yolk feeding to placental feeding) that occurs during the gestation of this placentatrophic species. Together these results suggest that at birth, the δ¹⁵N and δ¹³C values of R. terraenovae are likely higher than somewhat older neonates whose postpartum feeding habits have restructured their isotope profiles to reflect their postembryonic diet.     

Temporal variability in stable isotope ratios of C and N in the vibrissa of captive and wild adult South American sea lions Otaria byronia: More than just diet shifts

We analyzed the δ¹³C and δ¹⁵N values in the vibrissae of captive adult breeding South American sea lions (Otaria byronia) fed at a constant diet and then used this information to analyze the change in stable isotope values along the vibrissae from wild individuals. The overall diet‐to‐vibrissa discrimination factor of the captive animals was 3.0‰ ± 0.1‰ for δ¹³C and 3.6‰ ± 0.1‰ for δ¹⁵N, but the stable isotope ratios fluctuated periodically despite constant diet. The δ¹³C and δ¹⁵N values of the captive male declined at the end of the breeding season, whereas the δ¹³C values of the female increased during the central part of pregnancy and the δ¹⁵N values peaked during lactation. The δ¹³C and δ¹⁵N values of adult wild specimens also fluctuated periodically and vibrissae growth rate (0.15 mm/d in both sexes) was slightly lower than in captivity (0.17 mm/d), assuming an annual periodicity for oscillations. Similarities in the amplitude of the cycles of captive and wild males suggested that fasting was probably the main source of periodic variability in the δ¹⁵N of wild males, whereas pregnancy and lactation were probably the main source of periodic variability for the δ¹³C of wild females.     

Environmental and species‐specific controls on δ13C and δ15N in dominant woody plants from central‐western Argentinian drylands

Spatial variation in mean annual precipitation is the principal driver of plant water and nitrogen status in drylands. The natural abundance of carbon stable isotopes (δ¹³C) in photosynthetic tissues of C3 plants is an indicator of time‐integrated behaviour of stomatal conductance; while that of nitrogen stable isotopes (δ¹⁵N) is an indicator of the main source of plant N (soil N vs. atmospheric N₂). Previous studies in drylands have documented that plant δ¹³C and δ¹⁵N values increase with decreasing mean annual precipitation due to reductions in stomatal conductance, and soil enriched in ¹⁵N, respectively. However, evidence for this comes from studies focused on stable isotopes measurements integrated at the plant community level or on dominant plants at the site level, but little effort has been made to study C and N isotope variations within a species growing along rainfall gradients. We analysed plant δ¹³C, δ¹⁵N and C/N values of three woody species having different phenological leaf traits (deciduous, perennial and aphyllous) along a regional mean annual precipitation gradient from the central‐western Argentinian drylands. Noticeably, plant δ¹³C and δ¹⁵N values in the three woody species did not increase towards sites with low precipitation or at the start of the growing season (drier period), as we expected. These results suggest that environmental factors other than mean annual precipitation may be affecting plant δ¹³C and δ¹⁵N. The short‐term environmental conditions may interact with species‐specific plant traits related to water and nitrogen use strategies and override the predictive influence of the mean annual precipitation on plant δ¹³C and δ¹⁵N widely reported in drylands.     

Consumer‐resource stoichiometry as a predictor of trophic discrimination (Δ13C, Δ15N) in aquatic invertebrates

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Amino acids as a nitrogen source for tomato seedlings: The use of dual-labeled (C, N) glycine to test for direct uptake by tomato seedlings

Direct uptake of organic nitrogen (ON) compounds, rather than inorganic N, by plant roots has been hypothesized to constitute a significant pathway for plant nutrition. The aim of this study was to test whether tomatoes (Solanum lycopersicum cv. Huying932) can take up ON directly from the soil by using ¹⁵NH₄Cl, K¹⁵NO₃, 1, 2-¹³C₂¹⁵N-glycine labeling techniques. The ¹³C and ¹⁵N in the plants increased significantly indicating that a portion of the glycine-N was taken up in the form of intact amino acids by the tomatoes within 48 h after injection into the soil. Regression analysis of excess ¹³C against excess ¹⁵N showed that approximately 21% of the supplied glycine-N was taken up intact by the tomatoes. Atom% excesses of ¹⁵N and ¹³C in the roots were higher than in any shoots. Results also indicated rapid turnover of amino acids (e.g., glycine) by soil microorganisms, and the poor competitive ability of tomatoes in absorbing amino acids from the soil solution. This implies that tomatoes can take up ON in an intact form from the soil despite the rapid turnover of organic N usually found under such conditions. Given the influence of climatic change and N pollution, further studies investigating the functional ecological implications of ON in horticultural ecosystems are warranted.     

Using stable isotopes and C:N ratios to examine the life‐history strategies and nutritional sources of larval lampreys

Natural abundance stable‐isotope analysis (δ¹³C and δ¹⁵N) and C:N ratios were used to study the ammocoete phase of two common non‐parasitic lamprey species (least brook lamprey Lampetra aepyptera and American brook lamprey Lethenteron appendix) in two tributaries of the Ohio River (U.S.A.). The C:N ratios suggest that each species employs different lipid accumulation strategies to support its metamorphosis and recruitment into an adult animal. Ammocoete δ¹³C values generally increased with increasing C:N values. In contrast to δ¹³C, ammocoete δ¹⁵N values were weakly related to the total length (L_T) in L. aepyptera, but positively correlated to both L_T and C:N ratios in L. appendix. In L. appendix, C:N also correlated positively with L_T, and presumably age. A Bayesian mixing model using δ¹³C and δ¹⁵N was used to estimate nutritional subsidies of different potential food resources to ammocoetes at each site. The models suggested that although nutritional subsidies to ammocoetes varied as a function of site, ammocoetes were generally reliant on large contributions (42–62% at three sites) from aquatic plants. Contributions from aquatic sediment organic matter were also important at all sites (32–63%) for ammocoetes, with terrestrially derived plant materials contributing smaller amounts (4‐33%). These findings provide important insights into the feeding ecology and nutrition of two species of lampreys. They also suggest that similar and other quantitative approaches are required to (1) fully understand how the observed stable‐isotopes ratios are established in ammocoetes and (2) better assess ammocoete nutritional subsidies in different natal streams.     

Structural and Functional Characterization of the R-modules in Alginate C-5 Epimerases AlgE4 and AlgE6 from Azotobacter vinelandii

The bacterium Azotobacter vinelandii produces a family of seven secreted and calcium-dependent mannuronan C-5 epimerases (AlgE1–7). These epimerases are responsible for the epimerization of β-d-mannuronic acid (M) to α-l-guluronic acid (G) in alginate polymers. The epimerases display a modular structure composed of one or two catalytic A-modules and from one to seven R-modules having an activating effect on the A-module. In this study, we have determined the NMR structure of the three individual R-modules from AlgE6 (AR1R2R3) and the overall structure of both AlgE4 (AR) and AlgE6 using small angle x-ray scattering. Furthermore, the alginate binding ability of the R-modules of AlgE4 and AlgE6 has been studied with NMR and isothermal titration calorimetry. The AlgE6 R-modules fold into an elongated parallel β-roll with a shallow, positively charged groove across the module. Small angle x-ray scattering analyses of AlgE4 and AlgE6 show an overall elongated shape with some degree of flexibility between the modules for both enzymes. Titration of the R-modules with defined alginate oligomers shows strong interaction between AlgE4R and both oligo-M and MG, whereas no interaction was detected between these oligomers and the individual R-modules from AlgE6. A combination of all three R-modules from AlgE6 shows weak interaction with long M-oligomers. Exchanging the R-modules between AlgE4 and AlgE6 resulted in a novel epimerase called AlgE64 with increased G-block forming ability compared with AlgE6.     

Variations in stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) in different body parts and eggs of adult stoneflies (Plecoptera)

Variations in δ¹³C and δ¹⁵N might arise from differences in nutrient allocation. Residence times of δ¹³C and δ¹⁵N vary among tissues depending on metabolic turnover rates. However, because of their small size, entire individual insects are generally used as single samples in isotope analyses. The present study aimed to determine the degree of isotope similarity among regions of the adult body and eggs in four species of Plecoptera (Amphinemura sp., Sweltsa sp., Kamimuria tibialis Pictet and Ostrovus sp.). Levels of δ¹³C and δ¹⁵N differ between the four species, being lowest in Amphinemura sp., and with δ¹⁵N being highest in Sweltsa sp. Egg masses contain consistently the lowest values of δ¹³C in the four species, with the δ¹⁵N value of eggs being highest in K. tibialis and Ostrovus sp., and lower in Amphinemura and Sweltsa spp. In Sweltsa sp., the δ¹⁵N levels of the dermal layers and cuticle are lowest, whereas the δ¹³C values of the dermal layers and cuticle are almost equal to those in other regions of the body, except egg masses. Oviposited individuals of Amphinemura and Sweltsa spp. have lower δ¹⁵N levels than individuals that have not oviposited. The rates of metabolism and incorporation of dietary metabolites will differ depending on the body regions and species. Differences in egg ecology such as egg developmental period and egg buoyancy among species are considered to impact on the values of δ¹³C and δ¹⁵N. These results will be useful for understanding the nutritional status of aquatic insects and their energy allocation.     

1H, 15N and 13C resonance assignments,secondary structure,and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase

Summary By using fully ¹⁵N- and ¹⁵N/¹³C-labeled Escherichia coli dihydrofolate reductase, the sequence-specific ¹H and ¹⁵N NMR assignments were achieved for 95% of the backbone resonances and for 90% of the ¹³C resonances in the binary folate complex. These assignments were made through a variety of three-dimensional proton-detected ¹⁵N and ¹³C experiments. A smaller but significant subset of side-chain ¹H and ¹³C assignments were also determined. In this complex, only one ¹⁵N or ¹³C resonance was detected per ¹⁵N or ¹³C protein nucleus, which indicated a single conformation. Proton-detected ¹³C experiments were also performed with unlabeled DHFR, complexed with ¹³C-7/¹³C-9 folate to probe for multiple conformations of the substrate in its binary complex. As was found for the protein resonances, only a single bound resonance corresponding to a productive conformation could be detected for C-7. These results are consistent with an earlier report based on ¹H NMR data [Falzone, C.J. et al. (1990) Biochemistry, 29, 9667–9677] and suggest that the E. coli enzyme is not involved in any catalytically unproductive binding modes in the binary complex. This feature of the E. coli enzyme seems to be unique among the bacterial forms of DHFR that have been studied to date.