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.     

1H, 13C and 15N resonances of the AlgE62 subunit from Azotobacter vinelandii mannuronan C5-epimerase

The 17.7 kDa R2 module from Azotobacter vinelandii mannronan C5-epimerase AlgE6 has been isotopically labeled (¹³C,¹⁵N) and recombinantly expressed. Here we report the ¹H, ¹³C, ¹⁵N resonance assignment of AlgE6R2.     

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.     

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.     

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.     

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).     

Relationships between growth traits and scale stable isotopes (δ13C, δ15N) of adult chum salmon Oncorhynchus keta in Hokkaido,Japan

Stable isotope analysis (SIA) in combination with growth analysis using scales collected from adult chum salmon Oncorhynchus keta migrating back to Hokkaido, Japan, was performed to describe the variation of isotopic composition of carbon (δ¹³C) and nitrogen (δ¹⁵N) in scales and to examine relationships with growth traits [age, fork length (FL), and relative growth ratio in the last growth period [(RGR^last)]. Scale stable isotope (SI) values in 3‐ to 6‐year‐old fish were highly variable, ranging from ?17.6‰ to ?14.3‰ for δ¹³C and 9.5‰ to 13.4‰ for δ¹⁵N. The δ¹⁵N was positively correlated with FL, and this tendency may indicate changes in trophic level with growth. Significant effect was not detected between δ¹⁵N and RGR^last, it can be inferred that factors potentially yielding high δ¹⁵N may not necessarily result in higher growth rates. No trend found between FL and δ¹³C may imply that there is no clear segregation in feeding locations between the 3‐ to 6‐year groups. This study provided basic information for scale SI values of chum salmon adults and indicated that SIA using scales could be a new approach to elucidating the trophic ecology of chum salmon.     

Complete 1H, 15N and 13C assignments, secondary structure, and topology of recombinant human interleukin-6

Summary Essentially complete backbone and side-chain ¹H, ¹⁵N and ¹³C resonance assignments for the 185-aminoacid cytokine interleukin-6 (IL-6) are presented. NMR experiments were performed on uniformly [¹⁵N]-and [¹⁵N, ¹³C]-labeled recombinant human IL-6 (rIL-6) using a variety of heteronuclear NMR experiments. A combination of ¹³C-chemical shift, amide hydrogen-bond exchange, and ¹⁵N-edited NOESY data allowed for analysis of the secondary structure of IL-6. The observed secondary structure of IL-6 is composed of loop regions connecting five -helices, four of which are consistent in their length and disposition with the four-helix bundle motif present in other related cytokines and previously postulated for IL-6. In addition, the topology of the overall fold was found to be consistent with a left-handed up-up-down-down four-helix bundle based on a number of long-range interhelical NOEs. The results presented here provide deeper insight into structure-function relationships among members of the four-helix bundle family of proteins.     

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.     

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     

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.     

13C CP/MAS NMR Spectral Analysis of 6-O-Tosyl, 6-Deoxy-6-iodo,and 6-Deoxy Derivatives of N-Acetylchitosan in a Solid State

6-O-Tosyl (1, d.s. 0.94, 80% yield), 6-deoxy-6-iodo (2, d.s. 0.49, 86% yield) and 6-deoxy (3, d.s. 0.49, 50% yield) derivatives of N-acetylchitosan were prepared, and a ¹³C CP/MAS NMR spectral analysis was performed because no suitable solvent for 3 was found. The ¹³C signal for CH₃ at C-6 in 3 was detected at 18.9 ppm, and that for C-4 in 1–3 appeared at 72.2–72.7 ppm, which is in a higher magnetic field than those (82.5–86.0 ppm) in N-acetylchitosan, 6-O- (ethylthio), 6-O-(benzylthio)- and 6-O-(methylthio)-thiocarbonyl derivatives, chitosan, and chitin. This strongly suggests a different molecular conformation for 1–3.     

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.     

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.     

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

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Nonlinkage between C6 and chromosome 6 markers

Summary C6 typing was performed in a family material by two different techniques: serum or plasma samples were subjected either to high-voltage agarose gel electrophoresis or to isoelectric focusing in polyacrylamide gel slabs. Proteins with C6 activity were then visualized by a specific, hemolytic assay.In 81 unrelated adults within the family material the following allele frequencies were found: C6 ^A:0.61 and C6 ^B:0.39.Linkage studies exclude linkage between C6 and HLA region marker loci, and also between C6 and another chromosome 6 marker locus PGM3.     

C and N allocation in soil under ryegrass and alfalfa estimated by 13C and 15N labelling

Background and Aims

Below-ground translocated carbon (C) released as rhizodeposits is an important driver for microbial mobilization of nitrogen (N) for plants. We investigated how a limited substrate supply due to reduced photoassimilation alters the allocation of recently assimilated C in plant and soil pools under legume and non-legume species.

Methods

A non-legume (Lolium perenne) and a legume (Medicago sativa) were labelled with ¹⁵N before the plants were clipped or shaded, and labelled twice with ¹³CO₂ thereafter. Ten days after clipping and shading, the ¹⁵N and ¹³C in shoots, roots, soil, dissolved organic nitrogen (DON) and carbon (DOC) and in microbial biomass, as well as the ¹³C in soil CO₂ were analyzed.

Results

After clipping, about 50 % more ¹³C was allocated to regrowing shoots, resulting in a lower translocation to roots compared to the unclipped control. Clipping also reduced the total soil CO₂ efflux under both species and the ¹³C recovery of soil CO₂ under L. perenne. The ¹⁵N recovery increased in the shoots of M. sativa after clipping, because storage compounds were remobilized from the roots and/or the N uptake from the soil increased. After shading, the assimilated ¹³C was preferentially retained in the shoots of both species. This caused a decreased ¹³C recovery in the roots of M. sativa. Similarly, the total soil CO₂ efflux under M. sativa decreased more than 50 % after shading. The ¹⁵N recovery in plant and soil pools showed that shading has no effect on the N uptake and N remobilization for L. perenne, but, the ¹⁵N recovery increased in the shoot of M. sativa.

Conclusions

The experiment showed that the dominating effect on C and N allocation after clipping is the need of C and N for shoot regrowth, whereas the dominating effect after shading is the reduced substrate supply for growth and respiration. Only slight differences could be observed between L. perenne and M. sativa in the C and N distribution after clipping or shading.     

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.