1H, 13C, and 15N resonance assignment of photoactive yellow protein

Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue light of the bacterium Halorhodospira halophila. Here, we report nearly complete backbone and side chain ¹H, ¹³C and ¹⁵N resonance assignments at pH 5.8 and 20 °C of PYP in its electronic ground state.     

1H, 13C and 15N resonance assignments of S114A mutant of UVI31+ from Chlamydomonas reinhardtii

Almost complete sequence specific ¹H, ¹³C and ¹⁵N resonance assignments of S114A mutant of UVI31+ from Chlamydomonas reinhardtii are reported. The cDNA of S114A mutant of UVI31+ was cloned from a eukaryotic green algae (C. reinhardtii) and overexpressed in E.coli from where the protein was purified to homogeneity. The point mutation S114A in UVI31+ reduces its DNA endonuclease activity substantially as compared with its wild type. As a prelude to the structural characterization of S114A mutant of UVI31+, we report here complete sequence-specific ¹H, ¹³C and ¹⁵N NMR assignments.     

Interaction of N,N,N-trialkylammonioundecahydro-closo-dodecaborates with dipalmitoyl phosphatidylcholine liposomes

N,N,N-Trialkylammonioundecahydrododecaborates (1-), a novel class of compounds of interest for use as anions in ionic liquids, interact with DPPC liposomes. Increasing compound concentration causes an increasing negative ζ potential. Dissociation constants demonstrate that the binding capacity increases strongly with longer chain length. N,N,N-Trialkylammonioundecahydrododecaborates with longer alkyl chains show a detergent-like behavior: the compounds incorporate into the liposome membrane and differential scanning calorimetric experiment show already low concentrations cause a complete disappearance of the peak representing the gel-to-liquid crystalline phase transition. In contrast, compounds with shorter alkyl chains only interact with the headgroups of the lipids. Investigations by means of cryo-TEM reveal that all derivatives induce significant morphological changes of the liposomes. N,N,N-Trialkylammonioundecahydrododecaborates with short alkyl chains produce large bilayer sheets, whereas those with longer alkyl chains tend to induce the formation of open or multi-layered liposomes. We propose that the binding of N,N,N-trialkylammonioundecahydrododecaborates is mainly due to electrostatic interactions between the doubly negatively charged cluster unit and the positively charged choline headgroup; the positively charged ammonium group might be in contact with the deeper-lying negatively charged phosphate. For N,N,N-trialkylammonioundecahydrododecaborates with longer alkyl chains hydrophobic interactions with the non-polar hydrocarbon part of the membrane constitute an additional important driving force for the association of the compounds to the lipid bilayer.     

The Tail Sheath of Bacteriophage N4 Interacts with the Escherichia coli Receptor

Unlike other characterized phages, the lytic coliphage N4 must inject the 360-kDa virion RNA polymerase (vRNAP), in addition to its 72-kbp genome, into the host for successful infection. The process of adsorption to the host sets up and elicits the necessary conformational changes in the virion to allow genome and vRNAP injection. Infection of suppressor and nonsuppressor strains, Escherichia coli W3350 supF and E. coli W3350, with a mutant N4 isolate (N4am229) harboring an amber mutation in Orf65 yielded virions containing (N4gp65⁺) and lacking (N4gp65⁻) gp65, respectively. N4gp65⁺ but not N4gp65⁻ phage was able to adsorb to the host. Recombinant gp65 with a hexahistidine tag at the N terminus or hexahistidine and c-myc tags at the C terminus was able to complement N4gp65⁻ virions in vivo and in vitro. Immunogold detection of gp65 in vivo complemented virions revealed its localization at the N4 tail. Finally, we show both in vitro and in vivo that gp65 interacts with the previously determined N4 outer membrane receptor, NfrA.     

H-ATPase Activity from Storage Tissue of Beta vulgaris: IV. N,N'-Dicyclohexylcarbodiimide Binding and Inhibition of the Plasma Membrane H-ATPase

The molecular weight and isoelectric point of the plasma membrane H⁺-ATPase from red beet storage tissue were determined using N,N′-dicyclohexylcarbodiimide (DCCD) and a H⁺-ATPase antibody. When plasma membrane vesicles were incubated with 20 micromolar [¹⁴C]-DCCD at 0°C, a single 97,000 dalton protein was visualized on a fluorograph of a sodium dodecyl sulfate polyacrylamide gel. A close correlation between [¹⁴C]DCCD labeling of the 97,000 dalton protein and the extent of ATPase inhibition over a range of DCCD concentration suggests that this 97,000 dalton protein is a component of the plasma membrane H⁺-ATPase. An antibody raised against the plasma membrane H⁺-ATPase of Neurospora crassa cross-reacted with the 97,000 dalton DCCD-binding protein, further supporting the identity of this protein. Immunoblots of two-dimensional gels of red beet plasma membrane vesicles indicated the isoelectric point of the H⁺-ATPase to be 6.5.     

1H, 13C and 15N NMR assignments of inactive form of P1 endolysin Lyz

Lysozyme (Lyz) encoded by phage P1 is required for host cell lysis upon infection. Lyz has a N-terminal Signal Anchor Release (SAR) domain, responsible for its secretion into the periplasm and for its accumulation in a membrane tethered inactive form. Here, we report sequence-specific ¹H, ¹³C and ¹⁵N resonance assignments for secreted inactive form of Lyz at pH 4.5.     

1H, 13C and 15N assignments of CdnL, an essential protein in Myxococcus xanthus

CdnL, an essential protein in Myxococcus xanthus and several other bacteria, is a member of the large CarD_TRCF family of bacterial proteins that interact with RNA polymerase. Structural analyses of the 164-residue M. xanthus CdnL by NMR is complicated because of broadening, and hence overlap, of the signals due to the self-association and the monomer–dimer equilibrium that occurs in solution. Here, we report ¹H, ¹³C and ¹⁵N assignments for CdnL achieved by analyzing its NMR spectra on the basis of the complete assignment obtained in this study for the 68-residue N-terminal fragment of CdnL (CdnLNt) together with those we described previously for the stable, protease-resistant, 110-residue C-terminal domain (CdnLCt). This approach relied on our observation that many of the CdnLNt and CdnLCt chemical shifts matched closely with those of the equivalent residues in the full-length protein. Our assignments provide the crucial first step in the structural analysis of CdnL and this functionally important family of bacterial proteins.     

1H, 13C and 15N NMR assignment of CGC-19, a single domain proteic constituent of a non ribosomal peptide synthetase

CGC-19, a 14 kDa proteic constituent of a non ribosomal peptide synthetase implicated in the biosynthesis of a secondary metabolite in Streptomyces ambofaciens, has been isotopically enriched and recombinantly expressed. Its nearly complete ¹H, ¹³C and ¹⁵N resonance assignment is reported hereunder.     

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).     

1H, 13C and 15N resonance assignments of the C-terminal DNA-binding domain of RstA protein from Klebsiella pneumoniae

Bacterial cells often use two-component signal transduction systems to regulate genes in response to environmental stimuli. The RstA/RstB system is a two-component regulatory system consisting of the membrane sensor, RstB, and its cognate response regulator RstA. The RstA of Klebsiella pneumoniae consists of a N-terminal receiver domain (NRD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of the response regulator induces a conformational change in the regulatory domain of RstA, which results in activation of the effector domain to regulate the downstream genes, including the ferrous iron transport system (Feo), at low-pH condition. Here we report the ¹H, ¹³C and ¹⁵N resonance assignments and secondary structure identification of the DBD of RstA from K. pneumoniae as a first step for unraveling the structural and functional relationship of the RstA/RstB two component system.     

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.     

Structure and Membrane Interactions of the Antibiotic Peptide Dermadistinctin K by Multidimensional Solution and Oriented N and P Solid-State NMR Spectroscopy

DD K, a peptide first isolated from the skin secretion of the Phyllomedusa distincta frog, has been prepared by solid-phase chemical peptide synthesis and its conformation was studied in trifluoroethanol/water as well as in the presence of sodium dodecyl sulfate and dodecylphosphocholine micelles or small unilamellar vesicles. Multidimensional solution NMR spectroscopy indicates an α-helical conformation in membrane environments starting at residue 7 and extending to the C-terminal carboxyamide. Furthermore, DD K has been labeled with ¹⁵N at a single alanine position that is located within the helical core region of the sequence. When reconstituted into oriented phosphatidylcholine membranes the resulting ¹⁵N solid-state NMR spectrum shows a well-defined helix alignment parallel to the membrane surface in excellent agreement with the amphipathic character of DD K. Proton-decoupled ³¹P solid-state NMR spectroscopy indicates that the peptide creates a high level of disorder at the level of the phospholipid headgroup suggesting that DD K partitions into the bilayer where it severely disrupts membrane packing.     

15N fractionation between vegetation, soil, faeces and wool is not influenced by stocking rate

Understanding stable isotope fractionation in trophic networks is important for the interpretation of stable isotope composition of ecosystem components. This work explores the influence of grazing pressure on the nitrogen isotope composition (?? ¹⁵N) of vegetation (standing biomass), soil, and sheep??s faeces and wool in a three-years (2005?C2007) experiment with different stocking rates (0.375?C2.25 sheep ha^-1 year^-1) in semi-arid Inner Mongolia grassland. The ¹⁵N of wool (from a yearly shearing) reflects vegetation at the whole-year grazing grounds-scale while faeces reflect that of the area grazed within a few days. Stocking rate had no effect on ?? ¹⁵N of vegetation and soil, and sheep??s faeces and wool, although nitrogen content of bulk vegetation increased with stocking rate. Furthermore, ?? ¹⁵N of vegetation and diet did not differ between stocking rates. Hence, ¹⁵N fractionations between vegetation and faeces (??_veg-faeces), vegetation and wool (?? _veg-wool), faeces and soil (?? _faeces-soil) and soil and vegetation (?? _soil-veg) were constants, with ?? _veg-faeces?=?3.0?? (±0.1??, 95% confidence interval), ?? _veg-wool?=?5.3?? (±0.1??), ?? _faeces-soil?=?1.1?? (±0.4??) and ?? _soil-veg?=?-4.1?? (±0.3??). This finding is useful as it means that ?? ¹⁵N of wool or faeces can be used to estimate the ¹⁵N of grazed vegetation, even if grazing pressure is unknown.     

1H, 13C and 15N assignments of the holo-acyl carrier protein of Pseudomonas aeruginosa

Acyl carrier proteins (ACPs) are a group of highly conserved and abundant proteins in bacteria. ACPs play a central role as the acyl group carriers in bacterial fatty acid biosynthesis, providing building blocks for membrane biogenesis and the production of secondary metabolites. In the versatile human pathogen Pseudomonas aeruginosa, three ACP homologs have been identified. One homolog, AcpP, exhibits the strongest sequence homology to the canonical Escherichia coli ACP. Here we report the ¹H, ¹³C and ¹⁵N assignments of the holo-AcpP of P. aeruginosa.     

Estimating the contribution of nitrogen from legume cover crops to the nitrogen nutrition of grapevines using a 15N dilution technique

The aim of this controlled environment experiment was to quantify the distribution of leaf-fed-¹⁵N and canopy fed-¹³C within nodulating, non-nodulating or N fertilized non-nodulating Cicer arietinum L. and in their surrounding rhizosphere soil, excluding soil?+?root respiration. Nodulating chickpea partitioned 32% of its total N and 27% of its total recoverable C below-ground, of which only 50% of N and 36% of C were in the clean root fraction. Non-nodulating chickpea allocated equal recoverable C but slightly less N (28%) below-ground but lost less C from plant induced below-ground respiration. The importance of this below-ground partitioning for crop systems C and N balances is highlighted by their large (45% and 33%, for N and C, respectively) contribution to the total plant derived residue (recyclable) fraction. Recovered ¹⁵N and ¹³C were greater (P?<?0.05) in the outer-rhizosphere (459?µg ¹⁵N and 3.2 mg ¹³C core^?1) than in the inner-rhizosphere soil (detached from roots during freeze-drying; 18?µg ¹⁵N and 67?µg ¹³C core^?1) in relation with the relative size of these compartments. This highlights the significance of the outer-rhizosphere soil when estimating C and N budgets and quantifying rhizodeposition, and the benefit of a double (¹⁵N, ¹³C) isotope approach to determine this flow against large background soil C and N pools.     

1H, 13C and 15N assignment of the GNA1946 outer membrane lipoprotein from Neisseria meningitidis

GNA1946 (Genome-derived Neisseria Antigen 1946) is a highly conserved exposed outer membrane lipoprotein from Neisseria meningitidis bacteria of 287 amino acid length (31 kDa). Although the structure of NMB1946 has been solved recently by X-Ray crystallography, understanding the behaviour of GNA1946 in aqueuos solution is highly relevant for the discovery of the antigenic determinants of the protein that will possibly lead to a more efficient vaccine development against virulent serogroup B strain of N.meningitidis. Here we report almost complete ¹H, ¹³C and ¹⁵N resonance assignments of GNA1946 (residues 10–287) in aqueous buffer solution.     

Complete Genome Sequence of IME11, a New N4-Like Bacteriophage

N4-like bacteriophages are a class of virulent Podoviridae phages for which few genome sequences are present in GenBank. IME11, a novel lytic Escherichia bacteriophage with a wide host range, was isolated, and the whole genome was sequenced. It has a circular double-stranded DNA genome of 72,570 bp. Genomic analysis showed that it resembles another Escherichia phage, vB_EcoP_G7C. Here we announce its complete genome and major findings from its annotation.     

1H, 13C and 15N resonance assignments of the Onconase FL-G zymogen

Onconase^® FL-G zymogen is a 120 residue protein produced by circular permutation of the native Onconase^® sequence. In this construction, the wild type N- and C-termini are linked by a 16 residue segment and new N- and C-termini are generated at wild type positions R73 and S72. This novel segment linking the native N- and C-termini is designed to obstruct Onconase’s^® active site and encloses a cleavage site for the HIV-1 protease. As a first step towards the resolution of its 3D structure and the study of its structure–function relationships, we report here the nearly complete NMR ¹H, ¹³C and ¹⁵N resonance chemical shift assignments at pH 5.2 and 35°C (BMRB deposit no 17973). The results presented here clearly show that the structure of the wild type Onconase^® is conserved in the FL-G zymogen.