Quantitative proteomics reveals key pathways in the symbiotic interface and the likely extracellular property of soybean symbiosome

An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plant-rhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation. Here, we report a comprehensive proteome atlas of the soybean symbiosome membrane (SM), peribacteroid space (PBS), and root microsomal fraction (RMF) using state-of-the-art label-free quantitative proteomic technology. In total, 1759 soybean proteins with diverse functions are detected in the SM, and 1476 soybean proteins and 369 rhizobial proteins are detected in the PBS. The diversity of SM proteins detected suggests multiple origins of the SM. Quantitative comparative analysis highlights amino acid metabolism and nutrient uptake in the SM, indicative of the key pathways in nitrogen assimilation. The detection of soybean secretory proteins in the PBS and receptor-like kinases in the SM provides evidence for the likely extracellular property of the symbiosome and the potential signaling communication between both symbionts at the symbiotic interface. Our proteomic data provide clues for how some of the sophisticated regulation between soybean and rhizobium at the symbiotic interface is achieved, and suggest approaches for symbiosis engineering.

Hydrolase CehA and a Novel Two-Component 1-Naphthol Hydroxylase CehC1C2 are Responsible for the Two Initial Steps of Carbaryl Degradation in Rhizobium sp. X9

Carbaryl is a widely used carbamate pesticide in agriculture. The strain Rhizobium sp. X9 possesses the typical carbaryl degradation pathway in which carbaryl is mineralized via 1-naphthol, salicylate, and gentisate. In this study, we cloned a carbaryl hydrolase gene cehA and a novel two-component 1-naphthol hydroxylase gene cehC1C2. CehA mediates carbaryl hydrolysis to 1-naphthol and CehC1, an FMNH₂ or FADH₂-dependent monooxygenase belonging to the HpaB superfamily, and hydroxylates 1-naphthol in the presence of reduced nicotinamide-adenine dinucleotide (FMN)/flavin adenine dinucleotide (FAD), and the reductase CehC2. CehC1 has the highest amino acid similarity (58%) with the oxygenase component of a two-component 4-nitrophenol 2-monooxygenase, while CehC2 has the highest amino acid similarity (46%) with its reductase component. CehC1C2 could utilize both FAD and FMN as the cofactor during the hydroxylation, although higher catalytic activity was observed with FAD as the cofactor. The optimal molar ratio of CehC1 to CehC2 was 2:1. The K_m and K_cat/K_m values of CehC1 for 1-naphthol were 74.71 ± 16.07 μM and (8.29 ± 2.44) × 10^-4 s^-1·μM^-1, respectively. Moreover, the enzyme activities and substrate spectrum between CehC1C2 and previously reported 1-naphthol hydroxylase McbC were compared. The results suggested that McbC had a higher 1-naphthol hydroxylation activity, while CehC1C2 had a broader substrate spectrum.

Nitrogen-doped carbon dots from rhizobium as fluorescence probes for chlortetracycline hydrochloride

Fluorescent nitrogen-doped carbon dots (CDs) were prepared via hydrothermal method at 190 °C for 10 h using rhizobium from soy as the carbon and nitrogen source. Their optical properties, structure, morphology, and functional groups were characterized in detail and the results showed that they possess unique excitation-dependent fluorescence behavior, with average diameter 4.5 ± 2.0 nm and good water dispersibility. Due to the overlap of the UV-vis absorbance of chlortetracycline hydrochloride (CCH) and the fluorescence excitation band of CDs, the fluorescence of the prepared CDs can be quenched by CCH selectively and sensitively. The changes of the fluorescence intensity of CDs have a good linear relationship with the concentration of CCH in a wide concentration range of 5-100 μM, with a detection limit of 0.254 μM. This present method has been successfully applied to determine the CCH in water with recovery ranging from 96.0% to 100.7%.

Rhizobium ruizarguesonis sp. nov., isolated from nodules of Pisum sativum L

Four strains, coded as UPM1132, UPM1133T, UPM1134 and UPM1135, and isolated from nodules of Pisum sativum plants grown on Ni-rich soils were characterised through a polyphasic taxonomy approach. Their 16S rRNA gene sequences were identical and showed 100% similarity with their closest phylogenetic neighbors, the species included in the 'R. leguminosarum group': R. laguerreae FB206T, R. leguminosarum USDA 2370T, R. anhuiense CCBAU 23252T, R. sophoreae CCBAU 03386T, R. acidisoli FH13T and R. hidalgonense FH14T, and 99.6% sequence similarity with R. esperanzae CNPSo 668T. The analysis of combined housekeeping genes recA, atpD and glnII sequences showed similarities of 92-95% with the closest relatives. Whole genome average nucleotide identity (ANI) values were 97.5-99.7% ANIb similarity among the four strains, and less than 92.4% with closely related species, while digital DNA-DNA hybridization average values (dDDH) were 82-85% within our strains and 34-52% with closely related species. Major fatty acids in strain UPM1133T were C18:1 ω7c / C18:1 ω6c in summed feature 8, C14:0 3OH/ C16:1 iso I in summed feature 2 and C18:0. Colonies were small to medium, pearl-white coloured in YMA at 28°C and growth was observed in the ranges 8-34°C, pH 5.5-7.5 and 0-0.7% (w/v) NaCl. The DNA G+C content was 60.8mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains UPM1132, UPM1133T, UPM1134 and UPM1135 into a novel species of Rhizobium, for which the name Rhizobium ruizarguesonis sp. nov. is proposed. The type strain is UPM1133T (=CECT 9542T=LMG 30526T).

Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China

A Gram-stain-negative, facultative aerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped bacterium, designated strain NAU-18^T was isolated from an oil-contaminated soil in China. Strain NAU-18^T could grow at 10-42 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum, 0.5% NaCl in R2A). The predominant fatty acids were C_18:1ω7c (71.2%) and Summed feature 2 (5.1%), representing 76.3% of the total fatty acids. The major respiratory quinones were Q9 and Q10. The DNA G + C content of strain NAU-18^T was 61.4 mol% based on its draft genome sequence. Genome annotation of strain NAU-18^T predicted the presence of 6668 genes, of which 6588 are coding proteins and 80 are RNA genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NAU-18^T was a member of the genus Rhizobium and showed 96.93% (with 93.2% coverage) and 96.81% (with 100% coverage) identities with those of Neorhizobium alkalisoli CCBAU 01393^T and Rhizobium oryzicola ZYY136^T, respectively. In the phylogenetic analysis, strain NAU-18^T and R. oryzicola ZYY136^T are consistently placed in the same branch. Strain NAU-18^T represents a novel species within the genus Rhizobium, for which the name Rhizobium terrae sp. nov. is proposed, with the type strain NAU-18^T (=KCTC 62418^T = CCTCC AB 2018075^T).

Detection of Endogenous Phthalates in Bacterial Pathogens of Plants and Animals

The endogenous esters of orthophthalic acid, dibutyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP), have been first detected in bacterial pathogens of plants (Clavibacter michiganensis ssp. sepedonicus, Pectobacterium carotovorum ssp. carotovorum, Rhizobium rhizogenes, Rhizobium radiobacter) and bacterial pathogens of animal (Escherichia coli).

The potential of cadmium ion-immobilized Rhizobium pusense KG2 to prevent soybean root from absorbing cadmium in cadmium-contaminated soil

AIMS

Because the effect of Cd2+ -immobilized microbe on Cd uptake of plants in Cd-contaminated soil remains underexplored, this study focuses on the effect of Cd2+ -immobilized rhizobia on Cd uptake of soybean.

METHODS AND RESULTS

Strain KG2 from soybean nodule was identified as Rhizobium pusense KG2 by phylogenetic analysis. Rhizobium pusense KG2 showed the 120 mg l-1 of minimal lethal concentration for Cd2+ . In 50 and 100 mg l-1 of Cd2+ liquid, approximately 2 × 1010 cells removed 56·71 and 22·11% of Cd2+ , respectively. In pot soil containing 50 and 100 mg kg-1 of Cd2+ , strain KG2 caused a 45·9 and 35·3% decrease in soybean root Cd content, respectively. Meanwhile, KG2 improved the root and shoot length, nitrogen content and biomass of soybean plants and superoxide dismutase activity.

CONCLUSIONS

The Cd2+ -immobilized rhizobia could inhibit soybean plants to absorb Cd2+ from soil, promote plant growth and improve plant's tolerance against Cd. This study is the first time to report that R. pusense is an effective nodulating rhizobium of legume.

SIGNIFICANCE AND IMPACT OF THE STUDY

Some Cd2+ -immobilized microbe lowering Cd uptake of plant and promoting plant growth should be considered as an effective strategy for producing safety crops in the Cd-contaminated agricultural soil.

Potential Application of Saccharomyces cerevisiae and Rhizobium Immobilized in Multi Walled Carbon Nanotubes to Adsorb Hexavalent Chromium

The presence of harmful contaminants in the waste stream is an important concern worldwide. The convergence of biotechnology and nanoscience offers a sustainable alternative in treating contaminated waters. Hexavalent chromium, being carcinogenic deserves effective and sustainable methods for sequestration. Here in, we report the immobilization of a prokaryote (Rhizobium) and eukaryote (Saccharomyces cerevisiae) in multiwalled carbon nanotubes (MWCNTs) for the effective adsorption of hexavalent chromium. The carboxylic groups were introduced into the MWCNTs during oxidation using potassium permanganate and were subjected to EDC-HOBT coupling to bind with microbial cell surface. FTIR, TGA, BET, FESEM-EDAX, HRTEM, XPS and confocal microscopy were the investigative techniques used to characterize the developed biosorbents. Experimental variables such as pH, adsorbent dosage, kinetics, isotherms and thermodynamics were investigated and it was observed that the system follows pseudo second order kinetics with a best fit for Langmuir isotherm. Electrostatic interactions between the functional groups in the microbial cell wall and hydrochromate anion at pH 2.0 propel the adsorption mechanism. The lab scale column studies were performed with higher volumes of the Cr(VI) contaminated water. Sodium hydroxide was used as the desorbing agent for reuse of the biosorbents. The sustainable biosorbents show prospects to treat chromium contaminated water.

Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses

In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.

Rhizobium Lipo-chitooligosaccharide Signaling Triggers Accumulation of Cytokinins in Medicago truncatula Roots

Legume rhizobium symbiosis is initiated upon perception of bacterial secreted lipo-chitooligosaccharides (LCOs). Perception of these signals by the plant initiates a signaling cascade that leads to nodule formation. Several studies have implicated a function for cytokinin in this process. However, whether cytokinin accumulation and subsequent signaling are an integral part of rhizobium LCO signaling remains elusive. Here, we show that cytokinin signaling is required for the majority of transcriptional changes induced by rhizobium LCOs. In addition, we demonstrate that several cytokinins accumulate in the root susceptible zone 3 h after rhizobium LCO application, including the biologically most active cytokinins, trans-zeatin and isopentenyl adenine. These responses are dependent on calcium- and calmodulin-dependent protein kinase (CCaMK), a key protein in rhizobial LCO-induced signaling. Analysis of the ethylene-insensitive Mtein2/Mtsickle mutant showed that LCO-induced cytokinin accumulation is negatively regulated by ethylene. Together with transcriptional induction of ethylene biosynthesis genes, it suggests a feedback loop negatively regulating LCO signaling and subsequent cytokinin accumulation. We argue that cytokinin accumulation is a key step in the pathway leading to nodule organogenesis and that this is tightly controlled by feedback loops.

Proteomic analysis of the soybean symbiosome identifies new symbiotic proteins

Legumes form a symbiosis with rhizobia in which the plant provides an energy source to the rhizobia bacteria that it uses to fix atmospheric nitrogen. This nitrogen is provided to the legume plant, allowing it to grow without the addition of nitrogen fertilizer. As part of the symbiosis, the bacteria in the infected cells of a new root organ, the nodule, are surrounded by a plant-derived membrane, the symbiosome membrane, which becomes the interface between the symbionts. Fractions containing the symbiosome membrane (SM) and material from the lumen of the symbiosome (peribacteroid space or PBS) were isolated from soybean root nodules and analyzed using nongel proteomic techniques. Bicarbonate stripping and chloroform-methanol extraction of isolated SM were used to reduce complexity of the samples and enrich for hydrophobic integral membrane proteins. One hundred and ninety-seven proteins were identified as components of the SM, with an additional fifteen proteins identified from peripheral membrane and PBS protein fractions. Proteins involved in a range of cellular processes such as metabolism, protein folding and degradation, membrane trafficking, and solute transport were identified. These included a number of proteins previously localized to the SM, such as aquaglyceroporin nodulin 26, sulfate transporters, remorin, and Rab7 homologs. Among the proteome were a number of putative transporters for compounds such as sulfate, calcium, hydrogen ions, peptide/dicarboxylate, and nitrate, as well as transporters for which the substrate is not easy to predict. Analysis of the promoter activity for six genes encoding putative SM proteins showed nodule specific expression, with five showing expression only in infected cells. Localization of two proteins was confirmed using GFP-fusion experiments. The data have been deposited to the ProteomeXchange with identifier PXD001132. This proteome will provide a rich resource for the study of the legume-rhizobium symbiosis.

[Bioengineering of symbiotic systems: creation of new associative symbiosis with the use of lectins on the example of tobacco and colza]

"Barbate roots" in tobacco and colza transgenic on lectin gene were obtained with the use of a wild strain of Agrobacterium rhizogenes 15834 transformed with pCAMBIA1305.1 plasmid containing the full-size lectin gene (psl) from the Pisum sativum. Influence of expression oflectin gene on colonization oftransgenic roots with symbiont of pea (Rhizobium leguminosarum) was investigated. The number of adhered bacteria onto the roots transformed with lectin gene was 14-fold and 37-fold higher in comparison with the control; this confirms the interaction of R. leguminosarum with pea lectin at the surface of the transformed roots of tobacco and colza. The developed experimental approach, based on the simulation of recognition processes and early symbiotic interactions with lectins of pea plants, may, in perspective, be used for obtaining stable associations of economically valuable, nonsymbiotrophic plant species with rhizobia.

Enzymatic tailoring of ornithine in the biosynthesis of the Rhizobium cyclic trihydroxamate siderophore vicibactin

To acquire iron, the N(2)-fixing, symbiotic bacterium Rhizobium sp. produce the cyclic trihydroxamate siderophore vicibactin, containing a 30-membered trilactone scaffold. Herein we report the overproduction and purification of the six proteins VbsACGOLS in the bacterial host Escherichia coli and the reconstitution of the biosynthesis of vicibactin from primary metabolites. The flavoprotein VbsO acts as a pathway-initiating l-ornithine N(5)-hydroxylase, followed by VbsA, which transfers (R)-3-hydroxybutyryl- from the CoA thioester to N(5)-hydroxyornithine to yield N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-l-ornithine. VbsL is a PLP-dependent epimerase acting at C(2) of the 10 atom monomer unit. VbsS, a nonribosomal peptide synthetase free-standing module, then activates N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-d-ornithine as the AMP anhydride on the way to cyclotrimerization to the vicibactin scaffold. The last step, tris-acetylation of the C(2) amino group of desacetyl-d-vicibactin to the mature siderophore vicibactin, is catalyzed distributively by VbsC, using three molecules of acetyl-CoA.

Metal biosorption capability of Cupriavidus taiwanensis and its effects on heavy metal removal by nodulated Mimosa pudica

A novel metal biosorption system consisting of the symbiotic combination of an indigenous metal-resistant rhizobial strain, Cupriavidus taiwanensis TJ208, and its host plant Mimosa pudica has been developed for the removal of heavy-metal pollutants. Free-living C. taiwanensis TJ208 cells were able to adsorb 50.1, 19.0, and 19.6 mg/g of Pb, Cu, and Cd, respectively. After nodulation via inoculation with strain TJ208, the metal uptake ability of M. pudica markedly increased, as the nodulated M. pudica displayed a high metal uptake capacity (qmax) of 485, 25, and 43 mg/g, respectively, which is 86, 12, and 70% higher than that of nodule-free plants. Moreover, with TJ208 nodules, the M. pudica plant also displayed a 71, 81, and 33% enhancement in metal adsorption efficiency (eta) for Pb, Cu, and Cd, respectively. The nodulation appeared to give the greatest enhancing effect on the uptake of Pb, which is consistent with the preference of metal adsorption ability of TJ208. This seems to indicate the crucial role that the rhizobial strain may play in stimulating metal uptake of the nodulated plant. Furthermore, the results show that metal accumulation in the nodulated plant mainly occurred in the roots, accounting for 65-95% of total metal uptake. In contrast, the nodules and the shoots only contributed to 3-12 and 2-23% of total metal uptake, respectively. Nevertheless, the specific adsorption capacity of nodules is comparable to that of the roots. Hence, this work demonstrates the feasibility and effectiveness of using the nodulated plants to promote phyto-removal of heavy metals from the polluted environment as well as to restrict the metal contaminants in the unharmful region of the plant.

Protein-protein interactions within type III secretion system-dependent pili of Rhizobium sp. strain NGR234

Pili synthesized by the type III secretion system of Rhizobium species strain NGR234 are essential for protein secretion and thus for efficient symbiosis with many legumes. Isolation and partial purification of these pili showed that they are composed of at least three proteins, NopA, NopB, and NopX. Using biochemical assays, we show here that these proteins interact directly with one another.

The structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16 A resolution

The gating ring of cyclic nucleotide-modulated channels is proposed to be either a two-fold symmetric dimer of dimers or a four-fold symmetric tetramer based on high-resolution structure data of soluble cyclic nucleotide-binding domains and functional data on intact channels. We addressed this controversy by obtaining structural data on an intact, full-length, cyclic nucleotide-modulated potassium channel, MloK1, from Mesorhizobium loti, which also features a putative voltage-sensor. We present here the 3D single-particle structure by transmission electron microscopy and the projection map of membrane-reconstituted 2D crystals of MloK1 in the presence of cAMP. Our data show a four-fold symmetric arrangement of the CNBDs, separated by discrete gaps. A homology model for full-length MloK1 suggests a vertical orientation for the CNBDs. The 2D crystal packing in the membrane-embedded state is compatible with the S1-S4 domains in the vertical "up" state.

Antitumor effect of soluble beta-1,3-glucan from Agrobacterium sp. R259 KCTC 1019

Beta-1,3-glucans enhance immune reactions such as antitumor, antibacterial, antiviral, anticoagulatory, and wound healing activities. beta-1,3-Glucans have various functions depending on the molecular weight, degree of branching, conformation, water solubility, and intermolecular association. The molecular weight of the soluble glucan was about 15,000 as determined by a high-performance size exclusion chromatography. From the infrared (IR) and 13C NMR analytical data, the purified soluble glucan was found to exclusively consist of beta-D-glucopyranose with 1,3 linkage. We tested the immunestimulating activities of the soluble beta-1,3-glucan extracted from Agrobacterium sp. R259 KCTC 1019 and confirmed the following activities. IFN-gamma and each cytokines were induced in the spleens and thymus of mice treated with soluble beta-1,3-glucan. Adjuvant effect was observed on antibody production. Nitric oxide was synthesized in monocytic cell lines treated with beta-1,3-glucan. The cytotoxic and antitumor effects were observed on various cancer cell lines and ICR mice. These results strongly suggested that this soluble beta-1,3-glucan could be a good candidate for an immune-modulating agent.

Agonistic and antagonistic properties of a Rhizobium sin-1 lipid A modified by an ether-linked lipid

LPS from Rhizobium sin-1 (R. sin-1) can antagonize the production of tumor necrosis factor alpha (TNF-alpha) by E. coli LPS in human monocytic cells. Therefore these compounds provide interesting leads for the development of therapeutics for the prevention or treatment of septic shock. Detailed structure activity relationship studies have, however, been hampered by the propensity of these compounds to undergo beta-elimination to give biological inactive enone derivatives. To address this problem, we have chemically synthesized in a convergent manner a R. sin-1 lipid A derivative in which the beta-hydroxy ester at C-3 of the proximal sugar unit has been replaced by an ether linked moiety. As expected, this derivative exhibited a much-improved chemical stability. Furthermore, its ability to antagonize TNF-alpha production induced by enteric LPS was only slightly smaller than that of the parent ester modified derivative demonstrating that the ether-linked lipids affect biological activities only marginally. Furthermore, it has been shown for the first time that R. sin-1 LPS and the ether modified lipid A are also able to antagonize the production of the cytokine interferon-inducible protein 10, which arises from the TRIF-dependent pathway. The latter pathway was somewhat more potently inhibited than the MyD88-dependent pathway. Furthermore, it was observed that the natural LPS possesses much greater activity than the synthetic and isolated lipid As, which indicates that di-KDO moiety is important for optimal biological activity. It has also been found that isolated R. sin-1 LPS and lipid A agonize a mouse macrophage cell line to induce the production of TNF-alpha and interferon beta in a Toll-like receptor 4-dependent manner demonstrating species specific properties.

Rhizobialide: A New Stearolactone Produced byMesorhizobium sp. CCNWGX022, a Rhizobial Endophyte fromGlycyrrhiza uralensis

The endophytic strain Mesorhizobium sp. CCNWGX022 was isolated from licorice (Glycyrrhiza uralensis Fisch.) grown in the arid and semi-arid regions of Northwest China. The new stearic acid derived gamma-lactone 1, named rhizobialide (= (5S)-4,5-dihydro-5-(8-oxotetradecyl)furan-2(3H)-one), was isolated from the petroleum-ether extract of the fermentation broth of this strain. The structure of 1 was elucidated on the basis of spectroscopic and mass-spectrometric analysis. This is the first report of this type of compound from rhizobia.

Protein conformational changes of Agrobacterium phytochrome Agp1 during chromophore assembly and photoconversion

Phytochromes are widely distributed photochromic biliprotein photoreceptors. Typical bacterial phytochromes such as Agrobacterium Agp1 have a C-terminal histidine kinase module; the N-terminal chromophore module induces conformational changes in the protein that lead to modulation of kinase activity. We show by protein cross-linking that the C-terminal histidine kinase module of Agp1 mediates stable dimerization. The fragment Agp1-M15, which comprises the chromophore module but lacks the histidine kinase module, can also form dimers. In this fragment, dimer formation was stronger for the far-red-absorbing form Pfr than for the red-absorbing form Pr. The same or similar behavior was found for Agp1-M15Delta9N and Agp1-M15Delta18N, which lack 9 and 18 amino acids of the N-terminus, respectively. The fragment Agp1-M20, which is derived from Agp1-M15 by truncation of the C-terminal "PHY domain" (191 amino acids), can also form dimers, but dimerization is independent of irradiation conditions. The cross-linking data also showed that the PHY domain is in tight contact with Lys 16 of the protein and that the nine N-terminal amino acids mediate oligomer formation. Limited proteolysis shows that the hinge region between the chromophore module and the histidine kinase and a part of the PHY domain become exposed upon Pr to Pfr photoconversion.

Letter: influence of experimental parameters on identification of whole cell Rhizobium by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI ToF-MS) has been used to identify bacteria on the basis of its spectral nature. Identification of bacteria using MALDI ToF mass spectra depends on instrumental parameters and sample preparation protocol. Here we have optimized the sample preparation protocol for whole cell Rhizobium and evaluated the effect of its different growth phases to find out specific growth periods superior to the taxonomical approach. Sample preparation integrates the most important step influencing the quality and reproducibility of the spectra. The important factors in sample preparation include selection of matrix, solvent and acid concentration. A maximum numbers of peaks have been observed using 2,4- dihydroxy-phenylazobenzoic acid (HABA) rather than the commonly used alpha-cyano-4-hydroxy cinnamic acid (CHCA) or 3, 5-dimethoxy- 4-hydroxycinnamic acid (sinapinic acid) for whole cell Rhizobium identification. A protocol has been optimized after considering different experimental variables including various phases of bacterial growth and late log to stationary phase has been found to be best for identification of whole cell Rhizobium by this method.

Agrobacterium rhizogenes GALLS protein contains domains for ATP binding, nuclear localization, and type IV secretion

Agrobacterium tumefaciens and Agrobacterium rhizogenes are closely related plant pathogens that cause different diseases, crown gall and hairy root. Both diseases result from transfer, integration, and expression of plasmid-encoded bacterial genes located on the transferred DNA (T-DNA) in the plant genome. Bacterial virulence (Vir) proteins necessary for infection are also translocated into plant cells. Transfer of single-stranded DNA (ssDNA) and Vir proteins requires a type IV secretion system, a protein complex spanning the bacterial envelope. A. tumefaciens translocates the ssDNA-binding protein VirE2 into plant cells, where it binds single-stranded T-DNA and helps target it to the nucleus. Although some strains of A. rhizogenes lack VirE2, they are pathogenic and transfer T-DNA efficiently. Instead, these bacteria express the GALLS protein, which is essential for their virulence. The GALLS protein can complement an A. tumefaciens virE2 mutant for tumor formation, indicating that GALLS can substitute for VirE2. Unlike VirE2, GALLS contains ATP-binding and helicase motifs similar to those in TraA, a strand transferase involved in conjugation. Both GALLS and VirE2 contain nuclear localization sequences and a C-terminal type IV secretion signal. Here we show that mutations in any of these domains abolished the ability of GALLS to substitute for VirE2.

Nucleic acid extraction from Agrobacterium strains

Agrobacterium is routinely used as a tool for moving genetic constructs into plant cells. The successful use of Agrobacterium as a tool for the genetic engineering of plant cells often requires the manipulation and analysis of nucleic acids present in recombinant Agrobacterium strains. Here we present dependable methods for the isolation of genomic (total) DNA, mega-plasmid DNA, shuttle or binary plasmid DNA, and RNA. In addition, we provide a simple method for the electronic transfer of shuttle plasmids from Agrobacterium to E. coli for use when their low copy number in Agrobacterium impedes plasmid isolation from that strain.

Assembly of synthetic locked chromophores with agrobacterium phytochromes Agp1 and Agp2

Phytochromes are photoreceptors with a bilin chromophore in which light triggers the conversion between the red-absorbing form Pr and the far-red-absorbing form Pfr. Agrobacterium tumefaciens has two phytochromes, Agp1 and Agp2, with antagonistic properties: in darkness, Agp1 converts slowly from Pfr to Pr, whereas Agp2 converts slowly from Pr to Pfr. In a previous study, we have assembled Agp1 with synthetic locked chromophores 15Za, 15Zs, 15Ea, and 15Es in which the C15=C16 double bond is fixed in either the E or Z configuration and the C14-C15 single bond is fixed in either the syn (s) or anti (a) conformation. In the present study, the locked chromophores 5Za and 5Zs were used for assembly with Agp1; in these chromophores, the C4=C5 double bond is fixed in the Z configuration, and the C5-C6 single bond is fixed in either the syn or anti conformation. All locked chromophores were also assembled with Agp2. The data showed that in both phytochromes the Pr chromophore adopts a C4=C5 Z C5-C6 syn C15=C16 Z C14-C15 anti stereochemistry and that in the Pfr chromophore the C15=C16 double bond has isomerized to the E configuration, whereas the C14-C15 single bond remains in the anti conformation. Photoconversion shifted the absorption maxima of the 5Zs adducts to shorter wavelengths, whereas the 5Za adducts were shifted to longer wavelengths. Thus, the C5-C6 single bond of the Pfr chromophore is rather in an anti conformation, supporting the previous suggestion that during photoconversion of phytochromes, a rotation around the ring A-B connecting single bond occurs.

The 2-aminogluconate isomer of rhizobium sin-1 lipid A can antagonize TNF-alpha production induced by enteric LPS

The naturally occurring lipopolysaccharide (LPS) from Rhizobium sin-1, a nitrogen-fixing bacterial species, can prevent the induction of the tumor necrosis factor TNF-alpha induced by enteric LPS. The proximal saccharide moiety of R. sin-1 lipid A can exist in two forms, namely as a 2-aminogluconolactone or 2-aminogluconate. As it is unknown which of these forms is responsible for the antagonistic properties of R. sin-1 lipid A, compound 4 was prepared, and its inflammatory properties were studied. This compound contains a methyl ether at the C-5 hydroxyl, which prevents lactonization and therefore is ideally suited to determine whether the 2-aminogluconate possesses antagonistic properties. Compound 4 was synthesized by a highly convergent approach with a key disaccharide building block functionalized with a set of orthogonal protecting groups. The novel synthetic compound lacks proinflammatory properties, as indicated by an absence of TNF-alpha protein production. This compound was, however, able to antagonize the production of TNF-alpha induced by enteric LPS; this indicates that the 2-aminogluconate form of R. sin-1 lipid A is responsible for its biological properties.

Type IV secretion systems and their effectors in bacterial pathogenesis

Type IV secretion systems (T4SSs) are membrane-associated transporter complexes used by various bacteria to deliver substrate molecules to a wide range of target cells. T4SSs are involved in horizontal DNA transfer to other bacteria and eukaryotic cells, in DNA uptake from or release into the extracellular milieu, in toxin secretion and in the injection of virulence factors into eukaryotic host target cells by several mammalian pathogens. Rapid progress has been made towards defining the structures and functions of T4SSs, identifying the translocated effector molecules and elucidating the mechanisms by which the effectors subvert eukaryotic cellular processes during infection. These findings have had an important impact on our understanding of how these pathogens manipulate host cell functions to trigger bacterial uptake, facilitate intracellular growth and suppress defence mechanisms, thus facilitating bacterial colonization and disease development.

Structural determination of the Nod factors produced byRhizobium gallicumbv. gallicum R602

Rhizobium gallicum is a fast-growing bacterium found in European, Australian and African soils; it was first isolated in France. It is a microsymbiont which is able to nodulate plants of the genus Phaseolus. Rhizobium gallicum bv. gallicum R602 produces four extracellular signal molecules consisting of a linear backbone of N-acetyl glucosamine, bearing on the nonreducing terminal residue an N-methyl group and different N-acyl substituents. The four acyloligosaccharides terminate with a sulfated N-acetylglucosaminitol. This unit may be also acetylated. These structures were determined using carbohydrate and methylation analysis, mass spectrometric analysis and one-dimensional- and two-dimensional-nuclear magnetic resonance experiments. This work establishes the common structure that a lipochito-oligosaccharide must have so that the Rhizobium that produces and excretes it is able to nodulate plants of Phaseolus vulgaris. The substituents common to all the molecules are an N-methyl group and a C(18:1) fatty acid on the nonreducing terminal residue.

High temperature-induced changes in exopolysaccharides, lipopolysaccharides and protein profile of heat-resistant mutants of Rhizobium sp. (Cajanus)

A thermosensitive wild-type strain (PP201) of Rhizobium sp. (Cajanus) and its 14 heat-resistant mutants were characterized biochemically with regard to their cell surface (exopolysaccharides (EPSs) and lipopolysaccharides (LPSs)) properties and protein profile. Differences were observed between the parent strain and the mutants in all these parameters under high temperature conditions. At normal temperature (30 degrees C), only half of the mutant strains produced higher amounts of EPSs than the parent strain, but at 43 degrees C, all the mutants produced higher quantities of EPS. The LPS electrophoretic pattern of the parent strain PP201 and the heat-resistant mutants was almost identical at 30 degrees C. At 43 degrees C, the parent strain did not produce LPS but the mutants produced both kinds of LPSs. The protein electrophoretic pattern showed that the parent strain PP201 formed very few proteins at high temperature, whereas the mutants formed additional new proteins. A heat shock protein (Hsp) of 63-74 kDa was overproduced in all mutant strains.

Preparation of a lipid a derivative that contains a 27-hydroxyoctacosanoic acid moiety

[structure: see text] A general synthetic strategy for long-chain omega-1 hydroxy fatty acids has been developed, which employs as a key reaction step a cross metathesis between omega-unsaturated ester and 3-butene-2-ol. The resulting lipids were used for the preparation of lipid A derivatives of Rhizobium sin-1, which have the ability to inhibit the E. coli LPS-dependent synthesis of tumor necrosis factor by human monocytes.

[Lipopolysaccharides of rhizobiaceae: structure and biosynthesis]

The lipopolysaccharides (LPS) are major components of the outer membrane of Gram negative bacteria and, because of their location, are important mediators in the interaction between these bacteria and their environment and other organisms. The alpha-Proteobacterial family Rhizobiaceae includes the rhizobia and agrobacteria, microorganisms which establish symbiotic or parasitic relationships with plants. Mutants deficient in LPS biosynthesis show anomalous interactions with their hosts. The agronomical relevance of the relationship between rhizobia and agrobacteria with plants has promoted a large number of studies on the LPS from these bacteria. The complete structures of one or several domains of LPS from Rhizobiaceae have been determined in the last years. Additionally, several metabolic steps in the biosynthesis of these molecules have been elucidated. This review aims at the description of the more recent findings on the structure and biosynthesis of LPS in Rhizobium, Sinorhizobium and Agrobacterium.

[Infrared spectra analysis of chromium cation biosorbed by biosorbent ZL5-2]

Biosorption of Cr( VI) by the novel biosorbent ZL5-2 produced by Agrobacterium. sp was studied, and infrared spectra of native, absorbing and desorbing ZL5-2 were compared. The initial pH was important for biosorption. The optimum effect on Cr(VI) biosorption was acquired within initial pH 0.5-1.5, then with the pH increasing, the effect on Cr6+ biosorption was reduced. The biosorption for Cr(VI) was a quick process, only within 10 min 65.4% Cr(VI) was biosorbed, and the biosorption was in equilibrium after 60 min, then all the Cr(VI) was biosorbed after 80 min. The absorbed Cr(VI) could be recovered by desorption, and the desorption rate reached 13.6%-67.9%. The absorbance peak around 3 400 cm(-1), which reflected OH stretching vibration, moved about 8 cm(-1), and its absorbance decreased; the absorbance peak around 2 900 cm(-1) decreased, which reflected C-H stretching vibration; and the absorbance peak around 1 600 cm(-1), which reflected amide I group stretching vibration, moved about 13 cm(-1), and its absorbance decreased. After desorption, the absorbance peaks which reflected OH and C-H were increased to the initial degree, and the absorbance peak which reflected NH and amide I group did not increase. Therefore, authors presumed that the process of biosorption was reversible adsorption and irreversible adsorption simultaneously, however the reversible adsorption was more important in the biosorption.

Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium

Several human pathogens and the plant pathogen Agrobacterium tumefaciens use a type IV secretion system for translocation of effector proteins into host cells. How effector proteins are selected for transport is unknown, but a C-terminal transport signal is present in the proteins translocated by the A. tumefaciens VirB/D4 type IV secretion system. We characterized this signal in the virulence protein VirF by alanine scanning and further site-directed mutagenesis. The Cre recombinase was used as a reporter to measure the translocation efficiency of Cre-Vir fusions from A. tumefaciens to Arabidopsis. The data unambiguously showed that positive charge is an essential characteristic of the C-terminal transport signal. We increased the sensitivity of this translocation assay by modifying the Cre-induced readout in host cells from kanamycin resistance to GFP expression. This improvement allowed us to detect translocation of the VirD2 relaxase protein in the absence of transferred DNA, showing that attachment to the transferred DNA is not essential for transport by the VirB/D4 system. We also found another translocated effector protein, namely the VirD5 protein encoded by the tumor-inducing plasmid. According to secondary structure predictions, the C termini of all VirB/D4-translocated proteins identified so far are unstructured; however, they contain a characteristic hydropathic profile. Based on sequence alignments and mutational analysis of VirF, we conclude that the C-terminal transport signal for recruitment and translocation of effector proteins by the A. tumefaciens VirB/D4 system is hydrophilic and has a net positive charge with a consensus motif of R-X(7)-R-X-R-X-R-X-X(n)>.

Diversity in a promiscuous group of rhizobia from three Sesbania spp. colonizing ecologically distinct habitats of the semi-arid Delhi region

Sesbania-rhizobia associations have immense significance in soil amelioration programs for diverse habitats. Diversity in symbiotic properties, LPS profiles, Sym plasmid and rhizobiophage sensitivity of 28 root- and stem-nodulating bacterial isolates of three Sesbania species (S. sesban, S. aegyptica and S. rostrata) inhabiting six ecologically distinct sites of semi-arid Delhi region was analyzed. The isolates were highly promiscuous among the symbiotic partners (Sesbania spp.). The root nodules formed by all the isolates were morphologically similar but they differed in their symbiotic efficiency and effectiveness. 16S rDNA sequence analyses revealed that root nodule isolates of sesbanias belong to diverse rhizobial taxa (Sinorhizobium saheli, S. meliloti, Rhizobium huautlense) whereas stem-nodule isolates were strictly Azorhizobium caulinodans. Sinorhizobium spp. seem to dominate as microsymbiont partner of Sesbania in the Delhi region. The genetic diversity revealed by cluster analyses based on NPC-PCR reflects sorting of isolates across the ecological gradient. Parallel diversity was also observed in the grouping based on LPS profiles and sym plasmid (NPC-PCR). Segregation of different rhizobial taxa into distinct types/clusters based on LPS and NPC-PCR analyses suggest its significance in the circumscription of the taxa. However, subtypes and subclusters showed their sorting across the ecological gradients. Sesbania rhizobia showed extremely high specificity to rhizobiophages. Enormous diversity in LPS profiles and high specificity of rhizobiophages might be the result of environmental selection pressures operating in ecologically distinct habitats. The ability of sesbanias to enter into effective symbioses with different rhizobial taxa and colonize diverse habitats with various biotic and abiotic stresses appears to contribute to its wide ecological amplitude.

Why boron?

It is now more than 80 years since boron was convincingly demonstrated to be essential for normal growth of higher plants. However, its biochemical role is not well understood at the moment. Several recent reviews propose that B is implicated in three main processes: keeping cell wall structure, maintaining membrane function, and supporting metabolic activities. However, in the absence of conclusive evidence, the primary role of boron in plants remains elusive. Besides plants, growth of specific bacteria, such as heterocystous cyanobacteria and the recently reported actinomycetes of the genus Frankia, requires B, particularly for the stability of the envelopes that control the access of the nitrogenase-poisoning oxygen when they grow under N2-fixing conditions. Likewise, a role for B for animal embryogenesis and other developmental processes is being established. Finally, a new feature of the role of boron comes from signaling mechanisms for communication among bacteria and among legumes and rhizobia leading to N2-fixing symbiosis, and it is possible that new roles for B, based on its special chemistry and its interaction with Ca would appear in the world of signal transduction pathways. In conclusion, the diversity of roles played by B might indicate that either the micronutrient is involved in numerous processes or that its deficiency has a pleiotropic effect. The arising question is why such an element? Since all of the roles clearly established for B are related to its capacity to form diester bridges between cis-hydroxyl-containing molecules, we propose that the main reason for B essentiality is the stabilization of molecules with cis-diol groups turning them effective, irrespectively of their function.

Gas chromatography-mass spectrometry analysis of indoleacetic acid and tryptophan following aqueous chloroformate derivatisation of Rhizobium exudates

A new method for preparing alkyl esters of indole-3-acetic acid (IAA) in aqueous solution is adapted from the chloroformate method originally described by Husek for the analysis of amino acids. This method has the significant advantage of avoiding the generation and use of diazomethane, and is done in aqueous solution without the need to dry the sample with concomitant non-specific losses of IAA. The effectiveness of this method is demonstrated by its use in an isotope dilution gas chromatography-mass spectrometry (GC-MS) assay of IAA and L-tryptophan (Trp) in the culture supernatant of a series of Sinorhizobium meliloti and Rhizobium leguminosarum bv. trifolii strains that can interact with rice to either enhance or inhibit rice plant growth. We were testing the hypothesis that the rice growth inhibition was related to the biosynthesis of IAA. It was found that S. meliloti and Rhizobium strains produced high amounts of IAA in Trp supplemented BIII minimal medium compared to BIII media. All the strains produced more than the minimum amount of IAA required to inhibit rice growth and thus IAA is not the major inhibitory factor of rice seedling growth from S. meliloti and Rhizobium strains.

Rhizobial lipopolysaccharide as the receptor in lectin-Rhizobium interaction

Rhizobial specificity was examined on the basis of interaction between legume lectins (peanut, pea and soybean) and different rhizobial species (various bradyrhizobia specific for peanut, P 14-93 and SB16). Legume lectins showed higher affinity towards host-specific Rhizobium and lipopolysaccharides (LPS) isolated from those particular rhizobia. Two LPS mutants of peanut-specific Bradyrhizobiumn sp. (Arachis) strain GN17 were isolated by Tn5 mutagenesis. These mutants (GN17M1 and GN17M2) were characterized by their higher hydrophobicity with respect to the parent cells. The hexose content in exopolysaccharides (EPS) and LPS of the mutants was found reduced significantly, whereas 2-keto-3-deoxyoctulosonic acid (Kdo) and uronic acid in LPS were less by 20-times and thrice, respectively in the mutants. Glucose was the major sugar in LPS from all the strains. However, glucosamine appeared only in the mutants. Spectrofluorimetric analysis showed that LPS from GN17M1 mutant interacted most significantly with peanut root agglutinin or lectin (PRA II). The results indicate that LPS on the surface of rhizobial cells is the possible receptor for lectin.

Three-dimensional reconstruction of Agrobacterium VirE2 protein with single-stranded DNA

Agrobacterium tumefaciens infects plant cells by a unique mechanism involving an interkingdom genetic transfer. A single-stranded DNA substrate is transported across the two cell walls along with the bacterial virulence proteins VirD2 and VirE2. A single VirD2 molecule covalently binds to the 5'-end of the single-stranded DNA, while the VirE2 protein binds stoichiometrically along the length of the DNA, without sequence specificity. An earlier transmission/scanning transmission electron microscopy study indicated a solenoidal ("telephone coil") organization of the VirE2-DNA complex. Here we report a three-dimensional reconstruction of this complex using electron microscopy and single-particle image-processing methods. We find a hollow helical structure of 15.7-nm outer diameter, with a helical rise of 51.5 nm and 4.25 VirE2 proteins/turn. The inner face of the protein units contains a continuous wall and an inward protruding shelf. These structures appear to accommodate the DNA binding. Such a quaternary arrangement naturally sequesters the DNA from cytoplasmic nucleases and suggests a mechanism for its nuclear import by decoration with host cell factors. Coexisting with the helices, we also found VirE2 tetrameric ring structures. A two-dimensional average of the latter confirms the major features of the three-dimensional reconstruction.

The Biliverdin Chromophore Binds Covalently to a Conserved Cysteine Residue in the N-Terminus ofAgrobacteriumPhytochrome Agp1†

Phytochromes are widely distributed biliprotein photoreceptors. Typically, the chromophore becomes covalently linked to the protein during an autocatalytic lyase reaction. Plant and cyanobacterial phytochromes incorporate bilins with a ring A ethylidene side chain, whereas other bacterial phytochromes utilize biliverdin as chromophore, which has a vinyl ring A side chain. For Agrobacterium phytochrome Agp1, site-directed mutagenesis provided evidence that biliverdin is bound to cysteine 20. This cysteine is highly conserved within bacterial homologues, but its role as attachment site has as yet not been proven. We therefore performed mass spectrometry studies on proteolytic holopeptide fragments. For that purpose, an Agp1 expression vector was re-engineered to produce a protein with an N-terminal affinity tag. Following proteolysis, the chromophore co-purified with a ca. 5 kDa fragment during affinity chromatography, showing that the attachment site is located close to the N-terminus. Mass spectrometry analyses performed with the purified chromopeptide confirmed the role of the cysteine 20 as biliverdin attachment site. We also analyzed the role of the highly conserved histidine 250 by site-directed mutagenesis. The homologous amino acid plays an important but yet undefined role in plant phytochromes and has been proposed as chromophore attachment site of Deinococcus phytochrome. We found that in Agp1, this amino acid is dispensable for covalent attachment, but required for tight chromophore-protein interaction.

Cyclosophoraose as a catalytic carbohydrate for methanolysis

A novel catalytic methanolysis can be induced by a natural cyclooligosaccharide, a cyclosophoraose (cyclic-(1-->2)-beta-D-glucan, Cys), which is a member of a family of unbranched cyclooligosaccharides produced as intra- or extraoligosaccharides by soil microorganisms of the genus, Rhizobium. Cys catalyzed the methanolysis for 5(4H)-oxazolones and various phospholipids. Cys enhanced the methanolysis reaction about 9200-fold for a benzylidene oxazolone or 250-fold for dipalmitoylphosphatidylcholine comparing with control. In this study, we describe that natural cyclosophoraoses isolated from the Rhizobium species function as catalytic carbohydrates for the methanolysis.

A catalogue of molecular, physiological and symbiotic properties of soybean-nodulating rhizobial strains from different soybean cropping areas of China

We have analysed 198 fast-growing soybean-nodulating rhizobial strains from four different regions of China for the following characteristics: generation time; number of plasmids; lipopolysaccharide (LPS), nodulation factors (LCOs) and PCR profiles; acidification of growth medium; capacity to grow at acid, neutral, and alkaline pH; growth on LC medium; growth at 28 and 37 degrees C; melanin production capacity; Congo red absorption and symbiotic characteristics. These unbiased analyses of a total subset of strains isolated from specific soybean-cropping areas (an approach which could be called "strainomics") can be used to answer various biological questions. We illustrate this by a comparison of the molecular characteristics of five strains with interesting symbiotic properties. From this comparison we conclude, for instance, that differences in the efficiency of nitrogen fixation or competitiveness for nodulation of these strains are not apparently related to differences in Nod factor structure.

Fused RolA protein enhances beta-glucoronidase activity 50-fold: implication for RolA mechanism of action

We report that the plant oncoprotein RolA from Agrobacterium rhizogenes acts to stabilize beta-glucoronidase (Gus) when the two proteins are expressed as a fusion protein in transformed tobacco. The observed 50-fold increase of Gus activity was shown to be related to protein accumulation, with no significant changes in mRNA abundance, kinetic properties of the enzyme and thermostability. The entire RolA sequence is essential to achieve the full effect since both the N-terminal region, spanning a putative reverse signal-anchor and nuclear targeting sequences, or the contiguous C-terminal portion were shown to increase Gus activity only 10-fold. A possible interference of RolA in the protein degradation pathway regulated by auxin is discussed.

Synthesis and biological evaluation of Rhizobium sin-1 lipid A derivatives

A highly convergent strategy for the synthesis of several derivatives of the lipid A of Rhizobium sin-1 has been developed. The approach employed the advanced intermediate 3-O-acetyl-6-O-(3-O-acetyl-4,6-O-benzylidene-2-deoxy-2-phthalimido-beta-d-glucopyrano-syl)-2-azido-4-O-benzyl-2-deoxy-1-thio-alpha-d-glucopyranoside (5), which is protected in such a way that the anomeric center, the C-2 and C-2' amino groups, and the C-3 and C-3' hydroxyls can be selectively functionalized. The synthetic strategy was used for the preparation of 2-deoxy-6-O-[2-deoxy-3-O-[(R)-3-hydroxy-hexadecanoyl]-2-[(R)-3-octacosanoyloxy-hexadecan]amido-beta-d-glucopyranosyl]-2-[(R)-3-hydroxy-hexadecan]amido-3-O-[(R)-3-hydroxy-hexadecanoyl]-alpha-d-glucopyranose (11) and 2-deoxy-6-O-[2-deoxy-3-O-[(R)-3-hydroxy-hexadecanoyl]-2-[(R)-3-octacosanoyloxy-hexadecan]amido-beta-d-glucopyranosyl]-2-[(R)-3-hydroxy-hexadecan]amido-3-O-[(R)-3-hydroxy-hexadecanoyl]-d-glucono-1,5-lactone (13), which contain an unusual octacosanoic acid moiety and differ in the oxidation state of the anomeric center. The results of biological studies indicate that 11 and 13 lack the proinflammatory effects of Escherichia coli lipopolysaccharides (LPS). Furthermore, 13 emulated the ability of heterogeneous R. sin-1 LPS to antagonize enteric LPS, providing evidence for the critical role of the gluconolactone moiety of R. sin-1 LPS in mediating this antagonistic effect. Compound 13 is the first example of a lipid A derivative that is devoid of phosphate but possesses antagonistic properties, making it an attractive lead compound for development of a drug to use in the treatment of Gram-negative septicemia.

Enantioseparation using cyclosophoraoses as a novel chiral additive in capillary electrophoresis

Cyclosophoraoses, cyclic beta-(1-->2)-D-glucans produced by Rhizobium meliloti 2011, were used as a novel chiral additive for the separation of terbutaline, amethopterin, thyroxine and N-acetylphenylalanine enantiomers in aqueous capillary electrophoresis (CE). Enantioseparation took place in the normal- or reversed-polarity mode when a high concentration of neutral (60 mM) or anionic (40 mM) cyclosophoraoses was added to the background electrolyte (BGE).

The polar lipid composition of Mesorhizobium ciceri

The extractable lipid composition of Mesorhizobium ciceri strain HAMBI 1750 grown in a phosphate sufficient medium (79CA) is reported. Cardiolipin (CL-27% of total lipids), phosphatidylglycerol (PG-18%), phosphatidylethanolamine (PE-1%), phosphatidylcholine (PC-30%) and two methylated derivatives of PE, i.e. phosphatidyl-N, N-dimethylethanolamine (DMPE-1%) and phosphatidyl-N-monomethylethanolamine (MMPE-1%), were found to make up the phospholipids of the analysed bacteria. Nonphosphorus, ornithine-containing lipid (OL-10%) was also detected. Polar groups of phospholipids were predominantly acylated with cis-11,12-methyleneoctadecanoyl (lactobacillic) residues, whereas the ornithine lipid contained mainly 3-hexadecanoyloxy-11,12-methyleneoctadecanoic acid bound to the alpha-amino group.

Structural characterization of the lipid A component of Sinorhizobium sp. NGR234 rough and smooth form lipopolysaccharide. Demonstration that the distal amide-linked acyloxyacyl residue containing the long chain fatty acid is conserved in rhizobium and Sinorhizobium sp

A broad-host-range endosymbiont, Sinorhizobium sp. NGR234 is a component of several legume-symbiont model systems; however, there is little structural information on the cell surface glycoconjugates. NGR234 cells in free-living culture produce a major rough lipopolysaccharide (LPS, lacking O-chain) and a minor smooth LPS (containing O-chain), and the structure of the lipid A components was investigated by chemical analyses, mass spectrometry, and NMR spectroscopy of the underivatized lipids A. The lipid A from rough LPS is heterogeneous and consists of six major bisphosphorylated species that differ in acylation. Pentaacyl species (52%) are acylated at positions 2, 3, 2', and 3', and tetraacyl species (46%) lack an acyl group at C-3 of the proximal glucosamine. In contrast to Rhizobium etli and Rhizobium leguminosarum, the NGR234 lipid A contains a bisphosphorylated beta-(1' --> 6)-glucosamine disaccharide, typical of enterobacterial lipid A. However, NGR234 lipid A retains the unusual acylation pattern of R. etli lipid A, including the presence of a distal, amide-linked acyloxyacyl residue containing a long chain fatty acid (LCFA) (e.g. 29-hydroxytriacontanoate) attached as the secondary fatty acid. As in R. etli, a 4-carbon fatty acid, beta-hydroxybutyrate, is esterified to (omega - 1) of the LCFA forming an acyloxyacyl residue at that location. The NGR234 lipid A lacks all other ester-linked acyloxyacyl residues and shows extensive heterogeneity of the amide-linked fatty acids. The N-acyl heterogeneity, including unsaturation, is localized mainly to the proximal glucosamine. The lipid A from smooth LPS contains unique triacyl species (20%) that lack ester-linked fatty acids but retain bisphosphorylation and the LCFA-acyloxyacyl moiety. The unusual structural features shared with R. etli/R. leguminosarum lipid A may be essential for symbiosis.

Nod factors activate both heterotrimeric and monomeric G-proteins in Vigna unguiculata (L.) Walp

Nod factors are lipo-chito-oligosaccharides secreted by rhizobia that initiate many responses in the root hairs of the legume hosts, culminating in deformed hairs. The heterotrimeric G-protein agonists mastoparan, Mas7, melittin, compound 48/80 and cholera toxin provoke root hair deformation, whereas the heterotrimeric G-protein antagonist pertussis toxin inhibits mastoparan and Nod factor NodNGR[S]- (from Rhizobiumsp. NGR234) induced root hair deformation. Another heterotrimeric G-protein antagonist, isotetrandrine, only inhibited root hair deformation provoked by mastoparan and melittin. These results support the notion that G-proteins are implicated in Nod factor signalling. To study the role of G-proteins at a biochemical level, we examined the GTP-binding profiles of root microsomal membrane fractions isolated from the nodulation competent zone of Vigna unguiculata(L.) Walp. GTP competitively bound to the microsomal membrane fractions labelled with [(35)S]GTPgammaS, yielding a two-site displacement curve with displacement constants ( K(i)) of 0.58 micro M and 0.16 mM. Competition with either ATP or GDP revealed a one-site displacement curve with K(i) of 4.4 and 29 micro M, respectively, whereas ADP and UTP were ineffective competitors. The GTP-binding profiles of microsomal membrane fractions isolated from roots pretreated with either NodNGR[S] or the four-sugar, N- N'- N"- N'"-tetracetylchitotetraose (TACT) backbone of Nod factors were significantly altered compared with control microsomal fractions. To identify candidate proteins, membrane proteins were separated by SDS-PAGE and electrotransferred to nitrocellulose. GTP overlay experiments revealed that membrane fractions isolated from roots pretreated with NodNGR[S] or TACT contained two proteins (28 kDa and 25 kDa) with a higher affinity for GTPgammaS than control membrane fractions. Western analysis demonstrated that membranes from the pretreated roots contained more of another protein (~55 kDa) recognised by Galpha(common) antisera. These results provide pharmacological and biochemical evidence supporting the contention that G-proteins are involved in Nod factor signalling and, importantly, implicate monomeric G-proteins in this process.

Structural determination of the lipo-chitin oligosaccharide nodulation signals produced by Rhizobium giardinii bv. giardinii H152

Rhizobium giardinii bv. giardinii is a microsymbiont of plants of the genus Phaseolus and produces extracellular signal molecules that are able to induce deformation of root hairs and nodule organogenesis. We report here the structures of seven lipochitooligosaccharide (LCO) signal molecules secreted by R. giardinii bv. giardinii H152. Six of them are pentamers of GlcNAc carrying C 16:0, C 18:0, C 20:0 and C 18:1 fatty acyl chains on the non-reducing terminal residue. Four are sulfated at C-6 of the reducing terminal residue and one is acetylated in the same position. Six of them are N-methylated on the non-reducing GlcN residue and all the nodulation factors are carbamoylated on C-6 of the non-reducing terminal residue. The structures were determined using monosaccharide composition and methylation analyses, 1D- and 2D-NMR experiments and a range of mass spectrometric techniques. The position of the carbamoyl substituent on the non-reducing glucosamine residue was determined using a CID-MSMS experiment and an HMBC experiment.

Characterization of a novel lipid-A from Rhizobium species Sin-1. A unique lipid-A structure that is devoid of phosphate and has a glycosyl backbone consisting of glucosamine and 2-aminogluconic acid

The structure of the lipid-A from Rhizobium species Sin-1, a nitrogen-fixing Gram-negative bacterial symbiont of Sesbania, was determined by composition, nuclear magnetic resonance spectroscopic, and mass spectrometric analyses. The lipid-A preparation consisted of a mixture of structures due to differences in fatty acylation and in the glycosyl backbone. There were two different disaccharide backbones. One disaccharide consisted of a distal glucosaminosyl residue beta-linked to position 6 of a proximal 2-aminoglucono-1,5-lactonosyl residue, and in the second disaccharide, the proximal residue was 2-amino-2,3-dideoxy-d-erythro-hex-2-enono-1,5-lactone. For both disaccharides, the distal glucosamine was acylated at C-2' primarily with beta-hydroxypalmitate (beta-OHC16:0) which, in turn, was O-acylated with 27-hydroxyoctacosanoic acid. For some of the lipid-A molecules, the distal glucosaminosyl residue was also acylated at C-3' with beta-hydroxymyristate (beta-OHC14:0), whereas other molecules were devoid of this acyl substituent. Both the 2-aminoglucono-1,5-lactonosyl and 2-amino-2,3-dideoxy-d-erythro-hex-2-enono-1,5-lactonosyl residues were acylated at C-2, primarily with beta-OHC16:0. Minor amounts of lipid-A molecules contained beta-OHC14:0 at C-3 and/or beta-hydroxystearate (beta-OHC18:0) or beta-hydroxyoctadecenoate (beta-OHC18:1) as the C-2 and C-2' N-acyl substituents.

Molecular cloning and characterization of nodD genes from Rhizobium sp. SIN-1, a nitrogen-fixing symbiont of Sesbania and other tropical legumes

Rhizobium sp. SIN-1, a nitrogen-fixing symbiont of Sesbania aculeata and other tropical legumes, carries two copies of nodD, both on a sym plasmid. We have isolated these two nodD genes by screening a genomic library of Rhizobium sp. SIN-1 with a nodD probe from Sinorhizobium meliloti. Nucleotide sequence and the deduced amino acid sequence analysis indicated that the nodD genes of Rhizobium sp. SIN-1 are most closely related to those of R. tropici and Azorhziobium caulinodans. Rhizobium sp. SIN-1 nodD1 complemented a S. meliloti nodD1 D2 D3 negative mutant for nodulation on alfalfa, but failed to complement a nodD1 mutant of S. fredii USDA191 for soybean nodulation. A hybrid nodD gene, containing the N-terminus of S. fredii USDA191 nodD1 and the C-terminus of Rhizobium sp. SIN-1 nodD1, complemented the nodD1 negative mutant of USDA191 for nodulation on soybean.