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Identification of "nodule-specific" host proteins (nodoulins) involved in the development of rhizobium-legume symbiosis.

Infection of legume roots with Rhizobium species results in the development of a root nodule structure in which the bacteria form an intracellular symbiosis with the plant. We report here that the infection of soybean (Glycine max L.) roots with Rhizobium japonicum results in the synthesis by the plant of at least 18-20 polypeptides other than leghemoglobin during the development of root nodules. Identification of these "nodule-specific" host polypeptides (referred to as nodulins) was accomplished by two-dimensional gel analysis of the immunoprecipitates formed by a "nodule-specific" antiserum with in vitro translation products of root-nodule polysomes that are free of bacteroidal contaminations. Nodulins account for 7-11% of the total 35S-methionine-labeled protein synthesized in the host cell cytoplasm, and the majority of them are of 12,000-20,000 molecular weight. These proteins are absent from the uninfected roots, bacteroids and free-living Rhizobium, and appear to be coded for the plant genes that may be obligatory for the development of symbiosis in the legume root nodules. Analysis of nodulins in ineffective (unable to fix nitrogen) nodules developed due to Rhizobium strains SM5 and 61A24 showed that their synthesis is reduced and their expression differentially influenced by mutations in rhizobia. Two polypeptides of bacterial origin were also found to be cross-reactive with the "nodule-specific" antiserum, suggesting that they are secreted by Rhizobium into the host cell cytoplasm during symbiotic nitrogen fixation.

Fabaceae↗

Assignment of heme and distal amino acid resonances in the 1H-NMR spectra of the carbon monoxide and oxygen complexes of sperm whale myoglobin.

Assignments of resonances of the heme and distal amino acid protons in spectra of the CO and O2 complexes of sperm whale myoglobin are reported. These resonances provide information on the conformation of the heme pocket. For oxymyoglobin, the assignments of the heme meso protons disagree with those proposed previously on the basis of partial deuteration experiments. Rapid ring flips about the C beta-C gamma bond are detected for Phe-CD1. Recent claims for two conformational substates of valine-E11 in carbonmonoxymyoglobin (Bradbury, J.H. and Carver, J.A. (1984) Biochemistry 23, 4905-4913) are shown to be in error. The pK of His-97 (FG3) in carbonmonoxymyoglobin has been determined (pK = 5.9). This residue appears to influence many spectroscopic properties of myoglobin. The distal His-E7 in carbonmonoxymyoglobin has pK less than 5.0. Differences in the heme pocket conformation in the CO complexes of myoglobin and leghemoglobin are discussed. These differences may be influential in O2 and CO association reactions.

Amino Acids↗

Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula.

To construct macro- and microarray tools suitable for expression profiling in root endosymbioses of the model legume Medicago truncatula, we PCR-amplified a total of 6048 cDNA probes representing genes expressed in uninfected roots, mycorrhizal roots and young root nodules [Nucleic Acids Res. 30 (2002) 5579]. Including additional probes for either tissue-specific or constitutively expressed control genes, 5651 successfully amplified gene-specific probes were used to grid macro- and to spot microarrays designated Mt6k-RIT (M. truncatula 6k root interaction transcriptome). Subsequent to a technical validation of microarray printing, we performed two pilot expression profiling experiments using Cy-labeled targets from Sinorhizobium meliloti-induced root nodules and Glomus intraradices-colonized arbuscular mycorrhizal roots. These targets detected marker genes for nodule and arbuscular mycorrhiza development, amongst them different nodule-specific leghemoglobin and nodulin genes as well as a mycorrhiza-specific phosphate transporter gene. In addition, we identified several dozens of genes that have so far not been reported to be differentially expressed in nodules or arbuscular mycorrhiza thus demonstrating that Mt6k-RIT arrays serve as useful tools for an identification of genes relevant for legume root endosymbioses. A comprehensive profiling of such candidate genes will be very helpful to the development of breeding strategies and for the improvement of cultivation management targeted at increasing legume use in sustainable agricultural systems.

Equipment Design↗

Dioxygen affinity in heme proteins investigated by computer simulation.

We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O(2) binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O(2)-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O(2) storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c'.

Animals↗

A novel nodule-enhanced gene encoding a putative universal stress protein from Astragalus sinicus.

A nodule-enhanced gene, AsD243, was identified from infected roots of Astragalus sinicus using suppressive subtractive hybridization (SSH). It encodes a 20-kD protein related to the bacterial universal stress protein family (Usp). Sequence analysis showed that AsD243 is highly similar to the bacterial MJ0577-type of ATP-binding Usp proteins, which have been proposed to function as a molecular switch. Expression analyses revealed that AsD243 was transcribed in all plant organs, and progressively during all stages of nodulation. Its transcripts increased significantly at 7 days after inoculation, which is 2 days later than the onset of leghemoglobin expression in A. sinicus nodules. AsD243 was expressed more strongly in mature roots than in young roots regardless of inoculation status. We suggest that the AsD243 may have other functions in plant processes besides nodulation.

Amino Acid Sequence↗

Plant water status, ethylene evolution, N(2)-fixing efficiency, antioxidant activity and lipid peroxidation in Cicer arietinum L. nodules as affected by short-term salinization and desalinization.

Salinity induced changes in ethylene evolution, antioxidant defense system, N(2)-fixing efficiency and membrane integrity in relation to water and mineral status in chickpea (Cicer arietinum L.) nodules were studied under screen house conditions. At vegetative stage (55-65 DAS) plants were exposed to single saline irrigation (Cl(-) dominated) of levels 0, 2.5, 5.0 and 10.0dSm(-1) and sampled after 3d. The other set of treated plants was desalinized by flooding and the plants were sampled after further 3d. Water potential (Psiw) of leaf and osmotic potential (Psis) of leaf and nodules significantly decreased from -0.44 to -0.56MPa and from -0.65 to -1.15MPa and from -0.75 to -1.77MPa, respectively upon salinization. RWC of leaf and nodules also reduced from 86.05% to 73.30% and 94.70% to 89.98%, respectively. The decline in Psis of nodules was due to accumulation of proline and total soluble sugar. In comparison to control, the increase in ethylene (C(2)H(4)) production was 35-108% higher and correspondingly increase in 1-aminocycloprane-1-carboxylic acid (ACC) content (37-126%) and ACC oxidase activity (31-118%) was also noticed. Similarly, marked increase in H(2)O(2) (25-139%) and thiobarbituric acid substances (TBRAS, 11-133%) contents was seen. N(2)-fixing efficiency i.e. N(2)-ase activity, leghemoglobin and N contents of nodules declined significantly after saline irrigation. The induction in specific activity of antioxidant enzymes was confirmed by the increase in activity of superoxide dismutase, peroxidase, ascorbate peroxidase, glutathione reductase and glutathione transferase, whereas reverse was true for catalase. These activated enzymes could not overcome the accumulation of H(2)O(2) in nodules. Ascorbic acid content also declined from 20 to 38%, whereas Na(+)/K(+) ratio and Cl(-) content were significantly enhanced. Upon desalinization, a partial recovery in all above metabolic processes and water relations parameters was noticed. It is suggested that ethylene in relation to water status and lipid peroxidation and along with other metabolic processes has an important role in induced nodules senescence under salinity.

Antioxidants↗

Identification and expression regulation of symbiotically activated legume genes.

Legume plants are able to enter two different endosymbioses with soil prokaryotes and soil fungi, leading to nitrogen-fixing root nodules and to arbuscular mycorrhiza (AM), respectively. We applied in silico and microarray-based transcriptome profiling approaches to uncover the transcriptome of developing root nodules and AM roots of the model legume Medicago truncatula. Several hundred genes were found to be activated in different stages of either symbiosis, with almost 100 genes being co-induced during nodulation and in arbuscular mycorrhiza. These co-induced genes can be associated with different cellular functions required for symbiotic efficiency, such as the facilitation of transport processes across the perisymbiotic membranes that surround the endosymbiotic bacteroids in root nodules and the arbuscules in AM roots. To specify promoter elements required for gene expression in arbuscule-containing cells, reporter gene fusions of the promoter of the Vicia faba leghemoglobin gene VfLb29 were studied by loss-of-function and gain-of-function approaches in transgenic hairy roots. These analyses specified a 85-bp fragment that was necessary for gene expression in arbuscule-containing cells but was dispensible for gene activation in root nodules. In contrast to promoters mediating gene expression in the infected cells of root nodules, the activation of genes in AM appears to be governed by more complex regulatory systems requiring different promoter modules.

Fabaceae↗

Modeling the tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin.

The tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin (Hbm) was modeled using computer tools and the known tertiary structure of rice Hb1 as a template. This method was tested by predicting the tertiary structure of soybean leghemoglobin a (Lba) using rice Hb1 as a template. The tertiary structures of the predicted and native Lba were similar, indicating that our computer methods could reliably predict the tertiary structures of plant Hbs. We next predicted the tertiary structure of Hbm. Hbm appears to have a long pre-helix A and a large CD-loop. The positions of the distal and proximal His are identical in Hbm and rice Hb1, which suggests that heme-Fe is hexacoordinate in Hbm and that the kinetic properties of Hbm and rice Hb1 are expected to be very similar, i.e. that Hbm has a high O2-affinity. Thermostability analysis showed that Hbm CD-loop is unstable and may provide mobility to amino acids located at the heme pocket for both ligand binding and stabilization and heme-Fe coordination. Analysis of the C-terminal half of Hbm showed the existence of a pocket-like region (the N/C cavity) where interactions with organic molecules or proteins could be possible. Lys K94 protrudes into the N/C cavity, suggesting that K94 may sense the binding of molecules to the N/C cavity. Thus, it is likely that the instability of the CD-loop and the possibility of binding molecules to the N/C cavity are essential for positioning amino acids in the heme pocket and in regulating Hbm activity and function.

Amino Acids↗

Alterations induced by glyphosate on lupin photosynthetic apparatus and nodule ultrastructure and some oxygen diffusion related proteins.

The effects of glyphosate on protein metabolism, mesophyll cell ultrastructure and nodule ultrastructure and functioning of Lupinus albus cv. Multolupa inoculated with Bradyrhizobium sp. (Lupinus) were investigated. Young leaves and nodules were especially affected because these organs act as sinks of the herbicide. The alterations on nodular and chloroplast ultrastructure varied depending on herbicide concentration and time of exposure. After 3 days of 2.5 mM glyphosate application some toxic effects were detected. The most important alterations on nodules were the progressive cellular degradation of plant and bacteroidal cytosol and the rupture of bacteroidal membrane, whilst the peribacteroid membrane of the symbiosomes was preserved. This is the first report on the effect of glyphosate on legume-nodule ultrastructure. Glyphosate inhibited B. sp. (Lupinus) growth at concentrations higher than 62.5 microM. In the mesophyll cells, gradual disorganization of grana and intergrana was observed, loosing the parallel alignment with the chloroplast axis. As in nodules, degradation of membrane systems was observed, with the deformation, and even the rupture, of the tonoplast. These progressive effects were similar to those described in senescence processes. The adverse effects produced on infected zone can be due both to a direct effect of the herbicide on microsymbiont and to an indirect effect of glyphosate action on photosynthetic apparatus. Glyphosate produced changes in nodule cytosol and bacteroid proteins content and polypeptide pattern of leaves and nodules. With respect to proteins related to the oxygen diffusion mechanism, a large decrease in leghemoglobin and glycoproteins (recognized by antibodies MAC236 and MAC265) content was detected, which suggests that the oxygen diffusion mechanisms were also affected by glyphosate.

Diffusion↗

Comparative study of tyrosine radicals in hemoglobin and myoglobins treated with hydrogen peroxide.

The reactions of hydrogen peroxide with human methemoglobin, sperm whale metmyoglobin, and horse heart metmyoglobin were studied by electron paramagnetic resonance (EPR) spectroscopy at 10 K and room temperature. The singlet EPR signal, one of the three signals seen in these systems at 10 K, is characterized by a poorly resolved, but still detectable, hyperfine structure that can be used to assign it to a tyrosyl radical. The singlet is detectable as a quintet at room temperature in methemoglobin with identical spectral features to those of the well characterized tyrosyl radical in photosystem II. Hyperfine splitting constants found for Tyr radicals were used to find the rotation angle of the phenoxyl group. Analysis of these angles in the crystal structures suggests that the radical resides on Tyr151 in sperm whale myoglobin, Tyr133 in soybean leghemoglobin, and either alphaTyr42, betaTyr35, or betaTyr130 in hemoglobin. In the sperm whale metmyoglobin Tyr103Phe mutant, there is no detectable tyrosyl radical present. Yet the rotation angle of Tyr103 (134 degrees) is too large to account for the observed EPR spectrum in the wild type. Tyr103 is the closest to the heme. We suggest that Tyr103 is the initial site of the radical, which then rapidly migrates to Tyr151.

Animals↗

Modulation of the oxygen affinity of cobalt-porphyrin by globin.

We have combined two extreme effects which influence the oxygen affinity to obtain a cobalt-based oxygen carrier with an affinity similar to that of human adult hemoglobin (HbA). The goal was to obtain an oxygen transporter with a lower oxidation rate. Exchange of the heme group (Fe-protoporphyrin IX) in Hb with a cobalt-porphyrin leads to a reduction in oxygen affinity by over a factor of 10, an oxygen affinity too low for use as a blood substitute. At the other extreme, certain globin sequences are known to provide a very high oxygen affinity; for example, Hb Ascaris displays an oxygen affinity 1000 times higher than HbA. We demonstrate here that these opposing effects can be additive, yielding an oxygen affinity similar to that of HbA, but with oxygen binding to a cobalt atom. We have tested the effect of substitution of cobalt-porphyrin for heme in normal HbA, sperm whale (SW) Mb (Mb), and high affinity globins for leghemoglobin, two trematode Hbs: Paramphistomum epiclitum (Pe) and Gastrothylax crumenifer (Gc). As for HbA or SW Mb, the transition from heme to cobalt-porphyrin in the trematode Hbs leads to a large decrease in the oxygen affinity, with oxygen partial pressures for half saturation (P(50)) of 5 and 25 mm Hg at 37 degrees C for cobalt-Pe and cobalt-Gc, respectively. A critical parameter for Hb-based blood substitutes is the autoxidation rate; while both metals oxidize to an inactive state, we observed a decrease in the oxidation rate of over an order of magnitude for cobalt versus iron, for similar oxygen affinities. The time constants for autoxidation at 37 degrees C were 250 and 100 h for Pe and Gc, respectively.

Animals↗

Circular dichroism spectroscopy of Lucina I hemoglobin.

The monomeric hemoglobin from the mollusc Lucina pectinata (HbI) represents an interesting model system for the study of heme-related circular dichroic (CD) bands in view of the highly asymmetric distribution of aromatic residues around the heme pocket revealed by the X-ray crystal structure. The CD spectra of both ferrous and ferric HbI derivatives exhibit negative CD bands in the Soret and ultraviolet region with an enhanced ellipticity of the heme N and L bands in the near-UV region. In contrast, the magnitude of the Cotton effect in the visible and Soret regions is comparable to that observed in other hemoproteins. The spectrum of the carbon monoxide derivative shows a surprising similarity with that observed for the soybean leghemoglobin carbon monoxide adduct. A common structural feature in the two proteins is the presence in the distal pocket of two Phe residues (B9 and B10) the aromatic rings of which are perpendicular to the heme plane.

Animals↗

Iterated sequence databank search methods.

Iterated sequence databank search methods were assessed from the viewpoint of someone with the sequence of a novel gene product wishing to find distant relatives to their protein and, with the specific searches against the PDB, also hoping to find a relative of known structure. We examined three methods in detail, spanning a range from simple pattern-matching to sophisticated weighted profiles. Rather than apply these methods 'blindly' (with default parameters) to a large number of test queries, we have concentrated on the globins, so allowing a more detailed investigation of each method on different data subsets with different parameter settings. Despite their widespread use, regular-expression matching proved to be very limited-seldom extending beyond the sub-family from which the pattern was derived. To attain any generality, the patterns had to be 'stripped-down' to include only the most highly conserved parts. The QUEST program avoided these problems by introducing a more flexible (weighted) matching. On the PDB sequences this was highly effective, missing only a few globins with probes based on each sub-family or even a single representative from each sub-family. In addition, very few false-positives were encountered, and those that did match, often only did so for a few cycles before being lost again. On the larger sequence collection, however, QUEST encountered problems with maintaining (or achieving) the alignment of the full globin family. psi-BLAST also recognised almost all the globins when matching against the PDB sequences, typically, missing three or four of the most distantly related sequences while picking-up a few false-positives. In contrast to QUEST, psi-BLAST performed very well on the larger databank, getting almost a full collection of globins although still retaining the same proportion of false-positives. SAM applied to the PDB sequences performed reasonably well with the myoglobin and hemoglobin families as probes, missing, typically several of the more difficult proteins but performed poorly with the leghemoglobin probe. Only with the full family range as a probe did it produce results comparable to psi-BLAST and QUEST. With the larger databank, SAM produced a good result but, again, this was only achieved using the full range of sequence variation with the default regulariser and use of Dirichlet mixtures completely failed in this situation.

Amino Acid Sequence↗

Crystal structure of a nonsymbiotic plant hemoglobin.

BACKGROUND: Nonsymbiotic hemoglobins (nsHbs) form a new class of plant proteins that is distinct genetically and structurally from leghemoglobins. They are found ubiquitously in plants and are expressed in low concentrations in a variety of tissues including roots and leaves. Their function involves a biochemical response to growth under limited O(2) conditions. RESULTS: The first X-ray crystal structure of a member of this class of proteins, riceHb1, has been determined to 2.4 A resolution using a combination of phasing techniques. The active site of ferric riceHb1 differs significantly from those of traditional hemoglobins and myoglobins. The proximal and distal histidine sidechains coordinate directly to the heme iron, forming a hemichrome with spectral properties similar to those of cytochrome b(5). The crystal structure also shows that riceHb1 is a dimer with a novel interface formed by close contacts between the G helix and the region between the B and C helices of the partner subunit. CONCLUSIONS: The bis-histidyl heme coordination found in riceHb1 is unusual for a protein that binds O(2) reversibly. However, the distal His73 is rapidly displaced by ferrous ligands, and the overall O(2) affinity is ultra-high (K(D) approximately 1 nM). Our crystallographic model suggests that ligand binding occurs by an upward and outward movement of the E helix, concomitant dissociation of the distal histidine, possible repacking of the CD corner and folding of the D helix. Although the functional relevance of quaternary structure in nsHbs is unclear, the role of two conserved residues in stabilizing the dimer interface has been identified.

Amino Acid Sequence↗

Kinetics and thermodynamics of oxygen and carbon monoxide binding to the T-state hemoglobin of Urechis caupo.

The tetrameric hemoglobin from Urechis caupo is nearly ideal for studying ligation to the T-state. Our previous EXAFS study had shown that the Fe is displaced 0.35 A from the mean plane of the porphyrin in the HbCO derivative. We have carried out detailed kinetic studies of oxygen and CO ligation as a function of temperature in order to characterize both the kinetics and thermodynamics of ligation in this hemoglobin. The entropy change associated with ligation essentially corresponds to simple immobilization of the ligand and is virtually the same as that we have determined for leghemoglobin, an extreme R-state-type hemoglobin. The low ligand affinities thus derive from small enthalpies of ligation, which can be correlated with the large out of plane displacement of the Fe. Only oxygen pulse measurements revealed kinetic evidence for cooperative oxygen binding, but a direct measurement of oxygen binding gave a Hill number of 1.3. An allosteric analysis gave L = 2.6 and c = 0.048 (oxygen) and c = 0.77 (CO). The higher affinity state in this weakly cooperative hemoglobin is denoted T*, and it is for this state that thermodynamic quantities have been determined. The small differences between T and T* in CO binding were nevertheless sufficient to allow us to measure by flash photolysis the rate of the T*----T conformational change in terms of an allosteric model. The half-time for this transition was calculated to be 8-14 ms at 20 degrees C.

Allosteric Regulation↗

Effects of solvent on the absorption maxima of five-coordinate heme complexes and carbon monoxide-heme complexes as models for the differential spectral properties of hemoglobins and myoglobins.

Absorption spectra were recorded for 5- and 6-coordinate model ferrous heme complexes of hindered and unhindered ligands in aqueous, and detergent solutions. Heme complexes exhibited differences in absorption maxima up to 6 nm which were correlated with the polarity of the heme environment. Increasing polarity of the solvent resulted in a general blue shift of absorption maxima of both deoxy- and (carbon monoxy)heme complexes. The differences in absorption maxima of heme complexes with different heme environments are offered as a possible explanation for some of the differences in absorption maxima among hemoproteins such as hemoglobin, myoglobin, and leghemoglobin.

Carbon Monoxide↗

Proximal influences in two-on-two globins: effect of the Ala69Ser replacement on Synechocystis sp. PCC 6803 hemoglobin.

The cyanobacterium Synechocystis sp. PCC 6803 (S6803) expresses a two-on-two globin in which His46 (distal side) and His70 (proximal) function as heme iron axial ligands. His46 can be displaced by O2, CO, and CN-, among others, whereas His70 is not labile under native conditions. The residue preceding the proximal histidine has been implicated in controlling globin axial ligand reactivity; the details of the mechanism, however, are not well understood, and little information exists for bis-histidyl hexacoordinate proteins. In many vertebrate hemoglobins and in the Synechocystis protein, the position is occupied by an alanine, whereas, in myoglobins, it is a serine involved in an intricate hydrogen-bond network. We examined the role of Ala69 in S6803 hemoglobin through the effects of an Ala --> Ser replacement. The substitution resulted in minor structural perturbations, but the response of the holoprotein to temperature-, urea-, and acid-induced denaturation was measurably affected. Enhanced three-state behavior was manifested in the decoupling of heme binding and secondary-structure formation. Urea-gradient gel experiments revealed that the stability of the apoprotein was unchanged by the replacement and that a slight alteration of the folding kinetics occurred in the holoproteins. Cyanide-binding experiments were performed to assess trans effects. The apparent rate constant for association decreased 2-fold upon Ala69Ser replacement. This deceleration was attributed to a change in the lifetime of a state containing a decoordinated His46. The results demonstrated that, as in vertebrate globins and leghemoglobin, proximal influences operate to determine fundamental dynamic and thermodynamic properties of the protein.

Alanine↗

A cyanobacterial hemoglobin with unusual ligand binding kinetics and stability properties.

The glbN gene of the cyanobacterium Nostoc commune UTEX 584 encodes a hemoprotein, named cyanoglobin, that has high oxygen affinity. The basis for the high oxygen affinity of cyanoglobin was investigated through kinetic studies that utilized stopped-flow spectrophotometry and flash photolysis. Association and dissociation rate constants were measured at 20 degrees C for oxygen, carbon monoxide, nitric oxide, and methyl and ethyl isocyanides. The association rate constants for the binding of these five ligands to cyanoglobin are the highest reported for any naturally occurring hemoglobin, suggesting an unhindered and apolar ligand binding pocket. Cyanoglobin also shows high rates of autoxidation and hemin loss, indicating that the prosthetic group is readily accessible to solvent. The ligand binding behavior of cyanoglobin was more similar to that of leghemoglobin a than to that of sperm whale myoglobin. Collectively, the data support the model of cyanoglobin function described by Hill et al. [(1996) J. Bacteriol. 178, 6587-6598], in which cyanoglobin sequesters oxygen, and presents it to, or is a part of, a terminal cytochrome oxidase complex in Nostoc commune UTEX 584 under microaerobic conditions, when nitrogen fixation, and thus ATP demand, is maximal.

Bacterial Proteins↗