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PubMedDate not supplied

Primary sequence of a dimeric bacterial haemoglobin from Vitreoscilla.

Vitreoscilla, a filamentous bacterium in the Beggiatoa family, synthesizes a soluble haem-protein which has two identical subunits of relative molecular mass 15,775 and two b haems per molecule. It is synthesized in relatively large quantities when the organism, a strict aerobe, is grown under hypoxic conditions. It forms a relatively stable oxygenated form which is spectrally similar to oxymyoglobin (oxyHb) and oxyhaemoglobin (oxyHb). The amino acid sequence of this protein has been determined and aligned to fit the helical regions of several animal and plant globins. This alignment is consistent with its being a structural homologue of the eucaryotic haemoglobins although it diverged from the others in the N-terminal region and may lack an A-helix. It showed the maximum sequence homology (24%) with lupin leghaemoglobin (Lb). Vitreoscilla Hb is the first bacterial haemoglobin to be sequenced. It may function to enable the organism to survive in oxygen-limited environments by acting as an oxygen storage-trap or to facilitate oxygen diffusion.

Amino Acid Sequence↗
PubMed1977

Electron-paramagnetic-resonance studies of leghaemoglobins from soya-bean and cowpea root nodules. Identification of nitrosyl-leghaemoglobin in crude leghaemoglobin preparations.

1. Leghaemoglobins from soya-bean (Glycine max) and cowpea (Vigna unguiculata) root nodules were purified by chromatography on DEAE-cellulose phosphate columns at pH8.0 and pH5.8, to avoid the relatively low pH (5.2) commonly used to purify these proteins. 2. E.p.r. (electron-paramagnetic-resonance) spectra of the fluoride, azide, hydroxide and cyanide complexes of these ferric leghaemoglobins were very similar to the spectra of the corresponding myoglobin derivatives, indicating that the immediate environment of the iron in leghaemoglobin and myoglobin is similar, an imidazole moiety of histidine being the proximal ligand to the haem iron [cf. Appleby, Blumberg, Peisach, Wittenberg & Wittenberg (1976) J. Biol. Chem.251, 6090-6096]. 3. E.p.r. spectra of the acid-metleghaemoglobins showed prominent high-spin features very near g=6 and g=2 and, unlike myoglobin, small low-spin absorptions near g=2.26, 2.72 and 3.14. The width of the g=6 absorption derivative at 10-20K was about 4-4.5mT, similar to the value for acid-methaemoglobin. In contrast, a recently published (Appleby et al., 1976) spectrum of acid-metleghaemoglobin a had less high-spin character and a much broader absorption derivative around g=6. 4. E.p.r. spectra of ferric leghaemoglobin nicotinate and imidazole complexes suggest that the low-spin absorption near g=3.14 can be attributed to a trace of ferric leghaemoglobin nicotinate, and those near g=2.26 and 2.72 are from an endogenous dihistidyl haemichrome. 5. A large e.p.r. signal at g=2 in all samples of crude leghaemoglobin was shown to be from nitrosyl-leghaemoglobin. A soya-bean sample contained 27+/-3% of the latter. A previously unidentified form of soya-bean ferrous leghaemoglobin a was shown to be its nitrosyl derivative. If this is not an artifact, and occurs in the root nodule, the nitrosyl radical may interfere with the function of leghaemoglobin.

Chromatography, DEAE-Cellulose↗
PubMed1978

Oxidation of glycine by Phaseolus leghaemoglobin with associated catabolic reactions at the haem.

Leghaemoglobin from the root nodules of kidney bean (Phaseolus vulgaris) reacts in alkaline glycine solutions as a glycine oxidase in a reaction that may also be regarded as a coupled oxidation. Leghaemoglobin is reduced to the ferrous form by glycinate, the oxygen complex is formed, and finally the haem is attacked to yield a green reaction product. Glycine is simultaneously oxidized to glyoxylate, and hydrogen peroxide is generated. The initial velocity of the formation of the green product is proportional to the concentrations of leghaemoglobin and glycine, and the optimum pH for the reaction is 10.2. The green product is not formed if carbon monoxide, azide of imidazole is bound to the haem, whereas oxidation of glycine to glyoxylate is not inhibited by azide and not essentially by carbon monoxide. Haem breakdown is activated by digestion of leghaemoglobin by carboxypeptidase, and partly inhibited by catalase and superoxide dismutase.

Carboxypeptidases↗
PubMed1978

Bile-pigment formation from different leghaemoglobins. Methine-bridge specificity of coupled oxidation.

The coupled oxidation of leghaemoglobins with O(2) and ascorbate yielded oxyleghaemoglobin in the first reaction step, and the second step was the degradation of haem characterized by an A(675) increase. Leghaemoglobins were degraded to biliverdin isomers specifically, depending on the structure of the protein. The main leghaemoglobin components of Glycine (soya bean) and Phaseolus (kidney bean) were degraded to biliverdin mixtures containing about 50% of the beta-form, about 30% of the alpha-form and about 20% of the delta-isomer, whereas the leghaemoglobin I components of Vicia (broad bean) and Pisum (pea) were degraded almost exclusively to the beta-isomer, with traces of the alpha-isomer. The amino acid sequences of Glycine and Phaseolus leghaemoglobins resemble each other, as do those of Vicia and Pisum. The site specificity of bile-pigment formation from leghaemoglobins can be tentatively explained by specific differences in the amino acid sequences at those regions of the polypeptide chain that are in the vicinity of the appropriate methine bridges. The ligand-binding site in different leghaemoglobins may be outlined on the basis of the present results, supposing that the haem is degraded when a reduction product of haem-bound O(2) reacts with a methine bridge of the haem, and that the bridge specificity is regulated by hindering amino acid residues that determine the location of the bound O(2). The residue phenylalanine-CD1 appears to be further away from the haem plane or in a markedly more flexible position in leghaemoglobins than in mammalian globins. The haem-bound oxygen atom B, in Fe-O(A)-O(B), seems to be free to rotate in all directions except that of the gamma-bridge in Glycine and Phaseolus leghaemoglobins, but its position in Vicia and Pisum leghaemoglobin I might be restricted to the direction of the beta-methine bridge.

Bile Pigments↗
PubMed1992

Direct detection of a globin-derived radical in leghaemoglobin treated with peroxides.

The root nodules of leguminous plants contain an oxygen-carrying protein which is somewhat similar to myoglobin. Reaction of the Fe3+ form of this protein (metleghaemoglobin; MetLb) with H2O2 is known to generate a ferryl [iron(IV)-oxo] species. This intermediate, which is analogous to Compound II of peroxidases and ferryl myoglobin, is one oxidizing equivalent above the initial level. In the present study it is shown that the second oxidizing equivalent from the peroxide is rapidly transferred into the surrounding protein, generating a protein radical which has been detected by e.p.r. spectroscopy; this reaction is analogous to that observed with metmyoglobin. An identical protein-derived species is observed with all three forms of MetLb tested (a, c1, c3) and with a number of other hydroperoxides and two-electron oxidants. This latter result, the observation that the concentration of this species is not affected by certain hydroxyl-radical scavengers, and the loss of the radical when the oxy or deoxy forms are used, demonstrate that this species is formed by electron transfer within the protein rather than by the generation and subsequent reaction of hydroxyl radicals (and related species from the other hydroperoxides). The e.p.r. signal of this species, which decays rapidly with a half-life of approx. 40 s, is consistent with the formation of a sterically constrained tyrosine-derived phenoxyl radical; protein-iodination experiments lend support to this assignment. Reaction between the radical and a number of other compounds has been observed, demonstrating that it is at least partially exposed on the surface of the protein. Analysis of the protein structure suggest that the radical may be centred on a tyrosine residue present at position 132 in the protein; this residue is close to the haem prosthetic group, which would facilitate rapid electron transfer.

Electron Spin Resonance Spectroscopy↗
PubMed1993

Glutathione-dependent conversion of ferryl leghaemoglobin into the ferric form: a potential protective process in soybean (Glycine max) root nodules.

GSH is able to reduce soybean (Glycine max) ferryl-leghaemoglobin [Lb(IV)] formed by the reaction of ferric or ferrous Lb with H2O2; in both cases, ferric Lb is obtained and GSH is incapable of reducing ferric Lb to ferrous Lb. Furthermore, the addition of GSH before H2O2 to ferric Lb prevents side reactions which lead to a species whose spectrum differs markedly from that of Lb(IV). These reactions are likely to occur in vivo, as high GSH concentrations have been detected in soybean nodules. The GSH-dependent reduction of Lb(IV) is associated with the oxidation of GSH to GSSG. E.s.r. experiments show that the glutathione thiyl radical (GS.) is formed during this reaction. In the case of ferric Lb, both ferryl Lb and a globin-derived radical previously described appear to be involved in the formation of GS.. Both of these processes may be protective and can help account for the exclusive presence of ferrous (oxygenated or not) Lb in functioning nodules.

Electron Spin Resonance Spectroscopy↗
PubMed1998

Bacterial expression and spectroscopic characterization of soybean leghaemoglobin a.

A gene encoding leghaemoglobin a from soybean has been constructed and the soluble recombinant protein expressed in E. coli. The integrity of the recombinant protein has been assessed by a range of spectroscopic techniques. Electrospray mass spectrometry of the protein indicates that the molecular mass of the protein corresponds to the predicted amino acid sequence. Circular dichroism spectra of the ferric derivative and UV-visible spectra of various ferric and ferrous derivatives (pH 6.99, mu = 0.10 M, 25.0 degrees C) are consistent with published data for the wild-type protein. For the ferric derivative, UV-visible (298 and 77 K) and EPR (10 K) spectra indicate the existence of a thermal equilibrium between high- and low-spin forms. Titration of the protein (0.10 M NaCl, mu = 0.10 M, 25.0 degrees C) between pHs 6.68 and 10.35 indicate formation (pKa = 8.3+/-0.03) of a 6-coordinate, hydroxide-bound form of the protein at high pH. All of the above data are consistent with the behaviour of the wild-type protein.

Amino Acid Sequence↗
PubMed2000

Investigation of the haem-nicotinate interaction in leghaemoglobin. Role of hydrogen bonding.

A strategic assessment of the contributions of two active-site hydrogen bonds in the binding of nicotinate to recombinant ferric soybean leghaemoglobin a (rLb) was carried out by mutagenic replacement of the hydrogen-bonding residues (H61A and Y30A variants) and by complementary chemical substitution of the carboxylate functionality on the nicotinate ligand. Dissociation constants, Kd (pH 5.5, mu = 0.10 M, 25.0 +/- 0.1 degrees C), for binding of nicotinate to ferric rLb, H61A and Y30A were 1.4 +/- 0.3 microM, 19 +/- 1 microM and 11 +/- 1 microM, respectively; dissociation constants for binding of nicotinamide were, respectively, 38 +/- 1 mM, 50 +/- 2 mM and 12 +/- 1 mM, and for binding of pyridine were 260 +/- 50 microM, 4.5 +/- 0.5 microM and 66 +/- 8 microM, respectively. Binding of cyanide and azide to the H61A and Y30A variants was unaffected by the mutations. The pH-dependence of nicotinate binding for rLb and Y30A was consistent with a single titration process (pKa values 6.9 +/- 0.1 and 6.7 +/- 0.2, respectively); binding of nicotinate to H61A was independent of pH. Reduction potentials for the rLb and rLb-nicotinate derivatives were 29 +/- 2 mV (pH 5.40, 25.0 degrees C, mu = 0.10 M) and - 65 +/- 2 mV (pH 5.42, 25.0 degrees C, mu = 0.10 M), respectively. The experiments provide a quantitative assessment of the role of individual hydrogen bonds in the binding process, together with a definitive determination of the pKa of His61 and unambiguous evidence that titration of His61 controls binding in the neutral to alkaline region.

Base Sequence↗
PubMed1996

Foldons, protein structural modules, and exons.

Foldons, which are kinetically competent, quasi-independently folding units of a protein, may be defined using energy landscape analysis. Foldons can be identified by maxima in a scan of the ratio of a contiguous segment's energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of minimal frustration. The predicted foldons are compared with the exons and structural modules for 16 of the 30 proteins studied. Statistical analysis indicates a strong correlation between the energetically determined foldons and Go's geometrically defined structural modules, but there are marked sequence-dependent effects. There is only a weak correlation of foldons to exons. For gammaII-crystallin, myoglobin, barnase, alpha-lactalbumin, and cytochrome c the foldons and some noncontiguous clusters of foldons compare well with intermediates observed in experiment.

Algorithms↗
PubMed2004

Correlation of endogenous free polyamine levels with root nodule senescence in different genotypes in Vigna mungo L.

Endogenous free polyamines, nitrogenase (EC 1.1.8.6.1, acetylene reduction), and leghaemoglobin (pyridine-hemochrome assay) levels were compared among five genotypes of developing Vigna root nodules grown under field conditions. Nitrogenase activity and leghaemoglobin level attained a peak at the flowering stage and gradually declined thereafter. Individual and total polyamine also followed the same pattern. Ranking on the basis of legume yield and other morphometric attributes was PDU-2 > UH-28 > UH-82 > T-9 > Sardhomash. Except spermine, the levels of putrescine, spermidine, and total polyamine showed significant differences (p<0.05) amongst the genotypes, particularly from flowering to mid-pod development stage. Genotype, development stage, and their interaction between the two had significant (p<0.01) effects on individual as well as total polyamines. Moreover, significant high linear correlations were found between total free polyamine and putrescine with conventional nodule senescence marker like nitrogenase (R2 = 0.94 and R2 = 0.92, respectively). Putrescine had an overall positive correlation with high legume yield. The results strongly suggest a relationship between polyamine and nodule senescence. Endogenous free polyamine and putrescine may be considered as genotypic markers for nodule senescence in field grown V. mungo. It is suggested that the flowering stage is more suitable for selection.

Fabaceae↗
PubMed2004

The radical and redox chemistry of myoglobin and hemoglobin: from in vitro studies to human pathology.

Recent research has shown that myoglobin and hemoglobin play important roles in the pathology of certain disease states, such as renal dysfunction following rhabdomyolysis and vasospasm following subarachnoid hemorrhages. These pathologies are linked to the interaction of peroxides with heme proteins to initiate oxidative reactions, including generation of powerful vasoactive molecules (the isoprostanes) from free and membrane- bound lipids. This review focuses on the peroxide-induced formation of radicals, their assignment to specific protein residues, and the pseudoperoxidase and prooxidant activities of the heme proteins. The discovery of heme to protein cross-linked forms of myoglobin and hemoglobin in vivo, definitive markers of the participation of these heme proteins in oxidative reactions, and the recent results from heme oxygenase knockout/knockin animal model studies, indicate that higher oxidation states (ferryl) of heme proteins and their associated radicals play a major role in the mechanisms of pathology.

Animals↗
PubMed1999

Positional statistical significance in sequence alignment.

Beginning with the concept of near-optimal sequence alignments, we can assign a probability that each element in one sequence is paired in an alignment with each element in another sequence. This involves a sum over the set of all possible pairwise alignments. The method employs a designed hidden Markov model (HMM) and the rigorous forward and forward-backward algorithms of Rabiner. The approach can use any standard sequence-element-to-element probabilistic similarity measures and affine gap penalty functions. This allows the positional alignment statistical significance to be obtained as a function of such variables. A measure of the probabilistic relationship between any single sequence and a set of sequences can be directly obtained. In addition, the employed HMM with the Viterbi algorithm provides a simple link to the standard dynamic programming optimal alignment algorithms.

Adenylate Kinase↗
PubMed1998

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.

MOTIVATION: The discovery of motifs in biological sequences is an important problem. RESULTS: This paper presents a new algorithm for the discovery of rigid patterns (motifs) in biological sequences. Our method is combinatorial in nature and able to produce all patterns that appear in at least a (user-defined) minimum number of sequences, yet it manages to be very efficient by avoiding the enumeration of the entire pattern space. Furthermore, the reported patterns are maximal: any reported pattern cannot be made more specific and still keep on appearing at the exact same positions within the input sequences. The effectiveness of the proposed approach is showcased on a number of test cases which aim to: (i) validate the approach through the discovery of previously reported patterns; (ii) demonstrate the capability to identify automatically highly selective patterns particular to the sequences under consideration. Finally, experimental analysis indicates that the algorithm is output sensitive, i.e. its running time is quasi-linear to the size of the generated output.

Algorithms↗
PubMed2001

Abscisic acid induces a decline in nitrogen fixation that involves leghaemoglobin, but is independent of sucrose synthase activity.

Sucrose synthase (SS) activity has been suggested to be a key point of regulation in nodule metabolism since this enzyme is down-regulated in response to different stresses which lead to decreased nitrogen fixation. In soybean, a dramatic decline of SS transcripts has been observed within 1 d from the onset of drought. Such a quick response suggests mediation by a signal transduction molecule. Abscisic acid (ABA) is a likely candidate to act as such a molecule as it mediates in a significant number of plant responses to environmental constraints. The hypothesis of ABA controlling nodule metabolism was approached in this work by assessing nodule responses to exogenous ABA supply in pea. Under the experimental conditions, ABA did not affect plant biomass, nodule numbers or dry weight. However, nitrogen fixation rate was reduced by 70% within 5 d and by 80% after 9 d leading to a reduced plant organic nitrogen content. Leghaemoglobin (Lb) content declined in parallel with that of nitrogen fixation. SS activity, however, was not affected by ABA treatment, and neither were the activities of the enzymes aspartate amino transferase, alkaline invertase, malate dehydrogenase, glutamate synthase, uridine diphosphoglucose pyrophosphorylase, isocitrate dehydrogenase, and glutamine synthetase. Nodule bacteroid-soluble protein content was reduced in nodules only after 9 d of ABA treatment. These results do not support the hypothesis that ABA directly regulates SS activity. However, they do suggest the occurrence of at least two different control pathways in nodules under environmental constraints, which include ABA being involved in a Lb/oxygen-related control of nitrogen fixation.

Abscisic Acid↗
PubMed2002

Short-term metabolic responses of soybean root nodules to nitrate.

Soybean (Glycine max L. Merr.) plants exposed to 10 mM KNO(3) for a 4 d period were used to test the correlation between nitrogenase activity, gene expression and sucrose metabolism. Nitrate caused the down-regulation of sucrose synthase (SS) transcripts within 1 d, although a decline in nodule SS activity and an increase in nodule sucrose content only occurred after 3-4 d. In a second experiment, plants were exposed to (15)N-labelled nitrate for 48 h to determine the time period during which nitrate was taken up, and to relate this to the decline in apparent nitrogenase activity (H(2) production in air) and the reduction in SS gene transcript levels. The peak of nitrate uptake appeared to be between 8 h and 14 h whilst apparent nitrogenase activity began to decline at about 17.5 h. The SS mRNA signal declined markedly between 14 h and 24 h. The correlative association of these factors is clear. However, SS activity per se does not appear to be related to the initial decline in apparent nitrogenase activity as a result of nitrate uptake. These findings, therefore, do not support the hypothesis that the regulation of nodule function is mediated by the regulation of SS activity.

Blotting, Northern↗
PubMed2003

Leghaemoglobin oxygenation gradients in alfalfa and yellow sweetclover nodules.

Respiration in support of N(2) fixation by rhizobia in legume root nodules depends on an adequate supply of O(2), but excessive O(2) can damage nitrogenase, the key enzyme. The movement of O(2) into and within the nodule is driven by gradients in the concentration of O(2) or in the oxygenation of the O(2)-carrier, leghaemoglobin. Steeper gradients may increase flux to the sites of respiration, but gradients also raise the possibility of inadequate O(2) in some nodule zones and excessive O(2) in others. No detailed study of O(2) gradients in the interior of nodules has been published previously. Spectral changes in leghaemoglobin with oxygenation, previously used to measure the average O(2) status of the nodule interior, were used to map longitudinal gradients in O(2) and in respiratory capacity in the elongated nodules of alfalfa (Medicago sativa L.) and sweetclover (Melilotus officinalis L.). Variability among nodules under air in the magnitude and direction of internal O(2) gradients was seen in both species. Despite consistently higher respiratory capacity near the meristematic tip, a majority of nodules had higher O(2) towards the tip than towards the base. These results contrast with a previous report, apparently based on limited data, but they are consistent with anatomical and tracer studies showing higher gas permeability near the tip.

Algorithms↗