Aplysia oxymyoglobin with an unusual stability property

Molecular evolution of bacterial indoleamine 2,3-dioxygenase

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that catalyze the first step in L-Trp catabolism via the kynurenine pathway. In mammals, TDO is mainly expressed in the liver and primarily supplies nicotinamide adenine dinucleotide (NAD(+)). TDO is widely distributed from mammals to bacteria. Active IDO enzymes have been reported only in vertebrates and fungi. In mammals, IDO activity plays a significant role in the immune system while in fungal species, IDO is constitutively expressed and supplies NAD(+), like mammalian TDO. A search of genomic databases reveals that some bacterial species also have a putative IDO gene. A phylogenetic analysis clustered bacterial IDOs into two groups, group I or group II bacterial IDOs. The catalytic efficiencies of group I bacterial IDOs were very low and they are suspected not to contribute significantly to L-Trp metabolism. The bacterial species bearing the group I bacterial IDO are scattered across a few phyla and no phylogenetically close relationship is observed between them. This suggests that the group I bacterial IDOs might be acquired by horizontal gene transmission that occurred in each lineage independently. In contrast, group II bacterial IDOs showed rather high catalytic efficiency. Particularly, the enzymatic characteristics (K(m), V(max) and inhibitor selectivity) of the Gemmatimonas aurantiaca IDO are comparable to those of mammalian IDO1, although comparison of the IDO sequences does not suggest a close evolutionary relationship. In several bacteria, TDO and the kynureninase gene (kynU) are clustered on their chromosome suggesting that these genes could be transcribed in an operon. Interestingly, G. aurantiaca has no TDO, and the IDO is clustered with kynU on its chromosome. Although the G. aurantiaca also has NadA and NadB to synthesize a quinolinic acid (a precursor of NAD(+)) via the aspartate pathway, the high activity of the G. aurantiaca IDO flanking the kynU gene suggests its IDO has a function similar to eukaryotic enzymes.

Structure-Function Relationships in Unusual Nonvertebrate Globins

Based on the literature and our own results, this review summarizes the most recent state of nonvertebrate myoglobin (Mb) and hemoglobin (Hb) research, not as a general survey of the subject but as a case study. For this purpose, we have selected here four typical globins to discuss their unique structures and properties in detail. These include Aplysia myoglobin, which served as a prototype for the unusual globins lacking the distal histidine residue; midge larval hemoglobin showing a high degree of polymorphism; Tetrahymena hemoglobin evolved with a truncated structure; and yeast flavohemoglobin carrying an enigmatic two-domain structure. These proteins are not grouped by any common features other than the fact they have globin domains and heme groups. As a matter of course, various biochemical functions other than the conventional oxygen transport or storage have been proposed so far to these primitive or ancient hemoglobins or myoglobins, but the precise in vivo activity is still unclear. In this review, special emphasis is placed on the stability properties of the heme-bound O2. Whatever the possible roles of nonvertebrate myoglobins and hemoglobins may be (or might have been), the binding of molecular oxygen to iron(II) must be the primary event to manifest their physiological functions in vivo. However, the reversible and stable binding of O2 to iron(II) is not a simple process, since the oxygenated form of Mb or Hb is oxidized easily to its ferric met-form with the generation of superoxide anion. The metmyoglobin or methemoglobin thus produced cannot bind molecular oxygen and is therefore physiologically inactive. In this respect, protozoan ciliate myoglobin and yeast flavohemoglobin are of particular interest in their very unique structures. Indeed, both proteins have been found to have completely different strategies for overcoming many difficulties in the reversible and stable binding of molecular oxygen, as opposed to the irreversible oxidation of heme iron(II). Such comparative studies of the stability of MbO2 or HbO2 are of primary importance, not only for a full understanding of the globin evolution, but also for planning new molecular designs for synthetic oxygen carriers that may be able to function in aqueous solution and at physiological temperature.

Preparation of artificial 2-, 3-, 4- and 8-domain myoglobins and comparison of their autoxidation rates

Although most hemoglobins and myoglobins consist of 15-kDa single-domain subunits, structurally unusual hemoglobins, such as Artemia 9-domain and Barbatia 2-domain hemoglobins, occur naturally in several invertebrates. These hemoglobins appear to be the result of gene duplication and fusion. Using cDNA coding for the open reading frame of Aplysia kurodai myoglobin, artificial cDNA inserts corresponding to contiguous dimer, trimer, tetramer and octamer myoglobins (2-, 3-, 4- and 8-domain myoglobins) were prepared and cloned into pMAL or pQE plasmids. These artificial myoglobins and wild-type single-domain myoglobins were successfully expressed in Escherichia coli in the heme-attached, oxygenated form. Myoglobin was purified partially by ammonium sulfate fractionation and gel filtration, and autoxidation rates were examined. The autoxidation rates of recombinant wild-type myoglobins with MBP or hexameric His tag were comparable to those of native myoglobin, suggesting that the recombinant proteins appear to be properly folded and that the N-terminal MBP or His tag does not have an affect on the rate. On the other hand, the rates were significantly decreased in the 2- and 3-domain myoglobins (50% and 30% of the single-domain myoglobins, respectively). The rates for 4- and 8-domain myoglobins were similar to those for 3-domain myoglobin. These results indicate that the artificial poly-domain structure of myoglobin is more stable than the usual single-domain myoglobin from the viewpoint of storage of bound dioxygen.

Evidence of met-form myoglobin from Theliostyla albicilla radular muscle

Gastropod mollusc myoglobins provide interesting clues to the evolution of this family of proteins. In addition to conventional monomeric myoglobins, this group also has dimeric and unusual indoleamine dioxygenase-like myoglobins. We isolated myoglobin from the radular muscle of living gastropod mollusc Theliostyla albicilla. The myoglobin appeared to be present in an oxidized met-form, a physiologically inactive form that is not capable of binding oxygen. Under the same extraction conditions, myoglobins mainly of the physiologically active oxy-form have been isolated from other molluscs. The complete amino acid sequence of 157 residues of Theliostyla myoglobin shows that it has a long N-terminal extension of seven residues and contains three functional key residues: CD1-Phe, E7-His, and F8-His. The metmyoglobin can easily be reduced to a ferrous state with Na(2)S(2)O(4). The autoxidation rate of the oxy-form was comparable to other molluscan myoglobins over a wide pH range, and Theliostyla myoglobin was shown to be stable as an oxygen-binding protein. Thus, the predominantly met-form of myoglobin in Theliostyla can be attributed to the incomplete functioning of the myoglobin reduction system in the radular muscle. Although the function of Theliostyla myoglobin is unclear, it may be a scavenger of H(2)O(2).

Amino acid sequence, spectral, oxygen-binding, and autoxidation properties of indoleamine dioxygenase-like myoglobin from the gastropod mollusc Turbo cornutus

Myoglobin was isolated from the radular muscle of the archaeogastropod mollusc Turbo cornutus (Turbinidae). This myoglobin is a monomer carrying one protoheme group; the molecular mass was estimated by SDS-PAGE to be about 40 kDa, 2.5 times larger than that of usual myoglobin. The cDNA-derived amino acid sequence of 375 residues was determined, of which 327 residues were identified directly by chemical sequencing of internal peptides. The amino acid sequence of Turbo myoglobin showed no significant homology with any other usual 16-kDa globins, but showed 36% identity with the myoglobin from Sulculus diversicolor (Haliotiidae) and 27% identity with human indoleamine 2,3-dioxygenase, a tryptophan-degrading enzyme containing heme. Thus, the Turbo myoglobin can be counted among the myoglobins which evolved from the same ancestor as that of indoleamine 2,3-dioxygenase. The absorbance ratio of gamma to CT maximum (gamma/CT) of Turbo metmyoglobin was 17.8, indicating that this myoglobin probably possesses a histidine residue near the sixth coordination position of heme iron. The Turbo myoglobin binds oxygen reversibly. Its oxygen equilibrium properties are similar to those of Sulculus myoglobin, giving P50 = 3.5 mm Hg at pH 7.4 and 20 degrees C. The pH dependence of autoxidation of Turbo oxymyoglobin was quite different from that of mammalian myoglobin, suggesting a unique protein folding around the heme cavity of Turbo myoglobin. A kinetic analysis of autoxidation indicates that the amino acid residue with pKa = 5.4 is involved in the reaction. The autoxidation reaction was enhanced markedly at pH 7.6, but not at pH 5.5 and 6.3 in the presence of tryptophan. We suggest that a noncatalytic binding site for tryptophan, in which several dissociation groups with pKa > or = 7.6 are involved, remains in Turbo myoglobin as a relic of molecular evolution.

A myoglobin evolved from indoleamine 2,3-dioxygenase, a tryptophan-degrading enzyme

The distribution, isolation, spectral and oxygen-binding properties, stability of ferrous state (autoxidation), amino acid sequence and gene structure of indoleamine 2,3-dioxygenase (IDO)-like myoglobins are summarized, and their evolution is discussed. Although it has long been thought that all hemoglobins and myoglobins have evolved from a common ancestral gene encoding a 14-16 kDa polypeptide, the discovery of IDO-like myoglobin from several gastropod molluscs clearly indicates that there was an alternative pathway for myoglobin evolution.

Amino-acid sequence of the cooperative dimeric myoglobin from the radular muscles of the marine gastropod Nassa mutabilis

The complete amino-acid sequence of the dimeric and cooperative myoglobin from the radular muscles of Nassa mutabilis, a common edible gastropod mollusc on the Italian coast, has been determined. The molecule is a homodimer. The monomer is composed of 147 amino-acid residues, with a molecular mass of 15,760 Da. Its sequence is homologous with those of the dimeric myoglobins of the gastropod molluscs of the Prosobranchia subclass Busycon canaliculatum (63% conserved residues) and Cerithidea rhizophorarum (46% conserved residues). The rate of autoxidation to met-myoglobin of N. mutabilis oxymyoglobin at 25 degrees C is strongly pH-dependent with relative minimal rate values in the pH range 7 to 8.

The Soret magnetic circular dichroism of ferric high-spin myoglobins. A probe for the distal histidine residue

To find a simple criterion for the presence of the distal (E7) histidine residue in myoglobins and hemoglobins, the Soret magnetic-circular-dichroic spectra were examined for ferric metmyoglobins from various species. A distinct and symmetric dispersion-type curve was obtained for myoglobins containing the distal histidine, whereas a relatively weak and unsymmetric pattern was observed for myoglobins lacking this residue, such as those from three kinds of gastropodic sea molluscs, a shark and the African elephant. The magnetic-circular-dichroic spectra obtained would thus be a direct reflection of the presence or absence of a water molecule at the sixth coordinate position of the heme iron(III), this axial water ligand being stabilized by hydrogen-bond formation to the distal histidine residue. On the basis of these Soret magnetic-circular-dichroic signals, we also examined the structure of a protozoan myoglobin (or a monomeric hemoglobin) from Paramecium caudatum of particular interest for the evolution of these proteins from protozoa to higher animals.

Stability properties of Aplysia oxymyoglobin: effect of esterification of the heme propionates

When compared with sperm whale MbO2 as a reference Aplysia MbO2 is extremely susceptible to autoxidation, and its pH dependence for the reaction is also unusual. Kinetic and thermodynamic analyses have shown that two types of carboxyl group with pKa = 4.3 and 6.1 at 25 degrees C are involved in the stability property of Aplysia MbO2, the protonation of these groups being responsible for an increase in its autoxidation rate in the acidic pH range. Since protoheme has two carboxyl groups of the propionic acid side-chains, we have prepared Aplysia myoglobin containing the dimethylester of protohemin. The autoxidation of this derivative was found to be described by the involvement of only one type of carboxyl group with pKa = 4.4. A possible candidate for the protein residue was therefore discussed on the basis of the known amino acid sequences of three Aplysia myoglobins: it is suggested that Glu-94, next to the proximal His-95, is the most likely candidate.

Protozoan myoglobin from Paramecium caudatum. Its autoxidation reaction and hemichrome formation

Native oxymyoglobin (MbO2) was isolated directly from the cells of Paramecium caudatum with complete separation from metmyoglobin (metMb) on a DEAE-cellulose column. It was examined for its spectral and stability properties. When compared with sperm whale MbO2 used as a reference, Paramecium MbO2 was found to be much more susceptible to autoxidation over a wide range of pH (4-11) in 0.1 M buffer at 25 degrees C. Kinetic analysis has revealed that a proton-catalyzed displacement of O2- from MbO2 by an entering water molecule can play a dominant role in the autoxidation reaction of Paramecium MbO2 to metMb, as in the case of sperm whale MbO2 involving the distal histidine as its catalytic residue. At pH values higher than 9.5, however, Paramecium MbO2 was found to be oxidized to yield a hemichrome. The spontaneous formation of hemichromes is at variance with the other known myoglobins and is therefore discussed in relation to the unusual amino acid sequence of Paramecium myoglobin having a large number of deletion.

Amino acid sequence of myoglobin from the mollusc Bursatella leachii

The complete amino acid sequence of myoglobin from the triturative stomach of gastropodic mollusc Bursatella leachii has been determined. It is composed of 146 amino acid residues, is acetylated at the N-terminus, and contains a single histidine residue at position 95 which corresponds to the heme-binding proximal histidine. The E7 distal histidine, which is conserved widely in myoglobins and hemoglobins, is replaced by valine in Bursatella myoglobin. The amino acid sequence of Bursatella myoglobin shows strong homology (73-84%) with those of Aplysia and Dolabella myoglobins.

The ear-shell (Sulculus diversicolor aquatilis) myoglobin is composed of an unusual 39 kDA polypeptide chain

An unusual myoglobin was isolated from the buccal mass of the ear-shell Sulculus diversicolor aquatilis. The myoglobin consists of a 39 kDa polypeptide chain which is about double the size of the usual myoglobin subunit, contains one heme per molecule, and has an unusual spectral property ion the oxy-form. On the basis of these properties and partial amino acid sequencing, we propose that Sulculus myoglobin has a didomain structure, and that one of the two domains does not function as an oxygen-binding domain. So far, a myoglobin of this type has not been described in molluscs.

Spectral properties unique to the myoglobins lacking the usual distal histidine residue

Myoglobins can be divided into two groups. One group contains the usual myoglobins that have histidine at the distal (E7) position, and the other contains a few, but interesting myoglobins that lack the usual distal histidine residue. Spectroscopic examinations have shown that there is a remarkable difference in the Soret band between the two types of myoglobin, and an absorbance ratio of the Soret peak of the acidic met-form to that of the oxy-form seems to be very useful as a simple criterion for predicting whether or not a myoglobin has the usual distal histidine residue.

Aplysia oxymyoglobin with an unusual stability property: involvement of two kinds of carboxyl groups

Unlike mammalian oxymyoglobins, Aplysia MbO2 is extremely susceptible to autoxidation, and its pH dependence is also unusual. Kinetic formulation has revealed that two kinds of dissociable group with pK1 = 4.3 and pK2 = 6.1, respectively, at 25 degrees C are involved in the stability property of Aplysia MbO2. In order to characterize thermodynamically these dissociation processes involved, the effect of temperature on K1 and K2 was studied by analyzing the pH dependence for the autoxidation rate of Aplysia MbO2 in 0.1 M buffer over the pH range of 4-11, and at 15, 25 and 35 degrees C. The resulting thermodynamic parameters for each group were both those to be expected for the ionization of a carboxyl group; the delta H degrees value being numerically much less than 1 kcal.mol-1, or zero in practice, but being associated with a large negative value of delta S degrees of the order of -20 cal.mol-1.K-1. Taking into account the fact that Aplysia myoglobin contains only a single histidine residue corresponding to the heme-binding proximal one, we can unequivocally conclude that the two kinds of the dissociable group involved in the unusual stability of Aplysia MbO2 must both be carboxyl groups, the protonation of these groups being responsible for an increase in its autoxidation rate in the acidic pH range.

Forces between proteins and model polypeptides adsorbed on mica surfaces

The forces of interaction between proteins adsorbed onto mica have been measured as a function of the distance of separation between the two mica surfaces in aqueous solutions. The results for three proteins, myelin basic protein, concanavalin A and cytochrome c, are presented together with the results for a model basic protein, poly(L-lysine). With the exception of cytochrome c at large separations, the forces of interaction are due to charges on the protein surfaces and may be fitted closely to theoretical predictions. For cytochrome c, however, no long-range electrical repulsion is observed, indicating that the negatively charged mica surface has been neutralised by the adsorption of the positively charged protein. At short surface separations, an attraction between the protein surfaces was noted. For concanavalin A, a weak attraction was observed in the presence of calcium and manganese ions only. For poly(L-lysine) and cytochrome c the attraction can be explained simply in terms of van der Waals interactions between the proteins. However, for myelin basic protein the observed attraction was an order of magnitude larger than that predicted by van der Waals theory. We believe that this additional attraction may be due to hydrophobic interactions between the adsorbed myelin basic protein molecules.

Autoxidation of oxymyoglobin with the distal (E7) glutamine

We reported previously that the distal(E7) histidine is replaced by glutamine in myoglobin from the shark, Galeorhinus japonicus. The amino-acid sequence of myoglobin from another shark, Heterodontus japonicus, has been determined. The myoglobin is composed of 148 residues, is acetylated at the N-terminus, and contains the distal(E7) histidine at position 59. Although the sequence homologies between G. japonicus, H. japonicus, and sperm-whale myoglobins were about 40-55%, their hydropathy profiles were very similar, indicating that they have a similar geometry in their globin folding. The autoxidation rates of the two shark oxymyoglobins were examined in 0.1 M buffer at 25 degrees C over pH range 4.5-11.5. The pH dependence for the autoxidation of H. japonicus myoglobin was very similar to that of sperm-whale myoglobin, although the rate was about 10-times higher over the pH range examined. In both myoglobins, autoxidation was largely accelerated by H+. On the other hand, the pH dependence of G. japonicus myoglobin, which has the distal glutamine in the place of histidine, was quite different from those of sperm-whale and H. japonicus myoglobins. One of the most remarkable features is the fact that the autoxidation rate is not enhanced with an increase in the concentration of H+ in the acidic range of pH, where the autoxidation of sperm-whale and H. japonicus myoglobins is most accelerated. This finding suggests that the distal(E7) histidine participates in the autoxidation reaction as a catalytic residue facilitating the movement of a catalytic proton.

Stability properties of oxymyoglobin from chicken gizzard smooth muscle

1. Oxymyoglobin (MbO2) was isolated directly from the smooth muscle of chicken gizzard and was examined for its spectral and stability properties. 2. When compared with sperm whale MbO2 as a reference, chicken gizzard MbO2 was found to be much more susceptible to autoxidation. Its pH-dependence was therefore analyzed in terms of an "acid-catalyzed three-state model". 3. The complete amino acid sequence of the myoglobin was also determined. Its hydropathy profile revealed that the region corresponding to the distal side of the heme iron appears to be less hydrophobic.

Aplysia myoglobins with an unusual amino acid sequence

The complete amino acid sequence of the myoglobin from Aplysia juliana, a species distributed world-wide, has been determined and compared with the sequence of the myoglobin of Aplysia limacina, a Mediterranean species, and of Aplysia kurodai, a Japanese and Asian species. Unlike mammalian myoglobins, Aplysia myoglobins contain only a single histidine residue, lacking the distal one, the homology being 76% between A. juliana and A. limacina, 74% between A. juliana and A. kurodai, and 83% between A. limacina and A. kurodai. The hydropathy profiles of the Aplysia myoglobins are very similar, but completely different from that of sperm whale myoglobin, taken as the reference.