Unusual heme iron-lipid acyl chain coordination in Escherichia coli flavohemoglobin

Geometric isomerization of dietary monounsaturated fatty acids by a cis/trans fatty acid isomerase from Pseudomonas putida KT2440

Pseudomonas putida KT2440 encodes a defense system that rigidifies membranes by a cytochrome c-type cis/trans fatty acid isomerase (CTI). Despite its potential as an industrial biocatalyst for directly regulating the geometric isomerism of monounsaturated fatty acids, its original catalytic and structural properties have remained elusive. In this study, the catalytic nature of wild-type CTI purified P. putida KT2440 against dietary monounsaturated fatty acids was investigated. It showed substrate preference for palmitoleic acid (C16:1, cis-Δ9), along with substrate promiscuity with chain length and double bond position (palmitoleic acid>cis-vaccenic acid>oleic acid). Under determined optimum reaction conditions, its catalytic efficiency (kcat/Km) was evaluated as 5.13 × 102 M-1·sec-1 against palmitoleic acid. Furthermore, computational predictions of the protein structure revealed its monoheme cytochrome c-type domain and a parasol-like transmembrane domain, suggesting its catalytic mode of action. For effective cis/trans isomerization, the ethylene double bond of monounsaturated fatty acids should be precisely positioned at the heme center of CTI, indicating that its substrate specificity can be determined by the alkyl chain length and the double bond position of the fatty acid substrates. These findings shed light on the potential of CTI as a promising biocatalyst for the food and lipid industry.

Microbial Synthesis of Heme b: Biosynthetic Pathways, Current Strategies, Detection, and Future Prospects

Heme b, which is characterized by a ferrous ion and a porphyrin macrocycle, acts as a prosthetic group for many enzymes and contributes to various physiological processes. Consequently, it has wide applications in medicine, food, chemical production, and other burgeoning fields. Due to the shortcomings of chemical syntheses and bio-extraction techniques, alternative biotechnological methods have drawn increasing attention. In this review, we provide the first systematic summary of the progress in the microbial synthesis of heme b. Three different pathways are described in detail, and the metabolic engineering strategies for the biosynthesis of heme b via the protoporphyrin-dependent and coproporphyrin-dependent pathways are highlighted. The UV spectrophotometric detection of heme b is gradually being replaced by newly developed detection methods, such as HPLC and biosensors, and for the first time, this review summarizes the methods used in recent years. Finally, we discuss the future prospects, with an emphasis on the potential strategies for improving the biosynthesis of heme b and understanding the regulatory mechanisms for building efficient microbial cell factories.

Exciplex Formation in Lipid-bound Escherichia coli Flavohemoglobin

Flavohemoglobins have the particular capability of binding unsaturated and cyclopropanated fatty acids as free acids or phospholipids. Fatty acid binding to the ferric heme results in a weak but direct bonding interaction. Ferrous and ferric protein, in presence or absence of a bound lipid molecule, have been characterized by transient absorption spectroscopy. Measurements have been also carried out both on the ferrous deoxygenated and on the CO bound protein to investigate possible long-range interaction between the lipid acyl chain moiety and the ferrous heme. After excitation of the deoxygenated derivatives the relaxation process reveals a slow dynamics (350 ps) in lipid-bound protein but is not observed in the lipid-free protein. The latter feature and the presence of an extra contribution in the absorption spectrum, indicates that the interaction of iron heme with the acyl chain moiety occurs only in the excited electronic state and not in the ground electronic state. Data analysis highlights the formation of a charge-transfer complex in which the iron ion of the lipid-bound protein in the expanded electronic excited state, possibly represented by a high spin Fe III intermediate, is able to bind to the sixth coordination ligand placed at a distance of at 3.5 Å from the iron. A very small nanosecond geminate rebinding is observed for CO adduct in lipid-free but not in the lipid-bound protein. The presence of the lipid thus appears to inhibit the mobility of CO in the heme pocket.

Animal-free heme production for artificial meat in Corynebacterium glutamicum via systems metabolic and membrane engineering

Recently, heme has attracted much attention as a main ingredient that mimics meat flavor in artificial meat in the food industry. Here, we developed Corynebacterium glutamicum capable of high-yield production of heme with systems metabolic engineering and modification of membrane surface. The combination of two precursor pathways based on thermodynamic information increased carbon flux toward heme and porphyrin intermediate biosynthesis. The co-overexpression of genes involved in a noncanonical downstream pathway and the gene encoding the transcriptional regulator DtxR significantly enhanced heme production. The overexpression of the putative heme exporters, knockout of heme-binding proteins, modification of the cell wall by chemical treatment, and reduction of intermediate UP III substantially improved heme secretion. The fed-batch fermentation showed a maximum heme titer of 309.18 ± 16.43 mg l^-1, including secreted heme of 242.95 ± 11.45 mg l^-1, a yield on glucose of 0.61 mmol mol^-1, and productivity of 6.44 mg l^-1h^-1, which are the highest values reported to date. These results demonstrate that engineered C. glutamicum can be an attractive cell factory for animal-free heme production.

Rice phytoglobins regulate responses under low mineral nutrients and abiotic stresses in Arabidopsis thaliana

Just like animals, plants also contain haemoglobins (known as phytoglobins in plants). Plant phytoglobins (Pgbs) have been categorized into 6 different classes, namely, Phytogb0 (Pgb0), Phytogb1 (Pgb1), Phytogb2 (Pgb2), SymPhytogb (sPgb), Leghaemoglobin (Lb), and Phytogb3 (Pgb3). Among the 6 Phytogbs, sPgb and Lb have been functionally characterized, whereas understanding of the roles of other Pgbs is still evolving. In our present study, we have explored the function of 2 rice Pgbs (OsPgb1.1 and OsPgb1.2). OsPgb1.1, OsPgb1.2, OsPgb1.3, and OsPgb1.4 displayed increased level of transcript upon salt, drought, cold, and ABA treatment. The overexpression (OX) lines of OsPgb1.2 in Arabidopsis showed a tolerant phenotype in terms of better root growth in low potassium (K+ ) conditions. The expression of the known K+ gene markers such as LOX2, HAK5, and CAX3 was much higher in the OsPgb1.2 OX as compared to wild type. Furthermore, the OsPgb1.2 OX lines showed a decrease in reactive oxygen species (ROS) production and conversely an increase in the K+ content, both in root and shoot, as compared to wild type in K+ limiting condition. Our results indicated the potential involvement of OsPgb1.2 in signalling networks triggered by the nutrient deficiency stresses.

Structure and function of haemoglobins

Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O₂ transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O₂ binding affinity and selectivity between O₂/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O₂ binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.

Resonance Raman studies on the flavohemoglobin of the protist Giardia intestinalis: evidence of a type I/II-peroxidase-like heme environment and roles of the active site distal residues

Flavohemoglobins are microbial enzymes that counter nitrosative stress, but the details of their underlying enzymatic activities and structure-function relationships are not completely understood. These enzymes have been identified in Gram-negative bacteria, certain fungi, and the parasitic protist Giardia intestinalis (gFlHb) which, despite lacking the ability to make heme, encodes several hemeproteins. To gain knowledge about the biophysical properties of the active site of gFlHb, we used resonance Raman spectroscopy to probe the wild-type protein and variants at globin domain positions E11, E7, and B10 on the distal, ligand-binding side of the heme. The heme of gFlHb has a peroxidase-like environment resembling that of the well-characterized E. coli flavohemoglobin HMP. We provide evidence that gFlHb has two Fe-His stretching modes, a feature that also occurs in type I/II-peroxidases in which a proximal histidine with strong imidazolate character and a nearby carboxylic acid residue can exist as a tautomeric pair depending on the position of a shared proton. Characterization of the distal variants Tyr30Phe, Gln54Leu, and Leu59Ala shows that TyrB10 and GlnE7 but not LeuE11 are implicated in stabilisation of bound exogenous ligands such as CO and O₂. Our work revealed that several biophysical properties of the heme active site of gFlHb are highly conserved compared to HMP and suggest that they are conserved across the flavohemoglobin family.

Hydrated and Solvated Tin(II) Ions in Solution and the Solid State, and a Coordination Chemistry Overview of the d10 s2 Metal Ions

The coordination chemistry of d¹⁰ s² metal ions is strongly affected by an (at least partially) occupied d¹⁰ s² metal ion-ligand atom antibonding orbital, which may cause a void in the coordination sphere due to repulsion between the electrons in the antibonding orbital on the metal ion and those on the ligands. The character of the formed d¹⁰ s² metal ion-ligand atom bond plays an important role in the electron density in the antibonding orbital and thereby also in the coordination chemistry. The hydrated tin(II) ion, [Sn(H₂ O)₃ ]²⁺ , and the trihydroxidostannate ion, [Sn(OH)₃ ]^- , have very different mean Sn-O bond lengths (2.21 and 2.08 Å, respectively) and O-Sn-O angles (ca. 78 and 90°, respectively) both in the solid state and in solution. On increasing the covalency of the tin(II)-ligand bonds, the repulsion decreases and higher coordination numbers are obtained, as seen in the dimethylsulfoxide- and N,N-dimethylthioformamide-solvated tin(II) ions, both of which are five-coordinate with square-pyramidal structures.

Control of carotenoid biosynthesis through a heme-based cis-trans isomerase

Plants synthesize carotenoids essential for plant development and survival. These metabolites also serve as essential nutrients for human health. The biosynthetic pathway leading to all plant carotenoids occurs in chloroplasts and other plastids and requires 15-cis-ζ-carotene isomerase (Z-ISO). It was not certain whether isomerization was achieved by Z-ISO alone or in combination with other enzymes. Here we show that Z-ISO is a bona fide enzyme and integral membrane protein. Z-ISO independently catalyzes the cis-to-trans isomerization of the 15–15′ C=C bond in 9,15,9′-cis-ζ-carotene to produce the substrate required by the following biosynthetic pathway enzyme. We discovered that isomerization depends upon a ferrous heme b cofactor that undergoes redox-regulated ligand-switching between the heme iron and alternate Z-ISO amino acid residues. Heme b-dependent isomerization of a large, hydrophobic compound in a membrane is unprecedented. As an isomerase, Z-ISO represents a new prototype for heme b proteins and potentially utilizes a novel chemical mechanism.

Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin

The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a "U" shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state.

The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study

Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4+1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5+1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding.

Type I flavohemoglobin of mycobacterium smegmatis is a functional nitric oxide dioxygenase

Two flavohemoglobins, type I and type II, displaying distinct structural features and cofactor binding sites coexist in Mycobacterium smegmatis; however, none of these flavohemeproteins are characterized so far. We have cloned and expressed type I flavohemoglobin (FHb1) of Mycobacterium smegmatis, encoded by MSMEG_1336, and characterized its spectral and functional properties. FHb1 exists as a monomer and displays spectral and functional characteristics similar to HMP of E. coli. Specific NO dioxygenase (NOD) activity of FHb1 was estimated to be 63.5 nmol heme(-1) sec(-1) , which was nearly eightfold higher than the HbN of M. tuberculosis and matched closely to the HMP of E. coli on the basis of cellular heme content. FHb1 preferred NADH for the NO dioxygenation and exhibited rapid reduction of flavin adenine dinucleotide and heme iron using NADH as electron donor. Level of FHb1 transcript increased significantly in M. smegmatis in the presence of acidified nitrite, and a nitric oxide-responsive transcriptional regulator of Rrf2 family exists together with the FHb1 under the same operon. These results suggested that FHb1 of M. smegmatis is a functional NOD and may be involved in the stress management of its host toward nitric oxide and nitrosative stress.

The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions

Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.

An unconventional hexacoordinated flavohemoglobin from Mycobacterium tuberculosis

Being an obligate aerobe, Mycobacterium tuberculosis faces a number of energetic challenges when it encounters hypoxia and environmental stress during intracellular infection. Consequently, it has evolved innovative strategies to cope with these unfavorable conditions. Here, we report a novel flavohemoglobin (MtbFHb) from M. tuberculosis that exhibits unique features within its heme and reductase domains distinct from conventional FHbs, including the absence of the characteristic hydrogen bonding interactions within the proximal heme pocket and mutations in the FAD and NADH binding regions of the reductase domain. In contrast to conventional FHbs, it has a hexacoordinate low-spin heme with a proximal histidine ligand lacking imidazolate character and a distal heme pocket with a relatively low electrostatic potential. Additionally, MtbFHb carries a new FAD binding site in its reductase domain similar to that of D-lactate dehydrogenase (D-LDH). When overexpressed in Escherichia coli or Mycobacterium smegmatis, MtbFHb remained associated with the cell membrane and exhibited D-lactate:phenazine methosulfate reductase activity and oxidized D-lactate into pyruvate by converting the heme iron from Fe(3+) to Fe(2+) in a FAD-dependent manner, indicating electron transfer from D-lactate to the heme via FAD cofactor. Under oxidative stress, MtbFHb-expressing cells exhibited growth advantage with reduced levels of lipid peroxidation. Given the fact that D-lactate is a byproduct of lipid peroxidation and that M. tuberculosis lacks the gene encoding D-LDH, we propose that the novel D-lactate metabolizing activity of MtbFHb uniquely equips M. tuberculosis to balance the stress level by protecting the cell membrane from oxidative damage via cycling between the Fe(3+)/Fe(2+) redox states.

Plant hemoglobins: important players at the crossroads between oxygen and nitric oxide

Plant hemoglobins constitute a diverse group of hemeproteins and evolutionarily belong to three different classes. Class 1 hemoglobins possess an extremely high affinity to oxygen and their main function consists in scavenging of nitric oxide (NO) at very low oxygen levels. Class 2 hemoglobins have a lower oxygen affinity and they facilitate oxygen supply to developing tissues. Symbiotic hemoglobins in nodules have mostly evolved from class 2 hemoglobins. Class 3 hemoglobins are truncated and represent a clade with a very low similarity to class 1 and 2 hemoglobins. They may regulate oxygen delivery at high O(2) concentrations. Depending on their physical properties, hemoglobins belong either to hexacoordinate non-symbiotic or pentacoordinate symbiotic groups. Plant hemoglobins are plausible targets for improving resistance to multiple stresses.

Novel flavohemoglobins of mycobacteria

Flavohemoglobins (flavoHbs) constitute a distinct class of chimeric hemoglobins in which a globin domain is coupled with a ferredoxin reductase such as FAD- and NADH-binding modules. Structural features and active site of heme and reductase domains are highly conserved in various flavoHbs. A new class of flavoHbs, displaying crucial differences in functionally conserved regions of heme and reductase domains, have been identified in mycobacteria. Mining of microbial genome data indicated that the occurrence of such flavoHbs might be restricted to a small group of microbes unlike conventional flavoHbs that are widespread among prokaryotes and lower eukaryotes. One of the representative flavoHbs of this class, encoded by Rv0385 gene (MtbFHb) of Mycobacterium tuberculosis, has been cloned, expressed, and characterized. The ferric and deoxy spectra of MtbFHb displayed a hexacoordinate state indicating that its distal site may be occupied by an intrinsic amino acid or an external ligand and it may not be involved in nitric oxide detoxification. Phylogenetic analysis revealed that mycobacterial flavoHbs constitute a separate cluster distinct from conventional flavoHbs and may have novel function(s).

Nonsymbiotic hemoglobins and stress tolerance in plants

Hemoglobins (Hbs) are heme containing proteins found in most organisms including animals, bacteria, and plants. Their structure, size, and function are quite diverse among the different organisms. There are three different types of hemoglobins in plants: symbiotic (sHb), nonsymbiotic (nsHb), and truncated hemoglobins (trHb). The nonsymbiotic hemoglobins are divided into: class 1 hemoglobins (nsHb-1s), which have a very high affinity for oxygen: and class 2 hemoglobins (nsHb-2s), which have lower affinity for oxygen, are similar to the sHbs. nsHb-1s are expressed under hypoxia, osmotic stress, nutrient deprivation, cold stress, rhizobial infection, nitric oxide exposure, and fungal infection. Tolerance to stress is very important for the survival of the plant. Hemoglobins are one of many different strategies that plants have evolved to overcome stress conditions and survive. Hbs also react with NO produced under different stress conditions. Class 1 nsHbs are involved in a metabolic pathway involving NO. Those hemoglobins provide an alternative type of respiration to mitochondrial electron transport under limiting oxygen concentrations. Class 1 nsHbs in hypoxic plants act as part of a soluble, terminal, NO dioxygenase system, yielding nitrate from the reaction of oxyHb with NO. The overall reaction sequence, referred to as the nsHb/NO cycle, consumes NADH and maintains ATP levels via an as yet unknown mechanism. Class 2 nsHbs seem to scavenge NO in a similar fashion as class 1 Hbs and are involved in reducing flowering time in Arabidopsis. nsHbs also show peroxidase-like activity and NO metabolism and possibly protect against nitrosative stress in plant-pathogen interaction and in symbiotic interactions. nsHbs may be involved in other stress conditions such as osmotic, nutrient and cold stress together with NO and the function of nsHbs can be in NO metabolism and signal transduction. However, other possible functions cannot be precluded as Hbs have many different functions in other organisms.

Modulation of the heme electronic structure and cystathionine beta-synthase activity by second coordination sphere ligands: The role of heme ligand switching in redox regulation

In humans, cystathionine beta-synthase (CBS) is a hemeprotein, which catalyzes a pyridoxal phosphate (PLP)-dependent condensation reaction. Changes in the heme environment are communicated to the active site, which is approximately 20A away. In this study, we have examined the role of H67 and R266, which are in the second coordination sphere of the heme ligands, H65 and C52, respectively, in modulating the heme's electronic properties and in transmitting information between the heme and active sites. While the H67A mutation is comparable to wild-type CBS, interesting differences are revealed by mutations at the R266 site. The pathogenic mutant, R266K, is moderately PLP-responsive while the R266M mutation shows dramatic differences in the ferrous state. The electrostatic interaction between C52 and R266 is critical for stabilizing the ferrous heme and its disruption leads to the facile formation of a 424nm (C-424) absorbing ferrous species, which is inactive, compared to the active 449nm ferrous species for wild-type CBS. Resonance Raman studies on the R266M mutant reveal that the kinetics of C52 rebinding after Fe-CO photolysis are comparable to that of wild-type CBS. EXAFS studies on C-424 CBS are consistent with the presence of two axial N/O low Z scatters with only one being a rigid unit of a histidine residue while the other could be a solvent molecule, an oxygen atom from the peptide backbone or a side chain nitrogen. The redox potential for the heme in full-length CBS is -350+/-4mV and is substantially lower than the value of -287+/-2mV determined for truncated CBS. A redox-regulated ligand change has the potential to serve as an allosteric on/off switch in human CBS and the second sphere ligand, R266, plays an important role in this transition.

A survey of methods for the purification of microbial flavohemoglobins

Over the past decade, the flavohemoglobin Hmp has emerged as the most significant nitric oxide (NO)-detoxifying protein in many diverse organisms, including yeasts and fungi but particularly pathogenic bacteria. Flavohemoglobins--the best-characterized class of microbial globin--comprise two domains: a globin domain with a noncovalently bound heme B and a flavin domain with recognizable binding sites for FAD and NAD(P)H. Hmp was first identified in Escherichia coli and now has a clearly defined role in NO biology in that organism: its synthesis is markedly up-regulated by NO, and hmp knockout mutants of E. coli and Salmonella typhimurium are severely compromised for survival in the presence of NO in vitro and in pathogenic lifestyles. In the presence of molecular O2, Hmp catalyzes an oxygenase or denitrosylase reaction in which NO is stoichiometrically converted to nitrate ion, which is relatively innocuous. In this chapter, we present a survey of the methods used to express and purify the flavohemoglobins from diverse microorganisms and describe in more detail three methods developed and used in this laboratory for the E. coli protein. Particular problems are highlighted, particularly (a) the toxic consequences of Hmp overexpression that result from its ability to catalyze partial oxygen reduction and (b) the expression of protein with substoichiometric content of redox-active flavin and heme centers.

Analysis of the contribution of the globin and reductase domains to the ligand-binding properties of bacterial haemoglobins

Bacterial Hbs (haemoglobins), like VHb (Vitreoscilla sp. Hb), and flavoHbs (flavohaemoglobins), such as FHP (Ralstonia eutropha flavoHb), have different autoxidation and ligand-binding rates. To determine the influence of each domain of flavoHbs on ligand binding, we have studied the kinetic ligand-binding properties of oxygen, carbon monoxide and nitric oxide to the chimaeric proteins, FHPg (truncated form of FHP comprising the globin domain alone) and VHb-Red (fusion protein between VHb and the C-terminal reductase domain of FHP) and compared them with those of their natural counterparts, FHP and VHb. Moreover, we also analysed polarity and solvent accessibility to the haem pocket of these proteins. The rate constants for the engineered proteins, VHb-Red and FHPg, do not differ significantly from those of their natural counterparts, VHb and FHP respectively. Our results suggest that the globin domain structure controls the reactivity towards oxygen, carbon monoxide and nitric oxide. The presence or absence of a reductase domain does not affect the affinity to these ligands.

Plant hemoglobins: what we know six decades after their discovery

This review describes contributions to the study of plant hemoglobins (Hbs) from a historical perspective with emphasis on non-symbiotic Hbs (nsHbs). Plant Hbs were first identified in soybean root nodules, are known as leghemoglobins (Lbs) and have been characterized in detail. It is widely accepted that a function of Lbs in nodules is to facilitate the diffusion of O(2) to bacteroids. For many years Hbs could not be identified in plants other than N(2)-fixing legumes, however in the 1980s a Hb was isolated from the nodules of the non-legume dicot plant Parasponia, a hb gene was cloned from the non-nodulating Trema, and Hbs were detected in nodules of actinorhizal plants. Gene expression analysis showed that Trema Hb transcripts exist in non-symbiotic roots. In the 1990s nsHb sequences were also identified in monocot and primitive (bryophyte) plants. In addition to Lbs and nsHbs, Hb sequences that are similar to microbial truncated (2/2) Hbs were also detected in plants. Plant nsHbs have been characterized in detail. These proteins have very high O(2)-affinities because of an extremely low O(2)-dissociation constant. Analysis of rice Hb1 showed that distal His coordinates heme Fe and stabilizes bound O(2); this means that O(2) is not released easily from oxygenated nsHbs. Non-symbiotic hb genes are expressed in specific plant tissues, and overexpress in organs of stressed plants. These observations suggest that nsHbs have functions additional to O(2)-transport, such as to modulate levels of ATP and NO.

Characterization of the particulate methane monooxygenase metal centers in multiple redox states by X-ray absorption spectroscopy

The integral membrane enzyme particulate methane monooxygenase (pMMO) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. The 2.8-A resolution pMMO crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. Although not found in the crystal structure, solution samples of pMMO also contain iron. We have used X-ray absorption spectroscopy to analyze the oxidation states and coordination environments of the pMMO metal centers in as-isolated (pMMO(iso)), chemically reduced (pMMO(red)), and chemically oxidized (pMMO(ox)) samples. X-ray absorption near-edge spectra (XANES) indicate that pMMO(iso) contains both Cu(I) and Cu(II) and that the pMMO Cu centers can undergo redox chemistry. Extended X-ray absorption fine structure (EXAFS) analysis reveals a Cu-Cu interaction in all redox forms of the enzyme. The Cu-Cu distance increases from 2.51 to 2.65 A upon reduction, concomitant with an increase in the average Cu-O/N bond lengths. Appropriate Cu2 model complexes were used to refine and validate the EXAFS fitting protocols for pMMO(iso). Analysis of Fe EXAFS data combined with electron paramagnetic resonance (EPR) spectra indicates that Fe, present as Fe(III), is consistent with heme impurities. These findings are complementary to the crystallographic data and provide new insight into the oxidation states and possible electronic structures of the pMMO Cu ions.

Pentacoordinate and hexacoordinate ferric hemes in acid medium: EPR, UV–Vis and CD studies of the giant extracellular hemoglobin of Glossoscolex paulistus

The equilibrium complexity involving different axially coordinated hemes is peculiar to hemoglobins. The pH dependence of the spontaneous exchange of ligands in the extracellular hemoglobin from Glossoscolex paulistus was studied using UV-Vis, EPR, and CD spectroscopies. This protein has a complex oligomeric assembly with molecular weight of 3.1 MDa that presents an important cooperative effect. A complex coexistence of different species was observed in almost all pH values, except pH 7.0, where just aquomet species is present. Four new species were formed and coexist with the aquomethemoglobin upon acidification: (i) a "pure" low-spin hemichrome (Type II), also called hemichrome B, with an usual spin state (d(xy))(2)(d(xz),d(yz))(3); (ii) a strong g(max) hemichrome (Type I), also showing an usual spin state (d(xy))(2)(d(xz),d(yz))(3); (iii) a hemichrome with unusual spin state (d(xz),d(yz))(4)(d(xy))(1) (Type III); (iv) and a high-spin pentacoordinate species. CD measurements suggest that the mechanism of species formation could be related with an initial process of acid denaturation. However, it is worth mentioning that based on EPR the aquomet species remains even at acidic pH, indicating that the transitions are not complete. The "pure" low-spin hemichrome presents a parallel orientation of the imidazole ring planes but the strong g(max) hemichrome is a HALS (highly anisotropic low-spin) species indicating a reciprocally perpendicular orientation of the imidazole ring planes. The hemichromes and pentacoordinate formation mechanisms are discussed in detail.

A phylogenomic profile of globins

Background

Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FAD-binding domain and the gene-regulating globin coupled sensors, with variable C-terminal domains. The single-domain globins encompass sequences related to chimeric globins and «truncated» hemoglobins with a 2-over-2 instead of the canonical 3-over-3 α-helical fold.

Results

A census of globins in 26 archaeal, 245 bacterial and 49 eukaryote genomes was carried out. Only ~25% of archaea have globins, including globin coupled sensors, related single domain globins and 2-over-2 globins. From one to seven globins per genome were found in ~65% of the bacterial genomes: the presence and number of globins are positively correlated with genome size. Globins appear to be mostly absent in Bacteroidetes/Chlorobi, Chlamydia, Lactobacillales, Mollicutes, Rickettsiales, Pastorellales and Spirochaetes. Single domain globins occur in metazoans and flavohemoglobins are found in fungi, diplomonads and mycetozoans. Although red algae have single domain globins, including 2-over-2 globins, the green algae and ciliates have only 2-over-2 globins. Plants have symbiotic and nonsymbiotic single domain hemoglobins and 2-over-2 hemoglobins. Over 90% of eukaryotes have globins: the nematode Caenorhabditis has the most putative globins, ~33. No globins occur in the parasitic, unicellular eukaryotes such as Encephalitozoon, Entamoeba, Plasmodium and Trypanosoma.

Conclusion

Although Bacteria have all three types of globins, Archaeado not have flavohemoglobins and Eukaryotes lack globin coupled sensors. Since the hemoglobins in organisms other than animals are enzymes or sensors, it is likely that the evolution of an oxygen transport function accompanied the emergence of multicellular animals.