Evolutionary and Functional Relationships in the Truncated Hemoglobin Family.

Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends.

Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin.

Plant hemoglobins constitute three distinct groups: symbiotic, nonsymbiotic, and truncated hemoglobins. Structural investigation of symbiotic and nonsymbiotic (class I) hemoglobins revealed the presence of a vertebrate-like 3/3 globin fold in these proteins. In contrast, plant truncated hemoglobins are similar to bacterial truncated hemoglobins with a putative 2/2 α-helical globin fold. While multiple structures have been reported for plant hemoglobins of the first two categories, for plant truncated globins only one structure has been reported of late. Here, we report yet another crystal structure of the truncated hemoglobin from Arabidopsis thaliana (AHb3) with two water molecules in the heme pocket, of which one is distinctly coordinated to the heme iron, unlike the only available crystal structure of AHb3 with a hydroxyl ligand. AHb3 was monomeric in its crystallographic asymmetric unit; however, dimer was evident in the crystallographic symmetry, and the globin indeed existed as a stable dimer in solution. The tertiary structure of the protein exhibited a bacterial-like 2/2 α-helical globin fold with an additional N-terminal α-helical extension and disordered C-termini. To address the role of these extended termini in AHb3, which is yet unknown, N- and C-terminal deletion mutants were created and characterized and molecular dynamics simulations performed. The C-terminal deletion had an insignificant effect on most properties but perturbed the dimeric equilibrium of AHb3 and significantly influenced azide binding kinetics in the ferric state. These results along with the disordered nature of the C-terminus indicated its putative role in intramolecular or intermolecular interactions probably regulating protein-ligand and protein-protein interactions. While the N-terminal deletion did not change the overall globin fold, stability, or ligand binding kinetics, it seemed to have influenced coordination at the heme iron, the hydration status of the active site, and the quaternary structure of AHb3. Evidence indicated that the N-terminus is the predominant factor regulating the quaternary interaction appropriate to physiological requirements, dynamics of the side chains in the heme pocket, and tunnel organization in the protein matrix.

THB1, a truncated hemoglobin, modulates nitric oxide levels and nitrate reductase activity.

Hemoglobins are ubiquitous proteins that sense, store and transport oxygen, but the physiological processes in which they are implicated is currently expanding. Recent examples of previously unknown hemoglobin functions, which include scavenging of the signaling molecule nitric oxide (NO), illustrate how the implication of hemoglobins in different cell signaling processes is only starting to be unraveled. The extent and diversity of the hemoglobin protein family suggest that hemoglobins have diverged and have potentially evolved specialized functions in certain organisms. A unique model organism to study this functional diversity at the cellular level is the green alga Chlamydomonas reinhardtii because, among other reasons, it contains an unusually high number of a particular type of hemoglobins known as truncated hemoglobins (THB1-THB12). Here, we reveal a cell signaling function for a truncated hemoglobin of Chlamydomonas that affects the nitrogen assimilation pathway by simultaneously modulating NO levels and nitrate reductase (NR) activity. First, we found that THB1 and THB2 expression is modulated by the nitrogen source and depends on NIT2, a transcription factor required for nitrate assimilation genes expression. Furthermore, THB1 is highly expressed in the presence of NO and is able to convert NO into nitrate in vitro. Finally, THB1 is maintained on its active and reduced form by NR, and in vivo lower expression of THB1 results in increased NR activity. Thus, THB1 plays a dual role in NO detoxification and in the modulation of NR activity. This mechanism can partly explain how NO inhibits NR post-translationally.

Hemoglobins from Mycobacterium tuberculosis and Campylobacter jejuni: a comparative study with resonance Raman spectroscopy.

Three groups of hemoglobins (Hbs) have been identified in unicellular organisms: (1) the truncated Hbs (trHb) that display a novel two-over-two alpha-helical structure, (2) the flavohemoglobins (FHb) that comprise a Hb domain with a classical three-over-three alpha-helical structure and a covalently attached flavin-containing reductase domain, and (3) the single-domain Hbs (sdHb) that exhibit high sequence homology and structural similarity to the Hb domain of FHb. On the basis of phylogenetic analysis, the trHbs can be further divided into three subgroups: TrHb-I, TrHb-II, and TrHb-III. The various classes of Hbs may coexist in the same organism, suggesting distinct functions for each class of Hb. This chapter reviews the structural and functional properties of a TrHb-I (trHbN) and a TrHb-II (trHbO) from Mycobacterium tuberculosis, as well as a TrHb-III (trCtb) and a sdHb (Cgb) from Campylobacter jejuni on the basis of resonance Raman spectroscopic studies.

Truncated hemoglobin 1 is a new player in Chlamydomonas reinhardtii acclimation to sulfur deprivation.

Truncated hemoglobins constitute a large family, present in bacteria, in archaea and in eukaryotes. However, a majority of physiological functions of these proteins remains to be elucidated. Identification and characterization of a novel role of truncated hemoglobins in the model alga provides a framework for a more complete understanding of their biological functions. Here, we use quantitative RT-PCR to show that three truncated hemoglobins of Chlamydomonas reinhardtii, THB1, THB2 and THB12, are induced under conditions of depleted sulfur (S) supply. THB1 underexpression results in the decrease in cell size, as well in levels of proteins, chlorophylls and mRNA of several S-responsive genes under S starvation. We provide evidence that knock-down of THB1 enhances NO production under S deprivation. In S-deprived cells, a subset of S limitation-responsive genes is controlled by NO in THB1-dependent pathway. Moreover, we demonstrate that deficiency for S represses the nitrate reduction and that THB1 is involved in this control. Thus, our data support the idea that in S-deprived cells THB1 plays a dual role in NO detoxification and in coordinating sulfate limitation with nitrate assimilation. This study uncovers a new function for the Chlamydomonas reinhardtii THB1 in the control of proper response to S deprivation.

Role of PheE15 gate in ligand entry and nitric oxide detoxification function of mycobacterium tuberculosis truncated hemoglobin N.

The truncated hemoglobin N, HbN, of Mycobacterium tuberculosis is endowed with a potent nitric oxide dioxygenase (NOD) activity that allows it to relieve nitrosative stress and enhance in vivo survival of its host. Despite its small size, the protein matrix of HbN hosts a two-branched tunnel, consisting of orthogonal short and long channels, that connects the heme active site to the protein surface. A novel dual-path mechanism has been suggested to drive migration of O(2) and NO to the distal heme cavity. While oxygen migrates mainly by the short path, a ligand-induced conformational change regulates opening of the long tunnel branch for NO, via a phenylalanine (PheE15) residue that acts as a gate. Site-directed mutagenesis and molecular simulations have been used to examine the gating role played by PheE15 in modulating the NOD function of HbN. Mutants carrying replacement of PheE15 with alanine, isoleucine, tyrosine and tryptophan have similar O(2)/CO association kinetics, but display significant reduction in their NOD function. Molecular simulations substantiated that mutation at the PheE15 gate confers significant changes in the long tunnel, and therefore may affect the migration of ligands. These results support the pivotal role of PheE15 gate in modulating the diffusion of NO via the long tunnel branch in the oxygenated protein, and hence the NOD function of HbN.

Oxygen- and NssR-dependent globin expression and enhanced iron acquisition in the response of campylobacter to nitrosative stress.

Pathogenic bacteria experience nitrosative stress from NO generated in the host and from nitrosating species such as S-nitrosoglutathione. The food-borne pathogen Campylobacter jejuni responds by activating gene expression from a small regulon under the control of the NO-sensitive regulator, NssR. Here, we describe the full extent of the S-nitrosoglutathione response using transcriptomic and proteomic analysis of batch- and chemostat-cultured C. jejuni. In addition to the NssR regulon, which includes two hemoglobins (Cgb and Ctb), we identify more than 90 other up-regulated genes, notably those encoding heat shock proteins and proteins involved in oxidative stress tolerance and iron metabolism/transport. Up-regulation of a subset of these genes, including cgb, is also elicited by NO-releasing compounds. Mutation of the iron-responsive regulator Fur results in insensitivity of growth to NO, suggesting that derepression of iron-regulated genes and augmentation of iron acquisition is a physiological response to nitrosative damage. We describe the effect of oxygen availability on nitrosative stress tolerance; cells cultured at higher rates of oxygen diffusion have elevated levels of hemoglobins, are more resistant to inhibition by NO of both growth and respiration, and consume NO more rapidly. The oxygen response is mediated by NssR. Thus, in addition to NO detoxification catalyzed by the hemoglobins Cgb and possibly Ctb, C. jejuni mounts an extensive stress response. We suggest that inhibition of respiration by NO may increase availability of oxygen for Cgb synthesis and function.

[Expression of Vitreoscilla hemoglobin and nitrilase in the yeast Pichia pastoris].

The expression of the vgb gene in vivo could improve the fermentation density and then contribute the extracellular secretion of the product of bxn gene. Constructed the recombination plasmid pPIC9K-vgbbxn and transformed into Pichia pastoris GS115. The results of PCR and SDS-PAGE indicate that the vgb gene and bxn gene had integrated into the genome of Pichia pastoris GS115 and expressed in efficient level. Also, the protein activity of their products had been verified respectively. Shake flask fermentation experiments showed that the presence of VHb in yeast Pichia pastoris efficiently enhanced cell growth and secretive expression of bxn gene under hypoxic habitats.

[Recent advances in the study of Vitreoscilla hemoglobin(VHb) and related proteins - cloning, expression and physiological actions in heterologons hosts and in transgenic tobacco plants].

The first bacterial hemoglobin(VHb) was found in a strictly aerobic bacterium, Vitreoscilla strain C1, occurring in marshes low in oxygen, but rich in organic matter. The hemoglobin gene is induced under low oxygen tension and may amount to 20 times as high. The expression of VHb promotes cell growth, protein biosynthesis and primary and secondary metabolism of the host cells, because the increased intracellular oxygen accelerates both the function of respiratory chain and terminal oxidases. The serial action of increased oxygen concentration is elucidated through yeast two hybrid system and a model is proposed. In addition, novel globin proteins known as flavohemoglobins have been isolated from various procaryotes and eucaryotes, with a N-terminal similar to VHb and C-terminal with reductase activity. Primary study shows that flavohemoglobin proteins exhibit similar function as VHb and also protection effect to nitrosative stress. Further work is needed to learn more about the physiology of these flavohemoglobins. The most remarkable physiological effects of VHb are exihibited in transgenic tobacco plants, including accelerated seed germination and growth in plant, increased synthesis of chlorophyll and dry weight. Without doubt, these effects are brought about through the increased oxygen supply to plant cells. It is deemed that VHb transgenic tobacco is a forerunner for transgenic crops and VHb may be a valuable route for staple seed crops.

[Enhanced ergosterol production by recombinant Saccharomyces cerevisiae 1190 harboring Vitreoscilla hemoglobin gene (vgb)].

Ergosterol is a principal sterol of fungi. It is a raw material for production of vitamin D2, hydrocortisone, progesterone and brassinolide. Synthesis of ergosterol requires molecular oxygen, and low oxygen tensions was reported to dramatically reduce ergosterol concentration. Vitreoscilla Hemoglobin Gene (vgb), a homodimeric hemoglobin gene from Gram-negative obligate aerobic bacterium Vitreoscilla, enables a higher specific cellular oxygen uptake rate, it also improves the oxygen transportation. In this study, recombinant plasmid pVgb-kanMX4 containing Vitreoscilla Hemoglobin Gene (vgb) and geneticin (G418) was constructed and transformed into Saccharomyces cerevisiae 1190 for enhanced ergosterol production. With sufficient oxygen supply, the ergosterol contents of recombinant and wild type strains grown in shake flasks were 1.07% and 0.573%, respectively. Under oxygen limitation condition, ergosterol contents in recombinant and wild type strains were reduced to 0.39% and 0.25%, respectively. In a 30 hours fermentation study conducted in a 5 liter fermentor, 15.1 g/L Cell Dry Weight (CDW) containing 1.38% ergosterol was obtained from growth of the recombinant strains; Only 14.8 g/L CDW containing 0.9% ergosterol was produced by the wild type strain. These results demonstrated that vgb played a role in enhancing ergosterol production.