Heme-based gas sensor proteins have the ability to sense diatomic molecules such as O2 (FixL, EcDos or HemAT), CO (CooA, a CO-sensing protein of Rhodospirillum rubrum) and NO (guanylate cyclase) molecules and subsequently regulate numerous important biological processes in prokaryotic and eukaryotic organisms. The sensing function of these proteins is initiated by the binding of an effector (i.e., O2, CO, etc5) to the heme iron which then leads to a cascade of conformational events which gives rise to changes in kinase activity, DNA-binding activity, etc... In order to better understand the mechanism heme-based signaling, time resolved photothermal methods as well as transient optical techniques were utilized to obtain thermodynamic profiles for ligand binding/release in heme based signaling proteins including HemAT from Bacillus subtilis (aerotactic transducer), FixL from Sinorhizobium meliloti (regulation of the nitrogen fixation) and CooA from Rhodospirillum rubrum (transcriptional activator). In addition, a number of model systems were examined to understand the underlying thermodynamic processes involved in heme ligation. The variation of volume and enthalpy changes associated with spin state change of the iron from high-spin to low-spin where examined using the spin crossover Fe(III)(salten)(mepepy) complex. In addition, the experimental determination of the volume change due to electrostriction events were using Ru(II)(L)3 and the Debye-Hückel equation. Finally, different model heme proteins were studied to understand how a signal is conformationaly transmitted within a heme protein matrix. Sandbar shark hemoglobin was examined as an example of a non-signaling an allosteric protein. Two different peroxidases (horseradish and soybean) which have a direct channel between the heme pocket and the solvent involving no barrier energetic for the photodissociated ligand leaving the heme pocket were examined as example of non-signaling, non-allosteric proteins. The results show that each protein has a unique thermodynamic profile to conformationaly transmit signals subsequent to photodissociation of CO, even within the same class of protein (i.e. PAS domains, globins, etc...).

Heme-copper oxidases are transmembrane proteins that are found in aerobic and anaerobic respiratory chains. During aerobic respiration, these enzymes reduce dioxygen to water. The energy released in the reaction is used to transport protons across a biological membrane. Stored as proton electrochemical gradient, the energy can be used to regenerate ATP. It is known that aa3 oxidases, which are the most common oxidases, transport pumped protons and protons used for the catalytic reaction using two proton pathways. However, the molecular mechanism of pumping is still being debated. When oxygen is available in very small quantities, oxygen reductases with high affinity for oxygen are expressed by organisms like Thermus thermophilus. The proton pumping mechanism in the ba3 oxidase is slightly different from that of aa3 oxidases as this enzyme only uses a single proton uptake pathway. Here we analyzed the reaction mechanism of ba3 oxidase and found evidence that the first proton taken up by the four-electron reduced ba3 oxidase is transferred to a site distant from the catalytic site, the pump site, and that only every second proton taken up from solution is pumped. Data obtained from studies using site-directed mutagenesis and flow-flash spectroscopy suggest a probable location of the pump site. Under anaerobic conditions, some organisms are able to generate a proton- motive force using nitrate and nitrite as electron acceptors. In this process, the cytotoxic reaction intermediate nitric oxide is produced. Nitric oxide reductase (NOR), a deviant heme-copper oxidase that reduces NO to the rather harmless N2O, does not pump any protons. The catalytic mechanism of nitric oxide reduction by NOR is very poorly understood. Here we demonstrate that substrate inhibition, which occurs in NOR from Paracoccus denitrificans above 5 μM NO, can already be observed before the electrons from the low-spin hemes re-distribute to the active site. Furthermore, we found that a single specific proton pathway is used for proton-transfer leading from the periplasm to the active site.

Die Hämoxygenase-1 (HO-1) ist das geschwindigkeitsbestimmende Enzym des Hämabbaus und ist wichtiger Regulator inflammatorischer Prozesse. Der Verlauf einer experimentellen akuten Pankreatitis (AP) konnte im Tiermodell durch HO-1 Induktion abgemildert werden. Die Aktivierung und Proliferation pankreatischer Stellatum Zellen (PSC) wird durch eine experimentelle HO-1 Induktion inhibiert und kann so möglicherweise vor der Fibrosierung des Pankreasparenchyms bei chronischer Pankreatitis (CP) schützen. Die Transkription der HO-1 wird durch einen GT-Repeat beeinflusst, der im Promoter lokalisiert ist. Diese Arbeit untersuchte, ob Varianten des GT-Repeat oder weitere genetische Varianten der HO-1 mit verschiedenen Pankreatitisformen assoziiert sind. Der GT-Repeat und der SNP rs2071746 wurden mit fluoreszensmarkierten Primern bzw. mit Schmelzkurvenanalyse bei 285 Patienten mit AP, bei 208 Patienten mit alkoholischer CP (ACP), bei 207 mit idiopathischer/hereditärer CP (ICP/HCP), 147 Patienten mit Alkoholischer Leberzirrhose (ALZ) und bei 289 Kontrollen untersucht. Bei den ACP Patienten wurde die GT-Repeat Analyse auf insgesamt 446 Patienten erhöht. Zusätzlich wurden die kodierenden HO-1 Abschnitte mittels DNA-Sequenzierung bei 145 Patienten mit ACP, 138 Patienten mit ICP/HCP, 147 Patienten mit ALZ und bei 151 Kontrollen analysiert. Das Exon 3 wurde darüber hinaus bei zusätzlichen ICP/HP Patienten und Kontrollen untersucht. Die Längenverteilungen des GT-Repeat, die Allelverteilung des SNP rs2071746 und die Verteilung der bei der DNA-Sequenzierung gefundenen synonymen und nicht synonymen Varianten waren bei allen untersuchten Gruppen nicht signifikant unterschiedlich. Obwohl die funktionellen Daten einen Einfluss von HO-1 Varianten auf die Pathogenese der verschiedenen Pankreatitis-Formen nahelegen, konnte unsere umfangreiche genetische Analyse keine Assoziation nachweisen. Genetische Varianten der HO-1 haben keinen Einfluss auf die Entwicklung einer AP, ACP, ICP/HCP und ALZ.

<p>Nitric oxide (NO) is an endogenous gaseous signaling molecule produced by three NO synthase isoforms (NOS1, 2, 3) and important in host defense. The induction of NOS2 during bacterial sepsis is critical for pathogen clearance but its sustained activation has long been associated with increased mortality secondary to multiple organ dysfunction syndrome (MODS). High levels of NO produced by NOS2 incite intrinsic cellular dysfunction, in part by damaging macromolecules through nitration and/or nitrosylation. These include mitochondrial DNA (mtDNA) and enzymes of key mitochondrial pathways required for maintenance of normal O2 utilization and energy homeostasis. However, animal studies and clinical trials inhibiting NOS2 have demonstrated pronounced organ dysfunction and increased mortality in response to live bacterial infections, confirming that NOS2 confers pro-survival benefits. Of particular interest here, the constitutive NOS1 and NOS3 have been linked to the up-regulation of nuclear genes involved in mitochondrial biogenesis but no comparable role has been described for NOS2. <italic> Therefore, I hypothesized that NOS2 is indispensible for host protection but must be tightly regulated to ensure NO levels are high enough to activate mitochondrial and other pro-survival genes, but below the threshold for cellular damage.</italic></p><p>This hypothesis was explored with two major Aims. The <italic>first Aim</italic> was to define the role of NOS2 in the activation of mitochondrial biogenesis in the heart of <italic>E. coli</italic>-treated mice. The <italic>second</italic> was to investigate the ability of NOS2 to be transcriptionally regulated by an enzyme previously shown to induce mitochondrial biogenesis, heme oxygenase-1 (HO-1). This hypothesis was tested using an <italic>in vivo</italic> model of sublethal heat-killed <italic>E. coli</italic> (<italic>HkEC</italic>) peritonitis in C57B/L6 (Wt), NOS2-/-, and TLR4-/- mice. Additionally, <italic>in vitro</italic> systems of mouse AML-12 or Hepa 1-6 cells pretreated with HO-1 activators or <italic>Hmox1</italic> shRNA prior to inflammatory challenge with lipopolysaccharide (LPS) +/- tumor necrosis factor-&alpha; (TNF-&alpha;). For the first Aim, Wt, NOS2-/-, and TLR4-/- mice were treated with (<italic>HkEC</italic> and cardiac tissue analyzed for mitochondrial function, expression of nuclear and mitochondrial proteins needed for mitochondrial biogenesis, and histological expression of NOS2 and TLR4 relative to changes in mitochondrial mass. For the second Aim, Wt mice were pretreated with hemin or carbon monoxide (CO) to activate HO-1 prior to <italic>HkEC</italic>-peritonitis. Liver tissue in these animals was evaluated at four hours for HO-1 induction, <italic>Nos2</italic> mRNA expression, cytokine profiles, and nuclear factor (NF)-&kappa;B activation. Liver cell lines were pretreated with hemin, CO-releasing molecule (CORM), or bilirubin one hour before LPS exposure and the <italic>Nos2</italic> transcriptional response evaluated at two and 24 hours. The MTT assay was used to confirm that <italic>in vitro</italic> treatments were not lethal. </p><p>These studies demonstrated that <italic>HkEC</italic> induced mtDNA damage in the heart that was repaired in Wt mice but not in NOS2-deficient mice. In KO mice, sustained mtDNA damage was associated with the reduced expression of nuclear (NRF-1, PGC-1&alpha;) and mitochondrial (Tfam, Pol-&gamma;) proteins needed for mitochondrial biogenesis. The findings thus supported that NOS2 is required for mitochondrial biogenesis in the heart during Gram-negative challenge. Evaluation of the relationship between HO-1 and NOS2 in murine liver was more complex; HO-1 activation in <italic>HkEC</italic>-treated Wt mice attenuated 4-hour <italic>Nos2</italic> gene transcription. In liver cell lines, hemin, CORM, and bilirubin were unable to suppress <italic>Nos2</italic> expression at the time of maximal induction (2 hours). <italic>Nos2</italic> was, however, suppressed by 24 hours, suggesting that the regulatory impact of HO-1 induction was not engaged early enough to reduce <italic>Nos2</italic> transcription at 2 hours. It is concluded that NOS2 induction in bacterial sepsis optimizes the expression of the mitochondrial biogenesis transcriptional program, which subsequently can also be regulated by HO-1/CO in murine liver. This provides a potential new mechanism by which immune suppression and mitochondrial repair can occur in tandem during the acute inflammatory response.</p> / Dissertation

Angiotensin II (AngII), the major effector of the renin angiotensin system, mediates kidney disease progression by signalling through AT-1 receptor (AT-1R), but there are no specific measures of renal AngII activity. Accordingly, we sought to define an AngII-regulated proteome in primary human proximal tubular cells (PTEC) in order to identify potential AngII activity markers in the kidney. We utilized stable isotope labelling with amino acids (SILAC) in PTECs to compare proteomes of AngII-treated and control cells. Of 4618 quantified proteins, 83 were differentially regulated. SILAC ratios for 18 candidates were confirmed by Selected Reaction Monitoring (SRM) assays. Both SILAC and SRM revealed the nuclear factor erythroid 2-related 2 (Nrf2) target protein, heme oxygenase-1 (HO-1) as the most significantly upregulated protein in response to AngII stimulation. AngII-dependent regulation of HO-1 gene and protein was further verified by qRT-PCR and ELISA in PTECs. In order to extend these in vitro observations, we utilized a systems biology approach. We thus overlaid a network of significantly enriched gene ontology (GO) terms from our AngII-regulated proteins with a dataset of differentially expressed kidney genes from AngII-treated wild type mice and AT-1R knock-out mice. Five GO terms were enriched both in vitro and in vivo, and all included HO-1. Furthermore, four additional Nrf2 target proteins were functionally important in vitro and in vivo. We then studied HO-1 kidney expression and urinary excretion in AngII-treated wild type mice and mice with PTEC-specific AT-1R gene deletion. Deletion of the AT-1R gene in PTECs lowered both kidney expression and urine excretion of HO-1, confirming AngII/AT-1R mediated regulation of HO-1. In summary, our in vitro experiments identified novel molecular markers of AngII activity in PTECs and the animal studies demonstrated that these markers also reflect AngII activity in PTECs in vivo. These interesting proteins hold promise as specific markers of renal AngII activity in patients and in experimental models.

Microbial chlorate respiration plays an important role in the turnover of oxochlorates in nature and industrial waste management. This thesis deals with the characterization of the molecular components of chlorate respiration in Ideonella dechloratans. Chlorate respiration utilizes two soluble periplasmic enzymes, chlorate reductase and chlorite dismutase, to convert chlorate to chloride and oxygen. The genes encoding the enzymes participating in the chlorate degradation have been sequenced, and are found in close proximity, forming a gene cluster for chlorate metabolism. This work also includes the successful recombinant expression of three genes from Ideonella dechloratans. Two of the gene products, chlorite dismutase and the C subunit of chlorate reductase, participate in the chlorate respiration. The third gene, which is found close to the gene cluster for chlorate metabolism, encodes a soluble c-type cytochrome. The localization of the gene suggests the corresponding protein as a candidate for a role as electron donor to chlorate reductase. Also, the role of soluble periplasmic c cytochromes of Ideonella dechloratans in chlorate respiration was studied. At least one of the soluble c cytochromes was found capable of serving as electron donor for chlorate reduction. This c cytochrome, and several others, can also donate electrons to a terminal oxidase for subsequent reduction of oxygen, as required for the branched electron flow during chlorate respiration.

Primary chick embryo liver cells were used to explore the regulation of δ-aminolevulinic acid synthase and heme oxygenase, the enzymes that catalyze the rate-limiting reactions of heme anabolism and catabolism, respectively. The general focus of the work was the exploration of the novel observation in which glutethimide and iron synergistically induced both δ-aminolevulinic acid synthase and heme oxygenase, a phenomenon that would not be predicted a priori. The course of events appeared to be: first, that heme synthesis was increased after addition of the glutethimide and that iron potentiated heme synthesis; second, the heme induced heme oxygenase five to ten fold; and third, that heme oxygenase degraded the heme permitting an uncontrolled induction of δ-aminolevulinic acid synthase. This induction of δ-aminolevulinic acid synthase could be prevented by the addition of a metalloporphyrin inhibitor of heme oxygenase. Induced δ-aminolevulinic acid synthase activity could be dramatically reduced by the addition of nanomolar concentrations of a metalloporphyrin, inhibitory for heme oxygenase, and heme. Specific observations related to the synergistic induction of heme oxygenase by glutethimide and iron was that the induction of heme oxygenase activity by glutethimide and iron occurred rapidly, with maximal increases occurring four to six hours after original treatment. Induction of heme oxygenase by glutethimide and iron was shown to be dependent on de novoheme synthesis since 4,6-dioxoheptanoic acid, a potent and specific inhibitor of heme biosynthesis, prevented the activity of heme oxygenase from increasing in the presence of glutethimide and iron. Induction of activity was associated with increases in heme oxygenase mRNA and protein; and, when induction was prevented by 4,6-dioxoheptanoic acid, no increase in either mRNA or immunoreactive protein was observed. δ-Aminolevulinic acid synthase activity was also synergistically increased by glutethimide and iron; this increase occurred 4-6 hours after maximal heme oxygenase activity had been attained. The temporal relationship between the induction of δ-aminolevulinic acid synthase and heme oxygenase suggested that the oxygenase depleted a regulatory heme pool that would normally prevent uncontrolled induction of the synthase. When cultures were exposed to tin-mesoporphyrin, a potent inhibitor of heme oxygenase, induction of δ-aminolevulinic acid synthase, normally produced by glutethimide and iron, was prevented. Addition of tin-mesoporphyrin after δ-aminolevulinic acid synthase induction had already been established promptly halted any further induction. When heme or a combination of heme and tin-mesoporphyrin was added after induction of δ-aminolevulinic acid synthase was established, activity of the synthase was rapidly reduced. Finally, experiments in primary chick embryo liver cells with tin-, zinc- and copper- chelated porphyrins were done to assess their effects on activities of δ-aminolevulinic acid synthase, induced by prior treatment of cells with glutethimide and iron. Nanomolar concentrations of zinc- or tin porphyrins reduced δ-aminolevulinic acid synthase activities, while copper-chelated porphyrins did not. When nanomolar concentrations of heme were added with zinc- or tin-porphyrins, δ-aminolevulinic acid synthase activity was further reduced. Effects of the non-heme metalloporphyrins on δ-aminolevulinic acid synthase were closely correlated with their abilities to inhibit heme oxygenase (r=0.78). The largest decrease of δ-aminolevulinic acid synthase (67%) was obtained with zinc-mesoporphyrin and heme. There was a rapid appearance of the cytosolic, precursor form of δ-aminolevulinic acid synthase in the presence of both 10 μM heme or 50 nM zinc-mesoporphyrin and 200 nM heme. Reduction of the half-life of the mRNA from 5.2 hours to 2.2-2.5 hours was observed in the presence of both 10 μM heme or 50 nM zinc-mesoporphyrin and 200 nM heme. In summary, the chick embryo liver cell culture model treated with glutethimide and iron may serve as one experimental model for patients suffering from acute porphyrias, in whom uncontrolled induction of hepatic δ-aminolevulinic acid synthase plays a key role in pathogenesis of disease. The synergistic induction of δ-aminolevulinic acid synthase in the presence of glutethimide and iron may serve as an experimental paradigm for this disease. The reduction of δ-aminolevulinic acid synthase by low doses of zinc-mesoporphyrin and heme may help form the experimental foundation for eventual studies in patients suffering from acute porphyrias.

In this work, we have analysed the temporal dynamics of gut-dwelling bacteria and Borrelia in the gut of the deer tick Ixodes ricinus. Using quantitative PCR, we have shown that levels of the tick intestinal microflora are profoundly decreased at later stages of feeding on whole blood but not on serum. Even though we noted that host complement system manages to interfere with Borrelia viability in vitro, we did not see any effect of host complement on Borrelia acquisition in adult ticks in vivo. However, we revealed that host hemoglobin is essential for Borrelia proliferation in the tick gut. All together, these data imply that, during feeding, levels of gut-dwelling bacteria and Borrelia are determined by the host. While hemoglobin seems to be detrimental for gut-dwelling bacteria, Borrelia require it in order to proliferate. During off-host stage, we showed that levels of gut-dwelling microflora are regulated by an intestinal transmembrane enzyme Dual oxidase. In conclusion, we aimed, and mostly succeeded, to perform pilot experiments describing the biology of a complex process of regulating gut microflora in the vector Ixodes ricinus and extend it by its impact on Borrelia acquisition

Neuroglobin (Ngb) and cytoglobin (Cygb) are two new additions to the globin family, exhibiting heme iron hexa-coordination, a disulfide bond and large internal cavities. These proteins are implicated in cytoprotection under hypoxic-ischemic conditions, but the molecular basis of their cytoprotective function is unclear. Herein, a photothermal and spectroscopic study of the interactions of diatomic ligands with Ngb, Cygb, myoglobin and hemoglobin is presented. The impact of the disulfide bond in Ngb and Cygb and role of conserved residues in Ngb His64, Val68, Cys55, Cys120 and Tyr44 on conformational dynamics associated with ligand binding/dissociation were investigated. Transient absorption and photoacoustic calorimetry studies indicate that CO photo-dissociation from Ngb leads to a volume expansion (13.4±0.9 mL mol-1), whereas a smaller volume change was determined for Ngb with reduced Cys (ΔV=4.6±0.3 mL mol-1). Furthermore, Val68 side chain regulates ligand migration between the distal pocket and internal hydrophobic cavities since Val68Phe geminate quantum yield is ~2.7 times larger than that of WT Ngb. His64Gln and Tyr44Phe mutations alter the thermodynamic parameters associated with CO photo-release indicating that electrostatic/hydrogen binding network that includes heme propionate groups, Lys 67, His64, and Tyr 44 in Ngb modulates the energetics of CO photo-dissociation. In Cygb, CO escape from the protein matrix is fast (< 40 ns) with a ΔH of 18±2 kcal mol-1 in Cygbred, whereas disulfide bridge formation promotes a biphasic ligand escape associated with an overall enthalpy change of 9±4 kcal mol-1. Therefore, the disulfide bond modulates conformational dynamics in Ngb and Cygb. I propose that in Cygb with reduced Cys the photo-dissociated ligand escapes through the hydrophobic tunnel as occurs in Ngb, whereas the CO preferentially migrates through the His64 gate in Cygbox. To characterize Cygb surface 1,8-ANS interactions with Cygb were investigated employing fluorescence spectroscopy, ITC and docking simulations. Two 1,8-ANS binding sites were identified. One binding site is located close to the extended N-terminus of Cygb and was also identified as a binding site for oleate. Furthermore, guanidinium hydrochloride-induced unfolding studies of Cygb reveal that the disulfide bond does not impact Cygb stability, whereas binding of cyanide slightly increases the protein stability.

Presented work is focused on heme metabolism with the main interest in bile pigments. Recent data indicate that bilirubin is not only a waste product of the heme catabolic pathway, but also emphasize its important biological impacts, including possible antiproliferative effects. Until today metabolism of bilirubin has not been completely elucidated, which has prevented detailed evaluation of its potential anticancer action. The aim of this study was to clarify some aspects of heme catabolism with respect for antiproliferative properties of its products. Based on the fact that bilirubin potently affects carcinogenesis of the intestine, we initially investigated not properly known bilirubin metabolism by intestinal bacteria. We studied bilirubin neurotoxic effects in hyperbilirubinemic Gunn rats - its distribution in the brain tissue and its degradation during pathological conditions, such as severe newborn jaundice or Crigler-Najjar syndrome. Possible approaches to improve the treatment of severe unconjugated hyperbilirubinemias, combination of the phototherapy and human albumin administration were also investigated. The main reason of these studies was the fact that mechanisms of neurotoxic effects of bilirubin are predominantly identical with those, by which bilirubin inhibits cancer cells growth....